Starting phenix.real_space_refine on Tue Jun 10 21:31:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vv3_43548/06_2025/8vv3_43548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vv3_43548/06_2025/8vv3_43548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vv3_43548/06_2025/8vv3_43548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vv3_43548/06_2025/8vv3_43548.map" model { file = "/net/cci-nas-00/data/ceres_data/8vv3_43548/06_2025/8vv3_43548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vv3_43548/06_2025/8vv3_43548.cif" } resolution = 2.61 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= 0.002 sd= 0.369 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 132 5.16 5 C 7928 2.51 5 N 2028 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12172 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3031 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 6.99, per 1000 atoms: 0.57 Number of scatterers: 12172 At special positions: 0 Unit cell: (111.072, 110.004, 93.984, 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 132 16.00 O 2084 8.00 N 2028 7.00 C 7928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 83.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.605A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 80 removed outlier: 3.753A pdb=" N GLY A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 113 Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 140 through 173 removed outlier: 3.509A pdb=" N GLU A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 227 removed outlier: 3.557A pdb=" N ILE A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 341 removed outlier: 5.157A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Proline residue: A 331 - end of helix removed outlier: 3.530A pdb=" N SER A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 389 removed outlier: 3.579A pdb=" N LEU A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.882A pdb=" N GLU A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.641A pdb=" N SER A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 445 removed outlier: 3.504A pdb=" N MET A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.605A pdb=" N ILE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 26 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 80 removed outlier: 3.753A pdb=" N GLY B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 113 Processing helix chain 'B' and resid 113 through 136 Processing helix chain 'B' and resid 140 through 173 removed outlier: 3.510A pdb=" N GLU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 227 removed outlier: 3.557A pdb=" N ILE B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 341 removed outlier: 5.156A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix Proline residue: B 331 - end of helix removed outlier: 3.531A pdb=" N SER B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 389 removed outlier: 3.580A pdb=" N LEU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.883A pdb=" N GLU B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.642A pdb=" N SER B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 423 through 445 removed outlier: 3.504A pdb=" N MET B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.604A pdb=" N ILE C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 80 removed outlier: 3.754A pdb=" N GLY C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 113 through 136 Processing helix chain 'C' and resid 140 through 173 removed outlier: 3.510A pdb=" N GLU C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 227 removed outlier: 3.557A pdb=" N ILE C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 341 removed outlier: 5.156A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix Proline residue: C 331 - end of helix removed outlier: 3.531A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 389 removed outlier: 3.579A pdb=" N LEU C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.882A pdb=" N GLU C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 410 removed outlier: 3.642A pdb=" N SER C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 445 removed outlier: 3.504A pdb=" N MET C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.604A pdb=" N ILE D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 80 removed outlier: 3.754A pdb=" N GLY D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 113 Processing helix chain 'D' and resid 113 through 136 Processing helix chain 'D' and resid 140 through 173 removed outlier: 3.510A pdb=" N GLU D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 227 removed outlier: 3.557A pdb=" N ILE D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 341 removed outlier: 5.156A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Proline residue: D 331 - end of helix removed outlier: 3.531A pdb=" N SER D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 389 removed outlier: 3.580A pdb=" N LEU D 348 " --> pdb=" O ARG D 344 " (cutoff:3.500A) Proline residue: D 368 - end of helix removed outlier: 3.882A pdb=" N GLU D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.641A pdb=" N SER D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 423 through 445 removed outlier: 3.504A pdb=" N MET D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AA4, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AA7, first strand: chain 'D' and resid 37 through 41 Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 274 1028 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3767 1.34 - 1.46: 2167 1.46 - 1.58: 6274 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 12408 Sorted by residual: bond pdb=" C2 SOE D 501 " pdb=" O6 SOE D 501 " ideal model delta sigma weight residual 1.500 1.426 0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C2 SOE B 501 " pdb=" O6 SOE B 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C2 SOE A 501 " pdb=" O6 SOE A 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C2 SOE C 501 " pdb=" O6 SOE C 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C2 SOE A 501 " pdb=" O2 SOE A 501 " ideal model delta sigma weight residual 1.358 1.427 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 12403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 16347 1.23 - 2.45: 353 2.45 - 3.68: 83 3.68 - 4.91: 32 4.91 - 6.14: 21 Bond angle restraints: 16836 Sorted by residual: angle pdb=" CA TYR A 124 " pdb=" CB TYR A 124 " pdb=" CG TYR A 124 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.61e+00 angle pdb=" CA TYR B 124 " pdb=" CB TYR B 124 " pdb=" CG TYR B 124 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.60e+00 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 119.46 -5.56 1.80e+00 3.09e-01 9.53e+00 angle pdb=" CA TYR D 124 " pdb=" CB TYR D 124 " pdb=" CG TYR D 124 " ideal model delta sigma weight residual 113.90 119.44 -5.54 1.80e+00 3.09e-01 9.47e+00 angle pdb=" C SER C 123 " pdb=" N TYR C 124 " pdb=" CA TYR C 124 " ideal model delta sigma weight residual 120.72 115.72 5.00 1.67e+00 3.59e-01 8.98e+00 ... (remaining 16831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6680 16.96 - 33.92: 644 33.92 - 50.88: 108 50.88 - 67.84: 32 67.84 - 84.80: 20 Dihedral angle restraints: 7484 sinusoidal: 2968 harmonic: 4516 Sorted by residual: dihedral pdb=" CG ARG B 361 " pdb=" CD ARG B 361 " pdb=" NE ARG B 361 " pdb=" CZ ARG B 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.34 -44.66 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 361 " pdb=" CD ARG A 361 " pdb=" NE ARG A 361 " pdb=" CZ ARG A 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.37 -44.63 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG C 361 " pdb=" CD ARG C 361 " pdb=" NE ARG C 361 " pdb=" CZ ARG C 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.39 -44.61 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 7481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1509 0.035 - 0.070: 426 0.070 - 0.104: 104 0.104 - 0.139: 29 0.139 - 0.174: 8 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA TYR D 124 " pdb=" N TYR D 124 " pdb=" C TYR D 124 " pdb=" CB TYR D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA TYR C 124 " pdb=" N TYR C 124 " pdb=" C TYR C 124 " pdb=" CB TYR C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA TYR A 124 " pdb=" N TYR A 124 " pdb=" C TYR A 124 " pdb=" CB TYR A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 2073 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 124 " -0.002 2.00e-02 2.50e+03 1.20e-02 2.87e+00 pdb=" CG TYR A 124 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 124 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 124 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 124 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 124 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 124 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 124 " -0.002 2.00e-02 2.50e+03 1.19e-02 2.83e+00 pdb=" CG TYR B 124 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 124 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 124 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 124 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 124 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 124 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 124 " 0.002 2.00e-02 2.50e+03 1.19e-02 2.82e+00 pdb=" CG TYR C 124 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 124 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 124 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 124 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 124 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR C 124 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 124 " 0.002 2.00e-02 2.50e+03 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2154 2.77 - 3.30: 12336 3.30 - 3.83: 21645 3.83 - 4.37: 24698 4.37 - 4.90: 42896 Nonbonded interactions: 103729 Sorted by model distance: nonbonded pdb=" OD1 ASN A 222 " pdb=" NH2 ARG A 385 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN C 222 " pdb=" NH2 ARG C 385 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN D 222 " pdb=" NH2 ARG D 385 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN B 222 " pdb=" NH2 ARG B 385 " model vdw 2.234 3.120 nonbonded pdb=" OD1 ASP A 99 " pdb=" NE2 HIS A 326 " model vdw 2.249 3.120 ... (remaining 103724 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.740 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.004 0.074 12408 Z= 0.182 Angle : 0.523 6.136 16836 Z= 0.271 Chirality : 0.037 0.174 2076 Planarity : 0.004 0.025 2024 Dihedral : 14.374 84.801 4564 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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 (0.21), residues: 1524 helix: 2.35 (0.14), residues: 1216 sheet: -0.35 (0.86), residues: 40 loop : -2.60 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS A 22 PHE 0.014 0.001 PHE C 203 TYR 0.022 0.001 TYR A 124 ARG 0.002 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.12801 ( 1028) hydrogen bonds : angle 4.68954 ( 3048) covalent geometry : bond 0.00387 (12408) covalent geometry : angle 0.52309 (16836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6924 (ttt180) cc_final: 0.6094 (ttm-80) REVERT: A 91 MET cc_start: 0.5187 (tpp) cc_final: 0.4524 (ttt) REVERT: A 118 MET cc_start: 0.8008 (mmp) cc_final: 0.7797 (mmp) REVERT: A 133 ARG cc_start: 0.6573 (ttm110) cc_final: 0.5926 (ttp-110) REVERT: A 171 MET cc_start: 0.6591 (mtm) cc_final: 0.6209 (mmt) REVERT: A 197 MET cc_start: 0.7804 (tpt) cc_final: 0.7594 (tpp) REVERT: A 215 LYS cc_start: 0.8154 (tttm) cc_final: 0.7769 (ttmt) REVERT: A 289 GLU cc_start: 0.7077 (tt0) cc_final: 0.6539 (mm-30) REVERT: A 303 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 310 ASP cc_start: 0.7880 (m-30) cc_final: 0.7573 (m-30) REVERT: B 38 ARG cc_start: 0.6981 (ttt180) cc_final: 0.6170 (ttp-110) REVERT: B 46 TYR cc_start: 0.6974 (m-80) cc_final: 0.6355 (m-80) REVERT: B 52 LYS cc_start: 0.7290 (mttt) cc_final: 0.6998 (mmmt) REVERT: B 91 MET cc_start: 0.5277 (tpp) cc_final: 0.4652 (ttt) REVERT: B 133 ARG cc_start: 0.6975 (ttm110) cc_final: 0.6298 (ttp-110) REVERT: B 167 CYS cc_start: 0.7745 (m) cc_final: 0.7543 (m) REVERT: B 205 PHE cc_start: 0.7160 (m-80) cc_final: 0.6786 (m-80) REVERT: B 219 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7286 (mt-10) REVERT: B 303 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6798 (mt-10) REVERT: B 310 ASP cc_start: 0.7878 (m-30) cc_final: 0.7536 (m-30) REVERT: C 38 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6356 (ttp-110) REVERT: C 91 MET cc_start: 0.5131 (tpp) cc_final: 0.4731 (ttt) REVERT: C 118 MET cc_start: 0.8007 (mmp) cc_final: 0.7757 (mmp) REVERT: C 119 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6907 (mtm-85) REVERT: C 197 MET cc_start: 0.7816 (tpt) cc_final: 0.7522 (tpp) REVERT: C 215 LYS cc_start: 0.8143 (tttm) cc_final: 0.7653 (ttpt) REVERT: C 303 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6960 (mt-10) REVERT: D 38 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6296 (ttp-110) REVERT: D 46 TYR cc_start: 0.6785 (m-80) cc_final: 0.6304 (m-80) REVERT: D 60 ILE cc_start: 0.7859 (pt) cc_final: 0.7561 (mp) REVERT: D 91 MET cc_start: 0.5248 (tpp) cc_final: 0.4821 (ttt) REVERT: D 118 MET cc_start: 0.8186 (mmp) cc_final: 0.7947 (mmp) REVERT: D 119 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6733 (mtm-85) REVERT: D 133 ARG cc_start: 0.6714 (ttm110) cc_final: 0.5997 (ttp-110) REVERT: D 167 CYS cc_start: 0.7713 (m) cc_final: 0.7491 (m) REVERT: D 205 PHE cc_start: 0.7235 (m-80) cc_final: 0.6892 (m-80) REVERT: D 310 ASP cc_start: 0.7968 (m-30) cc_final: 0.7588 (m-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 1.2229 time to fit residues: 382.1765 Evaluate side-chains 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.262379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.233962 restraints weight = 10255.778| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 1.23 r_work: 0.4374 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4270 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12408 Z= 0.163 Angle : 0.552 7.394 16836 Z= 0.292 Chirality : 0.038 0.132 2076 Planarity : 0.004 0.029 2024 Dihedral : 3.892 15.349 1784 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.96 % Allowed : 9.25 % Favored : 87.80 % 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: 2.58 (0.21), residues: 1524 helix: 2.61 (0.14), residues: 1216 sheet: 0.46 (0.80), residues: 40 loop : -2.65 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.004 0.001 HIS B 22 PHE 0.016 0.002 PHE C 203 TYR 0.042 0.002 TYR C 124 ARG 0.005 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.05894 ( 1028) hydrogen bonds : angle 3.79083 ( 3048) covalent geometry : bond 0.00347 (12408) covalent geometry : angle 0.55197 (16836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7077 (ttt180) cc_final: 0.6270 (ttm-80) REVERT: A 46 TYR cc_start: 0.6885 (m-80) cc_final: 0.6149 (m-80) REVERT: A 60 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7581 (mt) REVERT: A 91 MET cc_start: 0.5329 (tpp) cc_final: 0.4770 (ttt) REVERT: A 133 ARG cc_start: 0.6966 (ttm110) cc_final: 0.6693 (ttm110) REVERT: A 171 MET cc_start: 0.7246 (mtm) cc_final: 0.6695 (mmt) REVERT: A 179 GLN cc_start: 0.7565 (pm20) cc_final: 0.7200 (pm20) REVERT: A 197 MET cc_start: 0.7925 (tpt) cc_final: 0.7709 (tpp) REVERT: A 215 LYS cc_start: 0.8517 (tttm) cc_final: 0.8303 (tttt) REVERT: A 289 GLU cc_start: 0.7638 (tt0) cc_final: 0.6645 (mm-30) REVERT: A 303 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 310 ASP cc_start: 0.7782 (m-30) cc_final: 0.7472 (m-30) REVERT: A 387 MET cc_start: 0.7570 (mmm) cc_final: 0.7220 (mtp) REVERT: B 38 ARG cc_start: 0.6892 (ttt180) cc_final: 0.6204 (ttp-110) REVERT: B 46 TYR cc_start: 0.6842 (m-80) cc_final: 0.6413 (m-80) REVERT: B 52 LYS cc_start: 0.7472 (mttt) cc_final: 0.6997 (mmmt) REVERT: B 91 MET cc_start: 0.5291 (tpp) cc_final: 0.4817 (ttt) REVERT: B 128 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6155 (mm) REVERT: B 133 ARG cc_start: 0.7158 (ttm110) cc_final: 0.6639 (ttp-110) REVERT: B 164 ASP cc_start: 0.8136 (t70) cc_final: 0.7924 (t70) REVERT: B 167 CYS cc_start: 0.8468 (m) cc_final: 0.8223 (m) REVERT: B 172 GLN cc_start: 0.6908 (mm110) cc_final: 0.6688 (mt0) REVERT: B 179 GLN cc_start: 0.7420 (pm20) cc_final: 0.7081 (pm20) REVERT: B 215 LYS cc_start: 0.8522 (mtpm) cc_final: 0.8277 (mtpt) REVERT: B 219 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7582 (mt-10) REVERT: B 284 GLN cc_start: 0.6077 (mt0) cc_final: 0.5474 (mt0) REVERT: B 303 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7128 (mt-10) REVERT: B 310 ASP cc_start: 0.7782 (m-30) cc_final: 0.7461 (m-30) REVERT: C 38 ARG cc_start: 0.7100 (ttt180) cc_final: 0.6320 (ttp-110) REVERT: C 49 THR cc_start: 0.7031 (t) cc_final: 0.6808 (t) REVERT: C 91 MET cc_start: 0.5101 (tpp) cc_final: 0.4759 (ttt) REVERT: C 119 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.6829 (mtm-85) REVERT: C 133 ARG cc_start: 0.6325 (ttm110) cc_final: 0.5802 (ttp-110) REVERT: C 179 GLN cc_start: 0.7399 (pm20) cc_final: 0.7027 (pm20) REVERT: C 197 MET cc_start: 0.7931 (tpt) cc_final: 0.7715 (tpp) REVERT: C 289 GLU cc_start: 0.7693 (tt0) cc_final: 0.6516 (mm-30) REVERT: C 303 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7320 (mt-10) REVERT: C 435 THR cc_start: 0.8052 (p) cc_final: 0.7701 (p) REVERT: D 38 ARG cc_start: 0.6899 (ttt180) cc_final: 0.6219 (ttp-110) REVERT: D 46 TYR cc_start: 0.6780 (m-80) cc_final: 0.6395 (m-80) REVERT: D 60 ILE cc_start: 0.7932 (pt) cc_final: 0.7697 (mp) REVERT: D 91 MET cc_start: 0.5322 (tpp) cc_final: 0.4914 (ttt) REVERT: D 119 ARG cc_start: 0.7304 (mtm-85) cc_final: 0.6706 (mtm-85) REVERT: D 133 ARG cc_start: 0.6796 (ttm110) cc_final: 0.6240 (ttp-110) REVERT: D 167 CYS cc_start: 0.8487 (m) cc_final: 0.8245 (m) REVERT: D 179 GLN cc_start: 0.7431 (pm20) cc_final: 0.7023 (pm20) REVERT: D 289 GLU cc_start: 0.7697 (tt0) cc_final: 0.6526 (mm-30) REVERT: D 310 ASP cc_start: 0.7914 (m-30) cc_final: 0.7551 (m-30) REVERT: D 387 MET cc_start: 0.7867 (mmm) cc_final: 0.7623 (mtt) REVERT: D 401 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7898 (tm-30) REVERT: D 435 THR cc_start: 0.8131 (p) cc_final: 0.7834 (p) outliers start: 40 outliers final: 19 residues processed: 249 average time/residue: 1.3190 time to fit residues: 354.7654 Evaluate side-chains 236 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN D 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.258827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.229911 restraints weight = 10325.048| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 1.22 r_work: 0.4317 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4210 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12408 Z= 0.180 Angle : 0.585 7.249 16836 Z= 0.307 Chirality : 0.039 0.134 2076 Planarity : 0.004 0.030 2024 Dihedral : 4.030 15.855 1784 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.48 % Allowed : 11.91 % Favored : 84.62 % 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: 2.55 (0.21), residues: 1524 helix: 2.58 (0.14), residues: 1220 sheet: 0.19 (0.79), residues: 40 loop : -2.68 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.004 0.001 HIS C 22 PHE 0.018 0.002 PHE A 203 TYR 0.033 0.002 TYR D 124 ARG 0.004 0.001 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.06249 ( 1028) hydrogen bonds : angle 3.75369 ( 3048) covalent geometry : bond 0.00409 (12408) covalent geometry : angle 0.58469 (16836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6941 (m-80) cc_final: 0.6186 (m-80) REVERT: A 60 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7734 (mt) REVERT: A 133 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6994 (ttm110) REVERT: A 171 MET cc_start: 0.7455 (mtm) cc_final: 0.6853 (mmt) REVERT: A 179 GLN cc_start: 0.7588 (pm20) cc_final: 0.7202 (pm20) REVERT: A 197 MET cc_start: 0.8028 (tpt) cc_final: 0.7818 (tpp) REVERT: A 289 GLU cc_start: 0.7853 (tt0) cc_final: 0.6885 (mm-30) REVERT: A 303 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 310 ASP cc_start: 0.7946 (m-30) cc_final: 0.7655 (m-30) REVERT: A 387 MET cc_start: 0.7770 (mmm) cc_final: 0.7418 (mtp) REVERT: B 38 ARG cc_start: 0.7058 (ttt180) cc_final: 0.6372 (ttm-80) REVERT: B 46 TYR cc_start: 0.6898 (m-80) cc_final: 0.6240 (m-80) REVERT: B 52 LYS cc_start: 0.7588 (mttt) cc_final: 0.7153 (mmmt) REVERT: B 91 MET cc_start: 0.5365 (tpp) cc_final: 0.4903 (ttt) REVERT: B 128 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6632 (mm) REVERT: B 133 ARG cc_start: 0.7358 (ttm110) cc_final: 0.7093 (ttm110) REVERT: B 179 GLN cc_start: 0.7371 (pm20) cc_final: 0.7085 (pm20) REVERT: B 219 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7834 (mt-10) REVERT: B 303 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7218 (mt-10) REVERT: B 310 ASP cc_start: 0.7917 (m-30) cc_final: 0.7590 (m-30) REVERT: C 38 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6436 (ttp-110) REVERT: C 52 LYS cc_start: 0.7446 (mttt) cc_final: 0.7070 (mmmt) REVERT: C 91 MET cc_start: 0.5313 (tpp) cc_final: 0.4933 (ttt) REVERT: C 119 ARG cc_start: 0.7393 (mtm-85) cc_final: 0.6785 (mtm-85) REVERT: C 133 ARG cc_start: 0.6805 (ttm110) cc_final: 0.6283 (ttp-110) REVERT: C 179 GLN cc_start: 0.7505 (pm20) cc_final: 0.7173 (pm20) REVERT: C 303 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7416 (mt-10) REVERT: C 310 ASP cc_start: 0.7775 (m-30) cc_final: 0.7493 (m-30) REVERT: C 435 THR cc_start: 0.8192 (p) cc_final: 0.7891 (p) REVERT: D 38 ARG cc_start: 0.7077 (ttt180) cc_final: 0.6419 (ttp-110) REVERT: D 46 TYR cc_start: 0.6822 (m-80) cc_final: 0.6309 (m-80) REVERT: D 52 LYS cc_start: 0.7565 (mttt) cc_final: 0.7133 (mmmt) REVERT: D 60 ILE cc_start: 0.7966 (pt) cc_final: 0.7761 (mp) REVERT: D 91 MET cc_start: 0.5478 (tpp) cc_final: 0.5086 (ttt) REVERT: D 119 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.6743 (mtm-85) REVERT: D 133 ARG cc_start: 0.7065 (ttm110) cc_final: 0.6840 (ttm110) REVERT: D 179 GLN cc_start: 0.7386 (pm20) cc_final: 0.7020 (pm20) REVERT: D 289 GLU cc_start: 0.7901 (tt0) cc_final: 0.7669 (tt0) REVERT: D 310 ASP cc_start: 0.8040 (m-30) cc_final: 0.7686 (m-30) REVERT: D 435 THR cc_start: 0.8176 (p) cc_final: 0.7882 (p) outliers start: 47 outliers final: 25 residues processed: 243 average time/residue: 1.3183 time to fit residues: 346.1600 Evaluate side-chains 242 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 121 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 134 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN C 172 GLN D 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.246711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.218909 restraints weight = 10006.441| |-----------------------------------------------------------------------------| r_work (start): 0.4612 rms_B_bonded: 1.13 r_work: 0.4413 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4307 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12408 Z= 0.147 Angle : 0.539 7.007 16836 Z= 0.283 Chirality : 0.037 0.132 2076 Planarity : 0.004 0.031 2024 Dihedral : 3.964 15.349 1784 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.55 % Allowed : 13.83 % Favored : 82.62 % 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: 2.72 (0.21), residues: 1524 helix: 2.71 (0.13), residues: 1220 sheet: 0.21 (0.76), residues: 40 loop : -2.65 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.000 HIS C 22 PHE 0.016 0.002 PHE A 203 TYR 0.027 0.001 TYR B 124 ARG 0.003 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.05678 ( 1028) hydrogen bonds : angle 3.60852 ( 3048) covalent geometry : bond 0.00311 (12408) covalent geometry : angle 0.53930 (16836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6878 (m-80) cc_final: 0.6107 (m-80) REVERT: A 60 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7710 (mt) REVERT: A 91 MET cc_start: 0.6148 (OUTLIER) cc_final: 0.4669 (ttt) REVERT: A 133 ARG cc_start: 0.7050 (ttm110) cc_final: 0.6784 (ttm110) REVERT: A 171 MET cc_start: 0.7371 (mtm) cc_final: 0.6855 (mmt) REVERT: A 179 GLN cc_start: 0.7562 (pm20) cc_final: 0.7232 (pm20) REVERT: A 197 MET cc_start: 0.7984 (tpt) cc_final: 0.7684 (tpp) REVERT: A 219 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7630 (mt-10) REVERT: A 289 GLU cc_start: 0.7670 (tt0) cc_final: 0.6674 (mm-30) REVERT: A 303 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 310 ASP cc_start: 0.7828 (m-30) cc_final: 0.7520 (m-30) REVERT: A 387 MET cc_start: 0.7650 (mmm) cc_final: 0.7242 (mtp) REVERT: B 38 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6264 (ttm-80) REVERT: B 46 TYR cc_start: 0.6738 (m-80) cc_final: 0.6102 (m-80) REVERT: B 52 LYS cc_start: 0.7528 (mttt) cc_final: 0.7013 (mmmt) REVERT: B 60 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7667 (mt) REVERT: B 91 MET cc_start: 0.5309 (tpp) cc_final: 0.4850 (ttt) REVERT: B 128 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6320 (mm) REVERT: B 133 ARG cc_start: 0.7171 (ttm110) cc_final: 0.6907 (ttm110) REVERT: B 179 GLN cc_start: 0.7357 (pm20) cc_final: 0.7034 (pm20) REVERT: B 219 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7762 (mt-10) REVERT: B 303 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7198 (mt-10) REVERT: B 310 ASP cc_start: 0.7830 (m-30) cc_final: 0.7521 (m-30) REVERT: C 38 ARG cc_start: 0.7037 (ttt180) cc_final: 0.6254 (ttp-110) REVERT: C 46 TYR cc_start: 0.6947 (m-80) cc_final: 0.6517 (m-80) REVERT: C 52 LYS cc_start: 0.7345 (mttt) cc_final: 0.6955 (mmmt) REVERT: C 91 MET cc_start: 0.5262 (tpp) cc_final: 0.4855 (ttt) REVERT: C 119 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6589 (mtm-85) REVERT: C 133 ARG cc_start: 0.6631 (ttm110) cc_final: 0.6152 (ttp-110) REVERT: C 179 GLN cc_start: 0.7476 (pm20) cc_final: 0.7143 (pm20) REVERT: C 215 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8169 (ttpp) REVERT: C 303 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7283 (mt-10) REVERT: C 310 ASP cc_start: 0.7694 (m-30) cc_final: 0.7432 (m-30) REVERT: C 435 THR cc_start: 0.8116 (p) cc_final: 0.7822 (p) REVERT: D 38 ARG cc_start: 0.6940 (ttt180) cc_final: 0.6208 (ttp-110) REVERT: D 46 TYR cc_start: 0.6895 (m-80) cc_final: 0.6356 (m-80) REVERT: D 52 LYS cc_start: 0.7547 (mttt) cc_final: 0.7038 (mmmt) REVERT: D 91 MET cc_start: 0.5421 (tpp) cc_final: 0.4992 (ttt) REVERT: D 119 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6565 (mtm-85) REVERT: D 133 ARG cc_start: 0.6919 (ttm110) cc_final: 0.6657 (ttm110) REVERT: D 179 GLN cc_start: 0.7271 (pm20) cc_final: 0.6940 (pm20) REVERT: D 310 ASP cc_start: 0.7822 (m-30) cc_final: 0.7498 (m-30) REVERT: D 435 THR cc_start: 0.8194 (p) cc_final: 0.7908 (p) outliers start: 48 outliers final: 36 residues processed: 257 average time/residue: 1.2698 time to fit residues: 354.0948 Evaluate side-chains 259 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.259951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.231770 restraints weight = 10240.688| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 1.18 r_work: 0.4329 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12408 Z= 0.158 Angle : 0.561 7.718 16836 Z= 0.292 Chirality : 0.038 0.180 2076 Planarity : 0.004 0.033 2024 Dihedral : 4.026 15.409 1784 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.73 % Allowed : 14.64 % Favored : 80.62 % 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: 2.70 (0.21), residues: 1524 helix: 2.68 (0.13), residues: 1220 sheet: 0.37 (0.75), residues: 40 loop : -2.66 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.003 0.001 HIS D 22 PHE 0.018 0.002 PHE A 203 TYR 0.026 0.002 TYR C 124 ARG 0.002 0.000 ARG D 385 Details of bonding type rmsd hydrogen bonds : bond 0.05825 ( 1028) hydrogen bonds : angle 3.63263 ( 3048) covalent geometry : bond 0.00349 (12408) covalent geometry : angle 0.56069 (16836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6845 (m-80) cc_final: 0.6102 (m-80) REVERT: A 60 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 91 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.4785 (ttt) REVERT: A 133 ARG cc_start: 0.7220 (ttm110) cc_final: 0.6964 (ttm110) REVERT: A 171 MET cc_start: 0.7514 (mtm) cc_final: 0.6983 (mmt) REVERT: A 179 GLN cc_start: 0.7651 (pm20) cc_final: 0.7330 (pm20) REVERT: A 197 MET cc_start: 0.8102 (tpt) cc_final: 0.7883 (tpp) REVERT: A 303 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7342 (mt-10) REVERT: A 310 ASP cc_start: 0.7883 (m-30) cc_final: 0.7568 (m-30) REVERT: A 387 MET cc_start: 0.7686 (mmm) cc_final: 0.7339 (OUTLIER) REVERT: B 38 ARG cc_start: 0.7013 (ttt180) cc_final: 0.6321 (ttm-80) REVERT: B 46 TYR cc_start: 0.6760 (m-80) cc_final: 0.6213 (m-80) REVERT: B 52 LYS cc_start: 0.7504 (mttt) cc_final: 0.7115 (mmmt) REVERT: B 60 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7755 (mt) REVERT: B 91 MET cc_start: 0.5359 (tpp) cc_final: 0.4898 (ttt) REVERT: B 133 ARG cc_start: 0.7305 (ttm110) cc_final: 0.7046 (ttm110) REVERT: B 179 GLN cc_start: 0.7451 (pm20) cc_final: 0.7167 (pm20) REVERT: B 303 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7263 (mt-10) REVERT: B 310 ASP cc_start: 0.7951 (m-30) cc_final: 0.7635 (m-30) REVERT: C 38 ARG cc_start: 0.7117 (ttt180) cc_final: 0.6365 (ttp-110) REVERT: C 46 TYR cc_start: 0.6988 (m-80) cc_final: 0.6591 (m-80) REVERT: C 52 LYS cc_start: 0.7418 (mttt) cc_final: 0.7069 (mmmt) REVERT: C 91 MET cc_start: 0.5369 (tpp) cc_final: 0.4957 (ttt) REVERT: C 119 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.6726 (mtm-85) REVERT: C 133 ARG cc_start: 0.6951 (ttm110) cc_final: 0.6417 (ttp-110) REVERT: C 179 GLN cc_start: 0.7538 (pm20) cc_final: 0.7221 (pm20) REVERT: C 303 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7398 (mt-10) REVERT: C 310 ASP cc_start: 0.7714 (m-30) cc_final: 0.7434 (m-30) REVERT: C 435 THR cc_start: 0.8160 (p) cc_final: 0.7864 (p) REVERT: D 38 ARG cc_start: 0.6992 (ttt180) cc_final: 0.6329 (ttm-80) REVERT: D 46 TYR cc_start: 0.6876 (m-80) cc_final: 0.6369 (m-80) REVERT: D 52 LYS cc_start: 0.7653 (mttt) cc_final: 0.7207 (mmmt) REVERT: D 91 MET cc_start: 0.5461 (tpp) cc_final: 0.5032 (ttt) REVERT: D 119 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.6722 (mtm-85) REVERT: D 133 ARG cc_start: 0.7023 (ttm110) cc_final: 0.6785 (ttm110) REVERT: D 179 GLN cc_start: 0.7390 (pm20) cc_final: 0.7143 (pm20) REVERT: D 289 GLU cc_start: 0.7901 (tt0) cc_final: 0.7506 (tt0) REVERT: D 310 ASP cc_start: 0.7848 (m-30) cc_final: 0.7503 (m-30) REVERT: D 435 THR cc_start: 0.8229 (p) cc_final: 0.7943 (p) outliers start: 64 outliers final: 47 residues processed: 262 average time/residue: 1.2439 time to fit residues: 353.7526 Evaluate side-chains 264 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 0.0670 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.245141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.216167 restraints weight = 10145.351| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 1.19 r_work: 0.4315 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4204 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12408 Z= 0.164 Angle : 0.579 8.368 16836 Z= 0.300 Chirality : 0.038 0.147 2076 Planarity : 0.004 0.033 2024 Dihedral : 4.107 15.977 1784 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.81 % Allowed : 15.31 % Favored : 79.88 % 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: 2.68 (0.21), residues: 1524 helix: 2.66 (0.13), residues: 1220 sheet: 0.60 (0.72), residues: 40 loop : -2.64 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS C 22 PHE 0.018 0.002 PHE A 203 TYR 0.025 0.002 TYR C 124 ARG 0.003 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05924 ( 1028) hydrogen bonds : angle 3.64343 ( 3048) covalent geometry : bond 0.00368 (12408) covalent geometry : angle 0.57906 (16836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6803 (m-80) cc_final: 0.6095 (m-80) REVERT: A 60 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 91 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.4757 (ttt) REVERT: A 133 ARG cc_start: 0.7242 (ttm110) cc_final: 0.6988 (ttm110) REVERT: A 171 MET cc_start: 0.7555 (mtm) cc_final: 0.6998 (mmt) REVERT: A 179 GLN cc_start: 0.7727 (pm20) cc_final: 0.7466 (pm20) REVERT: A 197 MET cc_start: 0.8114 (tpt) cc_final: 0.7897 (tpp) REVERT: A 303 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7340 (mt-10) REVERT: A 310 ASP cc_start: 0.7901 (m-30) cc_final: 0.7584 (m-30) REVERT: A 387 MET cc_start: 0.7726 (mmm) cc_final: 0.7337 (OUTLIER) REVERT: B 38 ARG cc_start: 0.7103 (ttt180) cc_final: 0.6382 (ttm-80) REVERT: B 46 TYR cc_start: 0.6742 (m-80) cc_final: 0.6184 (m-80) REVERT: B 52 LYS cc_start: 0.7512 (mttt) cc_final: 0.7141 (mmmt) REVERT: B 60 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7773 (mt) REVERT: B 91 MET cc_start: 0.5413 (tpp) cc_final: 0.4945 (ttt) REVERT: B 133 ARG cc_start: 0.7336 (ttm110) cc_final: 0.7071 (ttm110) REVERT: B 179 GLN cc_start: 0.7455 (pm20) cc_final: 0.7222 (pm20) REVERT: B 274 MET cc_start: 0.3213 (OUTLIER) cc_final: 0.2882 (ptp) REVERT: B 303 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 310 ASP cc_start: 0.7907 (m-30) cc_final: 0.7585 (m-30) REVERT: C 38 ARG cc_start: 0.7163 (ttt180) cc_final: 0.6395 (ttm-80) REVERT: C 46 TYR cc_start: 0.7015 (m-80) cc_final: 0.6613 (m-80) REVERT: C 52 LYS cc_start: 0.7500 (mttt) cc_final: 0.7140 (mmmt) REVERT: C 91 MET cc_start: 0.5414 (tpp) cc_final: 0.4991 (ttt) REVERT: C 119 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.6692 (mtm-85) REVERT: C 133 ARG cc_start: 0.7015 (ttm110) cc_final: 0.6781 (ttm110) REVERT: C 179 GLN cc_start: 0.7536 (pm20) cc_final: 0.7305 (pm20) REVERT: C 303 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7439 (mt-10) REVERT: C 310 ASP cc_start: 0.7756 (m-30) cc_final: 0.7472 (m-30) REVERT: C 435 THR cc_start: 0.8123 (p) cc_final: 0.7831 (p) REVERT: D 38 ARG cc_start: 0.6972 (ttt180) cc_final: 0.6380 (ttm-80) REVERT: D 46 TYR cc_start: 0.6903 (m-80) cc_final: 0.6402 (m-80) REVERT: D 52 LYS cc_start: 0.7623 (mttt) cc_final: 0.7192 (mmmt) REVERT: D 91 MET cc_start: 0.5585 (tpp) cc_final: 0.5151 (ttt) REVERT: D 119 ARG cc_start: 0.7395 (mtm-85) cc_final: 0.6707 (mtm-85) REVERT: D 133 ARG cc_start: 0.7085 (ttm110) cc_final: 0.6842 (ttm110) REVERT: D 179 GLN cc_start: 0.7401 (pm20) cc_final: 0.7191 (pm20) REVERT: D 310 ASP cc_start: 0.7856 (m-30) cc_final: 0.7519 (m-30) REVERT: D 435 THR cc_start: 0.8184 (p) cc_final: 0.7902 (p) outliers start: 65 outliers final: 48 residues processed: 262 average time/residue: 1.3389 time to fit residues: 381.3551 Evaluate side-chains 268 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 217 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.242900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.213814 restraints weight = 10140.419| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 1.18 r_work: 0.4287 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12408 Z= 0.195 Angle : 0.636 9.182 16836 Z= 0.327 Chirality : 0.040 0.185 2076 Planarity : 0.005 0.033 2024 Dihedral : 4.297 19.359 1784 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 5.25 % Allowed : 15.16 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1524 helix: 2.48 (0.13), residues: 1220 sheet: 0.53 (0.71), residues: 40 loop : -2.75 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS B 22 PHE 0.019 0.002 PHE A 203 TYR 0.025 0.002 TYR A 124 ARG 0.004 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.06405 ( 1028) hydrogen bonds : angle 3.74971 ( 3048) covalent geometry : bond 0.00455 (12408) covalent geometry : angle 0.63630 (16836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 219 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6911 (m-80) cc_final: 0.6229 (m-80) REVERT: A 60 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7826 (mt) REVERT: A 91 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.4858 (ttt) REVERT: A 119 ARG cc_start: 0.7152 (mtm-85) cc_final: 0.6545 (mtm-85) REVERT: A 133 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6969 (ttm110) REVERT: A 171 MET cc_start: 0.7595 (mtm) cc_final: 0.7072 (mmt) REVERT: A 197 MET cc_start: 0.7963 (tpt) cc_final: 0.7754 (tpp) REVERT: A 303 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7139 (mt-10) REVERT: A 310 ASP cc_start: 0.7818 (m-30) cc_final: 0.7490 (m-30) REVERT: B 38 ARG cc_start: 0.7057 (ttt180) cc_final: 0.6401 (ttm-80) REVERT: B 46 TYR cc_start: 0.6871 (m-80) cc_final: 0.6299 (m-80) REVERT: B 52 LYS cc_start: 0.7386 (mttt) cc_final: 0.7138 (mmmt) REVERT: B 60 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7791 (mt) REVERT: B 91 MET cc_start: 0.5384 (tpp) cc_final: 0.5026 (ttt) REVERT: B 119 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6608 (mtm-85) REVERT: B 133 ARG cc_start: 0.7270 (ttm110) cc_final: 0.6783 (ttp-110) REVERT: B 179 GLN cc_start: 0.7531 (pm20) cc_final: 0.7231 (pm20) REVERT: B 310 ASP cc_start: 0.7804 (m-30) cc_final: 0.7466 (m-30) REVERT: C 38 ARG cc_start: 0.7103 (ttt180) cc_final: 0.6388 (ttm-80) REVERT: C 46 TYR cc_start: 0.7071 (m-80) cc_final: 0.6680 (m-80) REVERT: C 52 LYS cc_start: 0.7423 (mttt) cc_final: 0.7155 (mmmt) REVERT: C 91 MET cc_start: 0.5374 (tpp) cc_final: 0.5094 (ttt) REVERT: C 119 ARG cc_start: 0.7155 (mtm-85) cc_final: 0.6680 (mtm-85) REVERT: C 303 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 310 ASP cc_start: 0.7776 (m-30) cc_final: 0.7461 (m-30) REVERT: C 435 THR cc_start: 0.8187 (p) cc_final: 0.7924 (p) REVERT: D 38 ARG cc_start: 0.6988 (ttt180) cc_final: 0.6398 (ttm-80) REVERT: D 46 TYR cc_start: 0.6922 (m-80) cc_final: 0.6448 (m-80) REVERT: D 52 LYS cc_start: 0.7423 (mttt) cc_final: 0.7161 (mmmt) REVERT: D 91 MET cc_start: 0.5472 (tpp) cc_final: 0.5154 (ttt) REVERT: D 119 ARG cc_start: 0.7284 (mtm-85) cc_final: 0.6691 (mtm-85) REVERT: D 133 ARG cc_start: 0.7087 (ttm110) cc_final: 0.6855 (ttm110) REVERT: D 303 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: D 310 ASP cc_start: 0.7790 (m-30) cc_final: 0.7435 (m-30) REVERT: D 435 THR cc_start: 0.8196 (p) cc_final: 0.7928 (p) outliers start: 71 outliers final: 46 residues processed: 271 average time/residue: 1.4393 time to fit residues: 424.5698 Evaluate side-chains 267 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.245269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.216617 restraints weight = 10154.930| |-----------------------------------------------------------------------------| r_work (start): 0.4516 rms_B_bonded: 1.18 r_work: 0.4316 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4206 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12408 Z= 0.158 Angle : 0.584 8.087 16836 Z= 0.302 Chirality : 0.038 0.191 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.203 18.777 1784 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.22 % Allowed : 16.49 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.21), residues: 1524 helix: 2.63 (0.13), residues: 1220 sheet: 0.64 (0.69), residues: 40 loop : -2.68 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 354 HIS 0.002 0.000 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.023 0.002 TYR C 124 ARG 0.003 0.000 ARG A 405 Details of bonding type rmsd hydrogen bonds : bond 0.05841 ( 1028) hydrogen bonds : angle 3.63844 ( 3048) covalent geometry : bond 0.00348 (12408) covalent geometry : angle 0.58370 (16836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 220 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6845 (m-80) cc_final: 0.6192 (m-80) REVERT: A 60 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7780 (mt) REVERT: A 91 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.4780 (ttt) REVERT: A 133 ARG cc_start: 0.7239 (ttm110) cc_final: 0.6984 (ttm110) REVERT: A 171 MET cc_start: 0.7635 (mtm) cc_final: 0.7020 (mmt) REVERT: A 197 MET cc_start: 0.8098 (tpt) cc_final: 0.7802 (tpp) REVERT: A 303 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7277 (mt-10) REVERT: A 310 ASP cc_start: 0.7897 (m-30) cc_final: 0.7587 (m-30) REVERT: B 38 ARG cc_start: 0.7180 (ttt180) cc_final: 0.6491 (ttm-80) REVERT: B 46 TYR cc_start: 0.6847 (m-80) cc_final: 0.6231 (m-80) REVERT: B 52 LYS cc_start: 0.7531 (mttt) cc_final: 0.7140 (mmmt) REVERT: B 60 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7785 (mt) REVERT: B 91 MET cc_start: 0.5443 (tpp) cc_final: 0.4969 (ttt) REVERT: B 133 ARG cc_start: 0.7276 (ttm110) cc_final: 0.7027 (ttm110) REVERT: B 179 GLN cc_start: 0.7474 (pm20) cc_final: 0.7268 (pm20) REVERT: B 310 ASP cc_start: 0.7937 (m-30) cc_final: 0.7623 (m-30) REVERT: B 435 THR cc_start: 0.8156 (p) cc_final: 0.7907 (p) REVERT: C 38 ARG cc_start: 0.7156 (ttt180) cc_final: 0.6429 (ttm-80) REVERT: C 46 TYR cc_start: 0.7027 (m-80) cc_final: 0.6649 (m-80) REVERT: C 52 LYS cc_start: 0.7472 (mttt) cc_final: 0.7124 (mmmt) REVERT: C 60 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7723 (mt) REVERT: C 91 MET cc_start: 0.5559 (tpp) cc_final: 0.5153 (ttt) REVERT: C 119 ARG cc_start: 0.7269 (mtm-85) cc_final: 0.6710 (mtm-85) REVERT: C 179 GLN cc_start: 0.7777 (pm20) cc_final: 0.7481 (pm20) REVERT: C 215 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8242 (ttpp) REVERT: C 274 MET cc_start: 0.4078 (mmt) cc_final: 0.1739 (tmt) REVERT: C 297 MET cc_start: 0.8521 (mtm) cc_final: 0.8182 (ttp) REVERT: C 303 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7473 (mt-10) REVERT: C 310 ASP cc_start: 0.7739 (m-30) cc_final: 0.7442 (m-30) REVERT: C 435 THR cc_start: 0.8124 (p) cc_final: 0.7840 (p) REVERT: D 38 ARG cc_start: 0.7081 (ttt180) cc_final: 0.6499 (ttm-80) REVERT: D 46 TYR cc_start: 0.6883 (m-80) cc_final: 0.6413 (m-80) REVERT: D 52 LYS cc_start: 0.7574 (mttt) cc_final: 0.7178 (mmmt) REVERT: D 60 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7881 (mt) REVERT: D 91 MET cc_start: 0.5568 (tpp) cc_final: 0.5124 (ttt) REVERT: D 119 ARG cc_start: 0.7400 (mtm-85) cc_final: 0.6723 (mtm-85) REVERT: D 133 ARG cc_start: 0.7085 (ttm110) cc_final: 0.6839 (ttm110) REVERT: D 179 GLN cc_start: 0.7637 (pm20) cc_final: 0.7389 (pm20) REVERT: D 310 ASP cc_start: 0.7865 (m-30) cc_final: 0.7526 (m-30) REVERT: D 435 THR cc_start: 0.8171 (p) cc_final: 0.7893 (p) outliers start: 57 outliers final: 45 residues processed: 264 average time/residue: 1.2865 time to fit residues: 370.9130 Evaluate side-chains 267 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 118 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 146 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.0010 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.247341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.218696 restraints weight = 10076.531| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 1.18 r_work: 0.4341 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4232 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12408 Z= 0.139 Angle : 0.556 9.297 16836 Z= 0.288 Chirality : 0.037 0.175 2076 Planarity : 0.004 0.033 2024 Dihedral : 4.100 18.534 1784 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.85 % Allowed : 17.31 % 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: 2.80 (0.21), residues: 1524 helix: 2.78 (0.13), residues: 1216 sheet: 0.83 (0.69), residues: 40 loop : -2.72 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.001 0.000 HIS C 326 PHE 0.016 0.002 PHE A 203 TYR 0.023 0.001 TYR C 124 ARG 0.004 0.000 ARG D 405 Details of bonding type rmsd hydrogen bonds : bond 0.05400 ( 1028) hydrogen bonds : angle 3.56041 ( 3048) covalent geometry : bond 0.00292 (12408) covalent geometry : angle 0.55634 (16836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 91 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.4775 (ttt) REVERT: A 133 ARG cc_start: 0.7087 (ttm110) cc_final: 0.6520 (ttp-110) REVERT: A 171 MET cc_start: 0.7620 (mtm) cc_final: 0.7020 (mmt) REVERT: A 197 MET cc_start: 0.8083 (tpt) cc_final: 0.7841 (tpp) REVERT: A 303 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7300 (mt-10) REVERT: A 310 ASP cc_start: 0.7908 (m-30) cc_final: 0.7590 (m-30) REVERT: B 38 ARG cc_start: 0.7150 (ttt180) cc_final: 0.6401 (ttm-80) REVERT: B 46 TYR cc_start: 0.6779 (m-80) cc_final: 0.6483 (m-80) REVERT: B 52 LYS cc_start: 0.7485 (mttt) cc_final: 0.7137 (mmmt) REVERT: B 60 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7819 (mt) REVERT: B 91 MET cc_start: 0.5410 (tpp) cc_final: 0.4953 (ttt) REVERT: B 133 ARG cc_start: 0.7127 (ttm110) cc_final: 0.6891 (ttm110) REVERT: B 310 ASP cc_start: 0.7812 (m-30) cc_final: 0.7479 (m-30) REVERT: B 435 THR cc_start: 0.8147 (p) cc_final: 0.7898 (p) REVERT: C 38 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6334 (ttm-80) REVERT: C 46 TYR cc_start: 0.6855 (m-80) cc_final: 0.6406 (m-80) REVERT: C 52 LYS cc_start: 0.7445 (mttt) cc_final: 0.7102 (mmmt) REVERT: C 60 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7745 (mt) REVERT: C 83 LYS cc_start: 0.7564 (mtpt) cc_final: 0.6830 (tppt) REVERT: C 133 ARG cc_start: 0.6907 (ttm110) cc_final: 0.6585 (ttp-110) REVERT: C 179 GLN cc_start: 0.7748 (pm20) cc_final: 0.7418 (pm20) REVERT: C 274 MET cc_start: 0.4006 (mmt) cc_final: 0.3558 (ttp) REVERT: C 303 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7425 (mt-10) REVERT: C 310 ASP cc_start: 0.7756 (m-30) cc_final: 0.7452 (m-30) REVERT: C 377 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7827 (mtmt) REVERT: C 435 THR cc_start: 0.8082 (p) cc_final: 0.7803 (p) REVERT: D 38 ARG cc_start: 0.6983 (ttt180) cc_final: 0.6384 (ttm-80) REVERT: D 46 TYR cc_start: 0.6849 (m-80) cc_final: 0.6323 (m-80) REVERT: D 52 LYS cc_start: 0.7535 (mttt) cc_final: 0.7135 (mmmt) REVERT: D 60 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7870 (mt) REVERT: D 91 MET cc_start: 0.5534 (tpp) cc_final: 0.5119 (ttt) REVERT: D 133 ARG cc_start: 0.7001 (ttm110) cc_final: 0.6744 (ttm110) REVERT: D 179 GLN cc_start: 0.7620 (pm20) cc_final: 0.7325 (pm20) REVERT: D 310 ASP cc_start: 0.7815 (m-30) cc_final: 0.7461 (m-30) REVERT: D 435 THR cc_start: 0.8113 (p) cc_final: 0.7879 (p) outliers start: 52 outliers final: 41 residues processed: 258 average time/residue: 1.3662 time to fit residues: 383.4080 Evaluate side-chains 257 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.244210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.215457 restraints weight = 10019.485| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 1.17 r_work: 0.4312 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4201 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12408 Z= 0.183 Angle : 0.638 10.306 16836 Z= 0.327 Chirality : 0.040 0.187 2076 Planarity : 0.004 0.033 2024 Dihedral : 4.309 25.081 1784 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.25 % Allowed : 18.34 % Favored : 78.40 % 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: 2.52 (0.21), residues: 1524 helix: 2.56 (0.13), residues: 1220 sheet: 0.71 (0.69), residues: 40 loop : -2.81 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 193 HIS 0.002 0.001 HIS A 22 PHE 0.019 0.002 PHE A 203 TYR 0.024 0.002 TYR C 124 ARG 0.003 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.06097 ( 1028) hydrogen bonds : angle 3.69962 ( 3048) covalent geometry : bond 0.00424 (12408) covalent geometry : angle 0.63825 (16836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6726 (m-80) cc_final: 0.6171 (m-80) REVERT: A 60 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 91 MET cc_start: 0.6240 (OUTLIER) cc_final: 0.4805 (ttt) REVERT: A 119 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.6636 (mtm-85) REVERT: A 133 ARG cc_start: 0.7170 (ttm110) cc_final: 0.6925 (ttm110) REVERT: A 171 MET cc_start: 0.7720 (mtm) cc_final: 0.7036 (mmt) REVERT: A 197 MET cc_start: 0.8089 (tpt) cc_final: 0.7874 (tpp) REVERT: A 303 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 310 ASP cc_start: 0.7930 (m-30) cc_final: 0.7620 (m-30) REVERT: A 435 THR cc_start: 0.8134 (p) cc_final: 0.7851 (p) REVERT: B 38 ARG cc_start: 0.7119 (ttt180) cc_final: 0.6434 (ttm-80) REVERT: B 46 TYR cc_start: 0.6848 (m-80) cc_final: 0.6274 (m-80) REVERT: B 52 LYS cc_start: 0.7546 (mttt) cc_final: 0.7173 (mmmt) REVERT: B 60 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7847 (mt) REVERT: B 91 MET cc_start: 0.5513 (tpp) cc_final: 0.5033 (ttt) REVERT: B 133 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6975 (ttm110) REVERT: B 310 ASP cc_start: 0.7882 (m-30) cc_final: 0.7561 (m-30) REVERT: B 435 THR cc_start: 0.8173 (p) cc_final: 0.7907 (p) REVERT: C 38 ARG cc_start: 0.7168 (ttt180) cc_final: 0.6458 (ttm-80) REVERT: C 46 TYR cc_start: 0.6927 (m-80) cc_final: 0.6475 (m-80) REVERT: C 52 LYS cc_start: 0.7471 (mttt) cc_final: 0.7116 (mmmt) REVERT: C 60 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7770 (mt) REVERT: C 83 LYS cc_start: 0.7608 (mtpt) cc_final: 0.6875 (tppt) REVERT: C 119 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.6690 (mtm-85) REVERT: C 303 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7465 (mt-10) REVERT: C 310 ASP cc_start: 0.7878 (m-30) cc_final: 0.7567 (m-30) REVERT: C 435 THR cc_start: 0.8148 (p) cc_final: 0.7875 (p) REVERT: D 38 ARG cc_start: 0.7103 (ttt180) cc_final: 0.6471 (ttm-80) REVERT: D 46 TYR cc_start: 0.6919 (m-80) cc_final: 0.6449 (m-80) REVERT: D 52 LYS cc_start: 0.7546 (mttt) cc_final: 0.7161 (mmmt) REVERT: D 60 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7857 (mt) REVERT: D 83 LYS cc_start: 0.7498 (mtpt) cc_final: 0.6791 (tppt) REVERT: D 91 MET cc_start: 0.5616 (tpp) cc_final: 0.5172 (ttt) REVERT: D 119 ARG cc_start: 0.7332 (mtm-85) cc_final: 0.6682 (mtm-85) REVERT: D 133 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6891 (ttm110) REVERT: D 179 GLN cc_start: 0.7662 (pm20) cc_final: 0.7347 (pm20) REVERT: D 310 ASP cc_start: 0.7860 (m-30) cc_final: 0.7527 (m-30) REVERT: D 435 THR cc_start: 0.8179 (p) cc_final: 0.7906 (p) outliers start: 44 outliers final: 38 residues processed: 248 average time/residue: 1.2395 time to fit residues: 334.0301 Evaluate side-chains 254 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 0.0970 chunk 73 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.246403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.218111 restraints weight = 9972.569| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 1.16 r_work: 0.4324 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4215 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12408 Z= 0.155 Angle : 0.592 9.192 16836 Z= 0.306 Chirality : 0.038 0.166 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.184 18.009 1784 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.40 % Allowed : 18.49 % Favored : 78.11 % 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: 2.62 (0.21), residues: 1524 helix: 2.65 (0.13), residues: 1216 sheet: 0.80 (0.69), residues: 40 loop : -2.76 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.002 0.000 HIS A 22 PHE 0.017 0.002 PHE A 203 TYR 0.023 0.002 TYR C 124 ARG 0.003 0.000 ARG C 405 Details of bonding type rmsd hydrogen bonds : bond 0.05689 ( 1028) hydrogen bonds : angle 3.62045 ( 3048) covalent geometry : bond 0.00341 (12408) covalent geometry : angle 0.59237 (16836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10049.82 seconds wall clock time: 174 minutes 35.22 seconds (10475.22 seconds total)