Starting phenix.real_space_refine on Wed Sep 17 23:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vv3_43548/09_2025/8vv3_43548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vv3_43548/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vv3_43548/09_2025/8vv3_43548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vv3_43548/09_2025/8vv3_43548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vv3_43548/09_2025/8vv3_43548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vv3_43548/09_2025/8vv3_43548.map" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D Time building chain proxies: 2.49, per 1000 atoms: 0.20 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: 1.24 Conformation dependent library (CDL) restraints added in 591.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 2.03 Time building geometry restraints manager: 1.62 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 4.760 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.23 (0.21), 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 ARG 0.002 0.000 ARG A 117 TYR 0.022 0.001 TYR A 124 PHE 0.014 0.001 PHE C 203 TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00387 (12408) covalent geometry : angle 0.52309 (16836) hydrogen bonds : bond 0.12801 ( 1028) hydrogen bonds : angle 4.68954 ( 3048) *********************** 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 : 0.622 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: 0.6092 (ttm-80) REVERT: A 91 MET cc_start: 0.5187 (tpp) cc_final: 0.4521 (ttt) REVERT: A 118 MET cc_start: 0.8008 (mmp) cc_final: 0.7798 (mmp) REVERT: A 133 ARG cc_start: 0.6573 (ttm110) cc_final: 0.5917 (ttp-110) REVERT: A 171 MET cc_start: 0.6591 (mtm) cc_final: 0.6212 (mmt) REVERT: A 197 MET cc_start: 0.7804 (tpt) cc_final: 0.7593 (tpp) REVERT: A 215 LYS cc_start: 0.8154 (tttm) cc_final: 0.7772 (ttmt) REVERT: A 289 GLU cc_start: 0.7077 (tt0) cc_final: 0.6547 (mm-30) REVERT: A 303 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6924 (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: 0.6172 (ttp-110) REVERT: B 46 TYR cc_start: 0.6974 (m-80) cc_final: 0.6352 (m-80) REVERT: B 52 LYS cc_start: 0.7290 (mttt) cc_final: 0.6997 (mmmt) REVERT: B 91 MET cc_start: 0.5277 (tpp) cc_final: 0.4649 (ttt) REVERT: B 133 ARG cc_start: 0.6975 (ttm110) cc_final: 0.6302 (ttp-110) REVERT: B 167 CYS cc_start: 0.7745 (m) cc_final: 0.7542 (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: 0.7287 (mt-10) REVERT: B 310 ASP cc_start: 0.7878 (m-30) cc_final: 0.7535 (m-30) REVERT: B 377 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7881 (mtmt) 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: 0.4726 (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: 0.7523 (tpp) REVERT: C 215 LYS cc_start: 0.8143 (tttm) cc_final: 0.7654 (ttpt) REVERT: C 303 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6964 (mt-10) REVERT: D 38 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6297 (ttp-110) REVERT: D 46 TYR cc_start: 0.6785 (m-80) cc_final: 0.6300 (m-80) REVERT: D 60 ILE cc_start: 0.7859 (pt) cc_final: 0.7563 (mp) REVERT: D 91 MET cc_start: 0.5248 (tpp) cc_final: 0.4818 (ttt) REVERT: D 118 MET cc_start: 0.8186 (mmp) cc_final: 0.7946 (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: 0.5999 (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: 0.6890 (m-80) REVERT: D 310 ASP cc_start: 0.7968 (m-30) cc_final: 0.7586 (m-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.5761 time to fit residues: 180.0012 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 : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.4922 r_free = 0.4922 target = 0.264026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.234884 restraints weight = 10446.397| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 1.28 r_work: 0.4381 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4278 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12408 Z= 0.150 Angle : 0.538 6.732 16836 Z= 0.284 Chirality : 0.037 0.141 2076 Planarity : 0.004 0.028 2024 Dihedral : 3.831 15.035 1784 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.18 % Allowed : 8.88 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.21), residues: 1524 helix: 2.67 (0.14), residues: 1216 sheet: 0.44 (0.79), residues: 40 loop : -2.63 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.040 0.002 TYR C 124 PHE 0.016 0.002 PHE C 203 TRP 0.005 0.001 TRP A 354 HIS 0.003 0.001 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00315 (12408) covalent geometry : angle 0.53783 (16836) hydrogen bonds : bond 0.05683 ( 1028) hydrogen bonds : angle 3.75207 ( 3048) *********************** 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 273 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6891 (m-80) cc_final: 0.6268 (m-80) REVERT: A 60 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7551 (mt) REVERT: A 91 MET cc_start: 0.5283 (tpp) cc_final: 0.4714 (ttt) REVERT: A 128 ILE cc_start: 0.6679 (OUTLIER) cc_final: 0.6262 (mm) REVERT: A 133 ARG cc_start: 0.6871 (ttm110) cc_final: 0.6312 (ttp-110) REVERT: A 171 MET cc_start: 0.7206 (mtm) cc_final: 0.6689 (mmt) REVERT: A 179 GLN cc_start: 0.7537 (pm20) cc_final: 0.7167 (pm20) REVERT: A 197 MET cc_start: 0.7880 (tpt) cc_final: 0.7581 (tpp) REVERT: A 215 LYS cc_start: 0.8501 (tttm) cc_final: 0.8281 (tttt) REVERT: A 289 GLU cc_start: 0.7603 (tt0) cc_final: 0.6563 (mm-30) REVERT: A 303 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7203 (mt-10) REVERT: A 310 ASP cc_start: 0.7749 (m-30) cc_final: 0.7449 (m-30) REVERT: B 38 ARG cc_start: 0.6825 (ttt180) cc_final: 0.6116 (ttp-110) REVERT: B 46 TYR cc_start: 0.6835 (m-80) cc_final: 0.6457 (m-80) REVERT: B 52 LYS cc_start: 0.7457 (mttt) cc_final: 0.6942 (mmmt) REVERT: B 91 MET cc_start: 0.5255 (tpp) cc_final: 0.4777 (ttt) REVERT: B 128 ILE cc_start: 0.6614 (OUTLIER) cc_final: 0.6088 (mm) REVERT: B 133 ARG cc_start: 0.7133 (ttm110) cc_final: 0.6625 (ttp-110) REVERT: B 164 ASP cc_start: 0.8112 (t70) cc_final: 0.7899 (t70) REVERT: B 167 CYS cc_start: 0.8493 (m) cc_final: 0.8239 (m) REVERT: B 172 GLN cc_start: 0.6761 (mm110) cc_final: 0.6534 (mt0) REVERT: B 179 GLN cc_start: 0.7389 (pm20) cc_final: 0.7044 (pm20) REVERT: B 219 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7640 (mt-10) REVERT: B 310 ASP cc_start: 0.7751 (m-30) cc_final: 0.7439 (m-30) REVERT: B 377 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7852 (mtmt) REVERT: C 38 ARG cc_start: 0.6970 (ttt180) cc_final: 0.6230 (ttp-110) REVERT: C 49 THR cc_start: 0.7077 (t) cc_final: 0.6829 (t) REVERT: C 91 MET cc_start: 0.5068 (tpp) cc_final: 0.4736 (ttt) REVERT: C 119 ARG cc_start: 0.7294 (mtm-85) cc_final: 0.6784 (mtm-85) REVERT: C 179 GLN cc_start: 0.7365 (pm20) cc_final: 0.6990 (pm20) REVERT: C 197 MET cc_start: 0.7874 (tpt) cc_final: 0.7543 (tpp) REVERT: C 289 GLU cc_start: 0.7616 (tt0) cc_final: 0.6443 (mm-30) REVERT: C 303 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 435 THR cc_start: 0.8104 (p) cc_final: 0.7777 (p) REVERT: D 38 ARG cc_start: 0.6904 (ttt180) cc_final: 0.6189 (ttp-110) REVERT: D 46 TYR cc_start: 0.6760 (m-80) cc_final: 0.6436 (m-80) REVERT: D 60 ILE cc_start: 0.7909 (pt) cc_final: 0.7667 (mp) REVERT: D 91 MET cc_start: 0.5319 (tpp) cc_final: 0.4895 (ttt) REVERT: D 118 MET cc_start: 0.8090 (mmp) cc_final: 0.7882 (mmp) REVERT: D 119 ARG cc_start: 0.7271 (mtm-85) cc_final: 0.6640 (mtm-85) REVERT: D 133 ARG cc_start: 0.6764 (ttm110) cc_final: 0.6152 (ttp-110) REVERT: D 167 CYS cc_start: 0.8488 (m) cc_final: 0.8235 (m) REVERT: D 179 GLN cc_start: 0.7417 (pm20) cc_final: 0.7003 (pm20) REVERT: D 205 PHE cc_start: 0.7562 (m-80) cc_final: 0.7144 (m-80) REVERT: D 215 LYS cc_start: 0.8364 (ttpt) cc_final: 0.8136 (ttpp) REVERT: D 289 GLU cc_start: 0.7638 (tt0) cc_final: 0.6505 (mm-30) REVERT: D 310 ASP cc_start: 0.7915 (m-30) cc_final: 0.7567 (m-30) REVERT: D 387 MET cc_start: 0.7878 (mmm) cc_final: 0.7517 (mtt) REVERT: D 401 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7843 (tm-30) REVERT: D 435 THR cc_start: 0.8080 (p) cc_final: 0.7785 (p) outliers start: 43 outliers final: 20 residues processed: 252 average time/residue: 0.5950 time to fit residues: 162.5358 Evaluate side-chains 238 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 B residue 222 ASN 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 210 LEU 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 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.0970 chunk 140 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.255944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.225280 restraints weight = 10343.267| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 1.32 r_work: 0.4306 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.4199 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1800 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= 0.167 Angle : 0.564 5.988 16836 Z= 0.297 Chirality : 0.038 0.149 2076 Planarity : 0.004 0.030 2024 Dihedral : 3.952 15.335 1784 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.40 % Allowed : 11.91 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.21), residues: 1524 helix: 2.66 (0.14), residues: 1220 sheet: 0.23 (0.77), residues: 40 loop : -2.73 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 293 TYR 0.034 0.002 TYR C 124 PHE 0.017 0.002 PHE A 203 TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00369 (12408) covalent geometry : angle 0.56387 (16836) hydrogen bonds : bond 0.06035 ( 1028) hydrogen bonds : angle 3.69490 ( 3048) *********************** 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: 46 poor density : 222 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6791 (m-80) cc_final: 0.5983 (m-80) REVERT: A 60 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7592 (mt) REVERT: A 91 MET cc_start: 0.5344 (tpp) cc_final: 0.4845 (ttt) REVERT: A 133 ARG cc_start: 0.7059 (ttm110) cc_final: 0.6779 (ttm110) REVERT: A 171 MET cc_start: 0.7258 (mtm) cc_final: 0.6699 (mmt) REVERT: A 179 GLN cc_start: 0.7500 (pm20) cc_final: 0.7069 (pm20) REVERT: A 197 MET cc_start: 0.7867 (tpt) cc_final: 0.7639 (tpp) REVERT: A 215 LYS cc_start: 0.8459 (tttm) cc_final: 0.8255 (ttpt) REVERT: A 289 GLU cc_start: 0.7646 (tt0) cc_final: 0.6670 (mm-30) REVERT: A 303 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 310 ASP cc_start: 0.7780 (m-30) cc_final: 0.7474 (m-30) REVERT: B 38 ARG cc_start: 0.6955 (ttt180) cc_final: 0.6211 (ttm-80) REVERT: B 46 TYR cc_start: 0.6819 (m-80) cc_final: 0.6144 (m-80) REVERT: B 52 LYS cc_start: 0.7481 (mttt) cc_final: 0.6993 (mmmt) REVERT: B 91 MET cc_start: 0.5310 (tpp) cc_final: 0.4827 (ttt) REVERT: B 128 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6258 (mm) REVERT: B 133 ARG cc_start: 0.7244 (ttm110) cc_final: 0.6965 (ttm110) REVERT: B 179 GLN cc_start: 0.7234 (pm20) cc_final: 0.6904 (pm20) REVERT: B 215 LYS cc_start: 0.8503 (mtpm) cc_final: 0.8274 (mtpt) REVERT: B 219 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7738 (mt-10) REVERT: B 310 ASP cc_start: 0.7837 (m-30) cc_final: 0.7518 (m-30) REVERT: B 387 MET cc_start: 0.7868 (mmm) cc_final: 0.7554 (mtt) REVERT: C 38 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6235 (ttp-110) REVERT: C 52 LYS cc_start: 0.7210 (mttt) cc_final: 0.6778 (mmmt) REVERT: C 91 MET cc_start: 0.5255 (tpp) cc_final: 0.4863 (ttt) REVERT: C 119 ARG cc_start: 0.7228 (mtm-85) cc_final: 0.6657 (mtm-85) REVERT: C 133 ARG cc_start: 0.6556 (ttm110) cc_final: 0.5991 (ttp-110) REVERT: C 179 GLN cc_start: 0.7440 (pm20) cc_final: 0.7060 (pm20) REVERT: C 197 MET cc_start: 0.7942 (tpt) cc_final: 0.7722 (tpp) REVERT: C 303 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7182 (mt-10) REVERT: C 310 ASP cc_start: 0.7623 (m-30) cc_final: 0.7369 (m-30) REVERT: C 435 THR cc_start: 0.8147 (p) cc_final: 0.7865 (p) REVERT: D 38 ARG cc_start: 0.6911 (ttt180) cc_final: 0.6216 (ttp-110) REVERT: D 46 TYR cc_start: 0.6753 (m-80) cc_final: 0.6225 (m-80) REVERT: D 52 LYS cc_start: 0.7479 (mttt) cc_final: 0.6975 (mmmt) REVERT: D 60 ILE cc_start: 0.7856 (pt) cc_final: 0.7611 (mp) REVERT: D 91 MET cc_start: 0.5329 (tpp) cc_final: 0.4955 (ttt) REVERT: D 118 MET cc_start: 0.7936 (mmp) cc_final: 0.7693 (mmp) REVERT: D 119 ARG cc_start: 0.7289 (mtm-85) cc_final: 0.6608 (mtm-85) REVERT: D 133 ARG cc_start: 0.6885 (ttm110) cc_final: 0.6638 (ttm110) REVERT: D 179 GLN cc_start: 0.7299 (pm20) cc_final: 0.6893 (pm20) REVERT: D 215 LYS cc_start: 0.8317 (ttpt) cc_final: 0.8005 (ttpp) REVERT: D 289 GLU cc_start: 0.7707 (tt0) cc_final: 0.6520 (mm-30) REVERT: D 310 ASP cc_start: 0.7795 (m-30) cc_final: 0.7474 (m-30) REVERT: D 387 MET cc_start: 0.7832 (mmm) cc_final: 0.7597 (mtt) REVERT: D 401 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7940 (tm-30) REVERT: D 435 THR cc_start: 0.8107 (p) cc_final: 0.7839 (p) outliers start: 46 outliers final: 25 residues processed: 242 average time/residue: 0.6072 time to fit residues: 158.3769 Evaluate side-chains 241 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 210 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 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 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 148 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 28 optimal weight: 0.0470 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4794 r_free = 0.4794 target = 0.246792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.218193 restraints weight = 10087.307| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 1.18 r_work: 0.4333 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12408 Z= 0.147 Angle : 0.532 6.948 16836 Z= 0.279 Chirality : 0.037 0.131 2076 Planarity : 0.004 0.030 2024 Dihedral : 3.955 15.431 1784 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.40 % Allowed : 14.20 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.21), residues: 1524 helix: 2.73 (0.13), residues: 1220 sheet: 0.26 (0.75), residues: 40 loop : -2.71 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 293 TYR 0.027 0.002 TYR B 124 PHE 0.017 0.002 PHE A 203 TRP 0.005 0.001 TRP D 354 HIS 0.002 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00316 (12408) covalent geometry : angle 0.53169 (16836) hydrogen bonds : bond 0.05661 ( 1028) hydrogen bonds : angle 3.60354 ( 3048) *********************** 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 269 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7755 (mt) REVERT: A 91 MET cc_start: 0.5365 (tpp) cc_final: 0.4806 (ttt) REVERT: A 133 ARG cc_start: 0.7182 (ttm110) cc_final: 0.6929 (ttm110) REVERT: A 171 MET cc_start: 0.7454 (mtm) cc_final: 0.6935 (mmt) REVERT: A 179 GLN cc_start: 0.7634 (pm20) cc_final: 0.7310 (pm20) REVERT: A 197 MET cc_start: 0.8075 (tpt) cc_final: 0.7793 (tpp) REVERT: A 219 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7939 (mt-10) REVERT: A 289 GLU cc_start: 0.7816 (tt0) cc_final: 0.6822 (mm-30) REVERT: A 303 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7351 (mt-10) REVERT: A 310 ASP cc_start: 0.7885 (m-30) cc_final: 0.7571 (m-30) REVERT: B 38 ARG cc_start: 0.7003 (ttt180) cc_final: 0.6360 (ttm-80) REVERT: B 46 TYR cc_start: 0.6793 (m-80) cc_final: 0.6246 (m-80) REVERT: B 52 LYS cc_start: 0.7501 (mttt) cc_final: 0.7097 (mmmt) REVERT: B 60 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7713 (mt) REVERT: B 91 MET cc_start: 0.5387 (tpp) cc_final: 0.4854 (ttt) REVERT: B 128 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6402 (mm) REVERT: B 133 ARG cc_start: 0.7321 (ttm110) cc_final: 0.7073 (ttm110) REVERT: B 179 GLN cc_start: 0.7379 (pm20) cc_final: 0.7058 (pm20) REVERT: B 219 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 310 ASP cc_start: 0.7910 (m-30) cc_final: 0.7587 (m-30) REVERT: B 387 MET cc_start: 0.7822 (mmm) cc_final: 0.7539 (mtt) REVERT: B 435 THR cc_start: 0.8150 (p) cc_final: 0.7882 (p) REVERT: C 38 ARG cc_start: 0.7011 (ttt180) cc_final: 0.6408 (ttp-110) REVERT: C 46 TYR cc_start: 0.6965 (m-80) cc_final: 0.6553 (m-80) REVERT: C 52 LYS cc_start: 0.7443 (mttt) cc_final: 0.7091 (mmmt) REVERT: C 91 MET cc_start: 0.5401 (tpp) cc_final: 0.4958 (ttt) REVERT: C 119 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.6933 (mtm-85) REVERT: C 133 ARG cc_start: 0.6781 (ttm110) cc_final: 0.6276 (ttp-110) REVERT: C 179 GLN cc_start: 0.7500 (pm20) cc_final: 0.7173 (pm20) REVERT: C 303 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7452 (mt-10) REVERT: C 310 ASP cc_start: 0.7824 (m-30) cc_final: 0.7537 (m-30) REVERT: C 435 THR cc_start: 0.8189 (p) cc_final: 0.7883 (p) REVERT: D 38 ARG cc_start: 0.6934 (ttt180) cc_final: 0.6347 (ttp-110) REVERT: D 46 TYR cc_start: 0.6932 (m-80) cc_final: 0.6421 (m-80) REVERT: D 52 LYS cc_start: 0.7617 (mttt) cc_final: 0.7145 (mmmt) REVERT: D 91 MET cc_start: 0.5467 (tpp) cc_final: 0.5005 (ttt) REVERT: D 119 ARG cc_start: 0.7440 (mtm-85) cc_final: 0.6826 (mtm-85) REVERT: D 133 ARG cc_start: 0.7034 (ttm110) cc_final: 0.6782 (ttm110) REVERT: D 179 GLN cc_start: 0.7325 (pm20) cc_final: 0.7009 (pm20) REVERT: D 215 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8204 (ttpp) REVERT: D 289 GLU cc_start: 0.7857 (tt0) cc_final: 0.7575 (tt0) REVERT: D 310 ASP cc_start: 0.7910 (m-30) cc_final: 0.7564 (m-30) REVERT: D 435 THR cc_start: 0.8247 (p) cc_final: 0.7963 (p) outliers start: 46 outliers final: 31 residues processed: 252 average time/residue: 0.6054 time to fit residues: 164.7416 Evaluate side-chains 251 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 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 = 0.4769 r_free = 0.4769 target = 0.243719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.214866 restraints weight = 10120.051| |-----------------------------------------------------------------------------| r_work (start): 0.4494 rms_B_bonded: 1.18 r_work: 0.4301 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4190 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2112 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= 0.182 Angle : 0.590 7.780 16836 Z= 0.308 Chirality : 0.039 0.181 2076 Planarity : 0.005 0.032 2024 Dihedral : 4.148 16.181 1784 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.81 % Allowed : 14.79 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.21), residues: 1524 helix: 2.62 (0.13), residues: 1216 sheet: 0.37 (0.73), residues: 40 loop : -2.79 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 385 TYR 0.026 0.002 TYR C 124 PHE 0.018 0.002 PHE A 203 TRP 0.005 0.001 TRP D 354 HIS 0.004 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00418 (12408) covalent geometry : angle 0.59015 (16836) hydrogen bonds : bond 0.06223 ( 1028) hydrogen bonds : angle 3.70187 ( 3048) *********************** 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 288 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6850 (m-80) cc_final: 0.6146 (m-80) REVERT: A 60 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7752 (mt) REVERT: A 91 MET cc_start: 0.5486 (tpp) cc_final: 0.4908 (ttt) REVERT: A 133 ARG cc_start: 0.7336 (ttm110) cc_final: 0.7071 (ttm110) REVERT: A 171 MET cc_start: 0.7576 (mtm) cc_final: 0.6958 (mmt) REVERT: A 179 GLN cc_start: 0.7678 (pm20) cc_final: 0.7411 (pm20) REVERT: A 197 MET cc_start: 0.8100 (tpt) cc_final: 0.7889 (tpp) REVERT: A 219 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 303 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 310 ASP cc_start: 0.7923 (m-30) cc_final: 0.7613 (m-30) REVERT: B 38 ARG cc_start: 0.7159 (ttt180) cc_final: 0.6446 (ttm-80) REVERT: B 46 TYR cc_start: 0.6685 (m-80) cc_final: 0.6086 (m-80) REVERT: B 52 LYS cc_start: 0.7484 (mttt) cc_final: 0.7102 (mmmt) REVERT: B 60 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7747 (mt) REVERT: B 91 MET cc_start: 0.5383 (tpp) cc_final: 0.4919 (ttt) REVERT: B 133 ARG cc_start: 0.7383 (ttm110) cc_final: 0.7122 (ttm110) REVERT: B 179 GLN cc_start: 0.7390 (pm20) cc_final: 0.7108 (pm20) REVERT: B 310 ASP cc_start: 0.7936 (m-30) cc_final: 0.7616 (m-30) REVERT: B 377 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7938 (mtmt) REVERT: B 387 MET cc_start: 0.7841 (mmm) cc_final: 0.7561 (mtt) REVERT: B 435 THR cc_start: 0.8145 (p) cc_final: 0.7875 (p) REVERT: C 38 ARG cc_start: 0.7220 (ttt180) cc_final: 0.6473 (ttp-110) REVERT: C 46 TYR cc_start: 0.7034 (m-80) cc_final: 0.6637 (m-80) REVERT: C 52 LYS cc_start: 0.7504 (mttt) cc_final: 0.7129 (mmmt) REVERT: C 91 MET cc_start: 0.5446 (tpp) cc_final: 0.5022 (ttt) REVERT: C 119 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.6952 (mtm-85) REVERT: C 126 GLU cc_start: 0.6165 (pt0) cc_final: 0.5833 (mm-30) REVERT: C 133 ARG cc_start: 0.7067 (ttm110) cc_final: 0.6817 (ttm110) REVERT: C 179 GLN cc_start: 0.7551 (pm20) cc_final: 0.7301 (pm20) REVERT: C 303 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7446 (mt-10) REVERT: C 310 ASP cc_start: 0.7883 (m-30) cc_final: 0.7584 (m-30) REVERT: C 435 THR cc_start: 0.8185 (p) cc_final: 0.7899 (p) REVERT: D 38 ARG cc_start: 0.6956 (ttt180) cc_final: 0.6404 (ttm-80) REVERT: D 46 TYR cc_start: 0.6927 (m-80) cc_final: 0.6425 (m-80) REVERT: D 52 LYS cc_start: 0.7655 (mttt) cc_final: 0.7181 (mmmt) REVERT: D 91 MET cc_start: 0.5607 (tpp) cc_final: 0.5169 (ttt) REVERT: D 119 ARG cc_start: 0.7474 (mtm-85) cc_final: 0.6826 (mtm-85) REVERT: D 133 ARG cc_start: 0.7186 (ttm110) cc_final: 0.6943 (ttm110) REVERT: D 179 GLN cc_start: 0.7416 (pm20) cc_final: 0.7180 (pm20) REVERT: D 289 GLU cc_start: 0.7959 (tt0) cc_final: 0.7662 (tt0) REVERT: D 310 ASP cc_start: 0.7867 (m-30) cc_final: 0.7533 (m-30) REVERT: D 435 THR cc_start: 0.8187 (p) cc_final: 0.7919 (p) outliers start: 65 outliers final: 41 residues processed: 265 average time/residue: 0.5703 time to fit residues: 163.8661 Evaluate side-chains 262 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE 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 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 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 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 37 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 146 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4886 r_free = 0.4886 target = 0.254888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.229832 restraints weight = 9753.798| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 0.99 r_work: 0.4389 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.4278 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12408 Z= 0.174 Angle : 0.585 8.980 16836 Z= 0.303 Chirality : 0.039 0.170 2076 Planarity : 0.004 0.033 2024 Dihedral : 4.162 17.817 1784 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.51 % Allowed : 15.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.20), residues: 1524 helix: 2.60 (0.13), residues: 1216 sheet: 0.48 (0.71), residues: 40 loop : -2.71 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.024 0.002 TYR A 124 PHE 0.018 0.002 PHE A 203 TRP 0.005 0.001 TRP A 354 HIS 0.003 0.001 HIS C 22 Details of bonding type rmsd covalent geometry : bond 0.00396 (12408) covalent geometry : angle 0.58454 (16836) hydrogen bonds : bond 0.06108 ( 1028) hydrogen bonds : angle 3.67510 ( 3048) *********************** 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 282 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 221 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6830 (m-80) cc_final: 0.6097 (m-80) REVERT: A 60 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7747 (mt) REVERT: A 91 MET cc_start: 0.5424 (tpp) cc_final: 0.4920 (ttt) REVERT: A 133 ARG cc_start: 0.7215 (ttm110) cc_final: 0.6963 (ttm110) REVERT: A 171 MET cc_start: 0.7645 (mtm) cc_final: 0.7055 (mmt) REVERT: A 197 MET cc_start: 0.8070 (tpt) cc_final: 0.7853 (tpp) REVERT: A 303 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 310 ASP cc_start: 0.7900 (m-30) cc_final: 0.7583 (m-30) REVERT: B 38 ARG cc_start: 0.7161 (ttt180) cc_final: 0.6431 (ttm-80) REVERT: B 46 TYR cc_start: 0.6681 (m-80) cc_final: 0.6065 (m-80) REVERT: B 52 LYS cc_start: 0.7521 (mttt) cc_final: 0.7099 (mmmt) REVERT: B 60 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7765 (mt) REVERT: B 91 MET cc_start: 0.5344 (tpp) cc_final: 0.4930 (ttt) REVERT: B 133 ARG cc_start: 0.7335 (ttm110) cc_final: 0.7072 (ttm110) REVERT: B 179 GLN cc_start: 0.7430 (pm20) cc_final: 0.7196 (pm20) REVERT: B 310 ASP cc_start: 0.7930 (m-30) cc_final: 0.7622 (m-30) REVERT: B 387 MET cc_start: 0.7813 (mmm) cc_final: 0.7590 (mtt) REVERT: B 435 THR cc_start: 0.8137 (p) cc_final: 0.7865 (p) REVERT: C 38 ARG cc_start: 0.7287 (ttt180) cc_final: 0.6448 (ttm-80) REVERT: C 46 TYR cc_start: 0.7041 (m-80) cc_final: 0.6647 (m-80) REVERT: C 52 LYS cc_start: 0.7497 (mttt) cc_final: 0.7097 (mmmt) REVERT: C 91 MET cc_start: 0.5491 (tpp) cc_final: 0.5100 (ttt) REVERT: C 119 ARG cc_start: 0.7259 (mtm-85) cc_final: 0.6918 (mtm-85) REVERT: C 133 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6774 (ttm110) REVERT: C 179 GLN cc_start: 0.7538 (pm20) cc_final: 0.7213 (pm20) REVERT: C 303 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7447 (mt-10) REVERT: C 310 ASP cc_start: 0.7870 (m-30) cc_final: 0.7583 (m-30) REVERT: C 435 THR cc_start: 0.8155 (p) cc_final: 0.7865 (p) REVERT: D 38 ARG cc_start: 0.7040 (ttt180) cc_final: 0.6421 (ttm-80) REVERT: D 46 TYR cc_start: 0.6865 (m-80) cc_final: 0.6375 (m-80) REVERT: D 52 LYS cc_start: 0.7612 (mttt) cc_final: 0.7144 (mmmt) REVERT: D 91 MET cc_start: 0.5514 (tpp) cc_final: 0.5121 (ttt) REVERT: D 119 ARG cc_start: 0.7449 (mtm-85) cc_final: 0.6990 (mtm-85) REVERT: D 133 ARG cc_start: 0.7091 (ttm110) cc_final: 0.6847 (ttm110) REVERT: D 179 GLN cc_start: 0.7427 (pm20) cc_final: 0.7117 (pm20) REVERT: D 289 GLU cc_start: 0.7891 (tt0) cc_final: 0.7581 (tt0) REVERT: D 310 ASP cc_start: 0.7853 (m-30) cc_final: 0.7515 (m-30) REVERT: D 435 THR cc_start: 0.8171 (p) cc_final: 0.7898 (p) outliers start: 61 outliers final: 41 residues processed: 266 average time/residue: 0.5564 time to fit residues: 160.7883 Evaluate side-chains 256 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 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 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU 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 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 22 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.258354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.230747 restraints weight = 10293.711| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 1.15 r_work: 0.4349 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4244 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2257 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= 0.168 Angle : 0.581 8.583 16836 Z= 0.302 Chirality : 0.038 0.190 2076 Planarity : 0.004 0.035 2024 Dihedral : 4.193 18.556 1784 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.66 % Allowed : 15.38 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.20), residues: 1524 helix: 2.57 (0.13), residues: 1220 sheet: 0.52 (0.70), residues: 40 loop : -2.69 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.023 0.002 TYR A 124 PHE 0.017 0.002 PHE A 203 TRP 0.005 0.001 TRP C 354 HIS 0.002 0.001 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00380 (12408) covalent geometry : angle 0.58149 (16836) hydrogen bonds : bond 0.06022 ( 1028) hydrogen bonds : angle 3.68001 ( 3048) *********************** 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 283 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6844 (m-80) cc_final: 0.6106 (m-80) REVERT: A 60 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7774 (mt) REVERT: A 91 MET cc_start: 0.5353 (tpp) cc_final: 0.4906 (ttt) REVERT: A 133 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6897 (ttm110) REVERT: A 171 MET cc_start: 0.7590 (mtm) cc_final: 0.7020 (mmt) REVERT: A 197 MET cc_start: 0.8023 (tpt) cc_final: 0.7797 (tpp) REVERT: A 303 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7186 (mt-10) REVERT: A 310 ASP cc_start: 0.7851 (m-30) cc_final: 0.7532 (m-30) REVERT: B 38 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6397 (ttm-80) REVERT: B 46 TYR cc_start: 0.6707 (m-80) cc_final: 0.6055 (m-80) REVERT: B 52 LYS cc_start: 0.7423 (mttt) cc_final: 0.7083 (mmmt) REVERT: B 60 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7739 (mt) REVERT: B 91 MET cc_start: 0.5338 (tpp) cc_final: 0.4963 (ttt) REVERT: B 133 ARG cc_start: 0.7251 (ttm110) cc_final: 0.7000 (ttm110) REVERT: B 179 GLN cc_start: 0.7475 (pm20) cc_final: 0.7141 (pm20) REVERT: B 310 ASP cc_start: 0.7870 (m-30) cc_final: 0.7560 (m-30) REVERT: B 387 MET cc_start: 0.7804 (mmm) cc_final: 0.7579 (mtt) REVERT: B 435 THR cc_start: 0.8154 (p) cc_final: 0.7891 (p) REVERT: C 38 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6369 (ttm-80) REVERT: C 46 TYR cc_start: 0.7054 (m-80) cc_final: 0.6671 (m-80) REVERT: C 52 LYS cc_start: 0.7449 (mttt) cc_final: 0.7086 (mmmt) REVERT: C 60 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7717 (mt) REVERT: C 91 MET cc_start: 0.5449 (tpp) cc_final: 0.5095 (ttt) REVERT: C 119 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6779 (mtm-85) REVERT: C 133 ARG cc_start: 0.6965 (ttm110) cc_final: 0.6730 (ttm110) REVERT: C 273 MET cc_start: 0.6171 (mmm) cc_final: 0.5916 (tpt) REVERT: C 274 MET cc_start: 0.3734 (OUTLIER) cc_final: 0.3006 (ttp) REVERT: C 303 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 310 ASP cc_start: 0.7841 (m-30) cc_final: 0.7534 (m-30) REVERT: C 435 THR cc_start: 0.8148 (p) cc_final: 0.7866 (p) REVERT: D 38 ARG cc_start: 0.6988 (ttt180) cc_final: 0.6384 (ttm-80) REVERT: D 46 TYR cc_start: 0.6896 (m-80) cc_final: 0.6416 (m-80) REVERT: D 52 LYS cc_start: 0.7497 (mttt) cc_final: 0.7112 (mmmt) REVERT: D 91 MET cc_start: 0.5492 (tpp) cc_final: 0.5112 (ttt) REVERT: D 119 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.6853 (mtm-85) REVERT: D 133 ARG cc_start: 0.7034 (ttm110) cc_final: 0.6795 (ttm110) REVERT: D 179 GLN cc_start: 0.7441 (pm20) cc_final: 0.7208 (pm20) REVERT: D 289 GLU cc_start: 0.7828 (tt0) cc_final: 0.7518 (tt0) REVERT: D 310 ASP cc_start: 0.7807 (m-30) cc_final: 0.7464 (m-30) REVERT: D 435 THR cc_start: 0.8151 (p) cc_final: 0.7881 (p) outliers start: 63 outliers final: 47 residues processed: 266 average time/residue: 0.5689 time to fit residues: 164.6711 Evaluate side-chains 267 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 96 SER 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 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 274 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4768 r_free = 0.4768 target = 0.243674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.215306 restraints weight = 10065.644| |-----------------------------------------------------------------------------| r_work (start): 0.4500 rms_B_bonded: 1.16 r_work: 0.4313 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4204 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12408 Z= 0.176 Angle : 0.602 9.354 16836 Z= 0.311 Chirality : 0.039 0.195 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.237 19.207 1784 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.51 % Allowed : 16.05 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.20), residues: 1524 helix: 2.53 (0.13), residues: 1220 sheet: 0.53 (0.69), residues: 40 loop : -2.82 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.023 0.002 TYR B 124 PHE 0.018 0.002 PHE A 203 TRP 0.005 0.001 TRP C 354 HIS 0.002 0.001 HIS B 22 Details of bonding type rmsd covalent geometry : bond 0.00403 (12408) covalent geometry : angle 0.60173 (16836) hydrogen bonds : bond 0.06123 ( 1028) hydrogen bonds : angle 3.70671 ( 3048) *********************** 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 278 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6801 (m-80) cc_final: 0.6152 (m-80) REVERT: A 60 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7782 (mt) REVERT: A 91 MET cc_start: 0.5480 (tpp) cc_final: 0.4986 (ttt) REVERT: A 133 ARG cc_start: 0.7219 (ttm110) cc_final: 0.6973 (ttm110) REVERT: A 171 MET cc_start: 0.7654 (mtm) cc_final: 0.7080 (mmt) REVERT: A 197 MET cc_start: 0.8071 (tpt) cc_final: 0.7858 (tpp) REVERT: A 303 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 310 ASP cc_start: 0.7882 (m-30) cc_final: 0.7562 (m-30) REVERT: B 38 ARG cc_start: 0.7200 (ttt180) cc_final: 0.6509 (ttm-80) REVERT: B 46 TYR cc_start: 0.6807 (m-80) cc_final: 0.6206 (m-80) REVERT: B 52 LYS cc_start: 0.7471 (mttt) cc_final: 0.7134 (mmmt) REVERT: B 60 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7780 (mt) REVERT: B 91 MET cc_start: 0.5417 (tpp) cc_final: 0.4996 (ttt) REVERT: B 133 ARG cc_start: 0.7321 (ttm110) cc_final: 0.7060 (ttm110) REVERT: B 179 GLN cc_start: 0.7525 (pm20) cc_final: 0.7218 (pm20) REVERT: B 310 ASP cc_start: 0.7950 (m-30) cc_final: 0.7639 (m-30) REVERT: B 387 MET cc_start: 0.7856 (mmm) cc_final: 0.7608 (mtt) REVERT: B 435 THR cc_start: 0.8173 (p) cc_final: 0.7906 (p) REVERT: C 38 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6440 (ttm-80) REVERT: C 46 TYR cc_start: 0.7034 (m-80) cc_final: 0.6666 (m-80) REVERT: C 52 LYS cc_start: 0.7499 (mttt) cc_final: 0.7116 (mmmt) REVERT: C 60 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7738 (mt) REVERT: C 91 MET cc_start: 0.5544 (tpp) cc_final: 0.5155 (ttt) REVERT: C 119 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.6824 (mtm-85) REVERT: C 133 ARG cc_start: 0.7037 (ttm110) cc_final: 0.6795 (ttm110) REVERT: C 179 GLN cc_start: 0.7785 (pm20) cc_final: 0.7505 (pm20) REVERT: C 215 LYS cc_start: 0.8500 (tttm) cc_final: 0.8241 (ttpp) REVERT: C 273 MET cc_start: 0.6283 (mmm) cc_final: 0.6064 (tpt) REVERT: C 274 MET cc_start: 0.3799 (OUTLIER) cc_final: 0.2934 (ttp) REVERT: C 303 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7454 (mt-10) REVERT: C 310 ASP cc_start: 0.7872 (m-30) cc_final: 0.7557 (m-30) REVERT: C 435 THR cc_start: 0.8161 (p) cc_final: 0.7887 (p) REVERT: D 38 ARG cc_start: 0.7070 (ttt180) cc_final: 0.6449 (ttm-80) REVERT: D 46 TYR cc_start: 0.6905 (m-80) cc_final: 0.6435 (m-80) REVERT: D 52 LYS cc_start: 0.7532 (mttt) cc_final: 0.7146 (mmmt) REVERT: D 60 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7830 (mt) REVERT: D 91 MET cc_start: 0.5541 (tpp) cc_final: 0.5129 (ttt) REVERT: D 119 ARG cc_start: 0.7370 (mtm-85) cc_final: 0.6863 (mtm-85) REVERT: D 133 ARG cc_start: 0.7126 (ttm110) cc_final: 0.6887 (ttm110) REVERT: D 310 ASP cc_start: 0.7852 (m-30) cc_final: 0.7512 (m-30) REVERT: D 435 THR cc_start: 0.8197 (p) cc_final: 0.7930 (p) outliers start: 61 outliers final: 47 residues processed: 265 average time/residue: 0.5592 time to fit residues: 161.0821 Evaluate side-chains 267 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 27 LYS 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 274 MET 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 40 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 22 optimal weight: 0.0030 chunk 59 optimal weight: 0.0060 chunk 120 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 351 GLN D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.247776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.220201 restraints weight = 10025.937| |-----------------------------------------------------------------------------| r_work (start): 0.4556 rms_B_bonded: 1.13 r_work: 0.4388 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4284 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12408 Z= 0.136 Angle : 0.542 8.901 16836 Z= 0.283 Chirality : 0.036 0.155 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.080 20.082 1784 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.07 % Allowed : 16.49 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.21), residues: 1524 helix: 2.79 (0.13), residues: 1216 sheet: 0.81 (0.68), residues: 40 loop : -2.71 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 405 TYR 0.022 0.001 TYR A 124 PHE 0.015 0.002 PHE A 203 TRP 0.005 0.001 TRP C 354 HIS 0.001 0.000 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00280 (12408) covalent geometry : angle 0.54185 (16836) hydrogen bonds : bond 0.05343 ( 1028) hydrogen bonds : angle 3.56024 ( 3048) *********************** 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 284 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7778 (mt) REVERT: A 91 MET cc_start: 0.5341 (tpp) cc_final: 0.4903 (ttt) REVERT: A 133 ARG cc_start: 0.6962 (ttm110) cc_final: 0.6404 (ttp-110) REVERT: A 171 MET cc_start: 0.7523 (mtm) cc_final: 0.6993 (mmt) REVERT: A 197 MET cc_start: 0.7999 (tpt) cc_final: 0.7768 (tpp) REVERT: A 215 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8091 (ttpp) REVERT: A 303 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7198 (mt-10) REVERT: A 310 ASP cc_start: 0.7869 (m-30) cc_final: 0.7537 (m-30) REVERT: B 38 ARG cc_start: 0.6974 (ttt180) cc_final: 0.6309 (ttm-80) REVERT: B 46 TYR cc_start: 0.6756 (m-80) cc_final: 0.6450 (m-80) REVERT: B 52 LYS cc_start: 0.7454 (mttt) cc_final: 0.7113 (mmmt) REVERT: B 60 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7770 (mt) REVERT: B 91 MET cc_start: 0.5360 (tpp) cc_final: 0.4941 (ttt) REVERT: B 133 ARG cc_start: 0.7071 (ttm110) cc_final: 0.6839 (ttm110) REVERT: B 310 ASP cc_start: 0.7853 (m-30) cc_final: 0.7527 (m-30) REVERT: B 387 MET cc_start: 0.7745 (mmm) cc_final: 0.7512 (mtt) REVERT: B 435 THR cc_start: 0.8057 (p) cc_final: 0.7828 (p) REVERT: C 38 ARG cc_start: 0.6983 (ttt180) cc_final: 0.6268 (ttm-80) REVERT: C 46 TYR cc_start: 0.6922 (m-80) cc_final: 0.6465 (m-80) REVERT: C 52 LYS cc_start: 0.7411 (mttt) cc_final: 0.7041 (mmmt) REVERT: C 60 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7704 (mt) REVERT: C 91 MET cc_start: 0.5455 (tpp) cc_final: 0.5095 (ttt) REVERT: C 133 ARG cc_start: 0.6851 (ttm110) cc_final: 0.6609 (ttm110) REVERT: C 179 GLN cc_start: 0.7741 (pm20) cc_final: 0.7474 (pm20) REVERT: C 215 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8178 (ttpp) REVERT: C 274 MET cc_start: 0.4075 (OUTLIER) cc_final: 0.3103 (ttp) REVERT: C 303 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 310 ASP cc_start: 0.7717 (m-30) cc_final: 0.7428 (m-30) REVERT: C 435 THR cc_start: 0.8089 (p) cc_final: 0.7863 (p) REVERT: D 38 ARG cc_start: 0.6908 (ttt180) cc_final: 0.6289 (ttm-80) REVERT: D 46 TYR cc_start: 0.6909 (m-80) cc_final: 0.6389 (m-80) REVERT: D 52 LYS cc_start: 0.7491 (mttt) cc_final: 0.7114 (mmmt) REVERT: D 60 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7843 (mt) REVERT: D 91 MET cc_start: 0.5447 (tpp) cc_final: 0.5073 (ttt) REVERT: D 133 ARG cc_start: 0.6889 (ttm110) cc_final: 0.6643 (ttm110) REVERT: D 310 ASP cc_start: 0.7804 (m-30) cc_final: 0.7463 (m-30) REVERT: D 435 THR cc_start: 0.8084 (p) cc_final: 0.7855 (p) outliers start: 55 outliers final: 40 residues processed: 270 average time/residue: 0.5489 time to fit residues: 161.4132 Evaluate side-chains 260 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 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 210 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 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 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR 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 215 LYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 395 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 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 54 optimal weight: 0.1980 chunk 70 optimal weight: 0.0870 chunk 86 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 0.0020 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.248389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.220901 restraints weight = 10057.604| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 1.13 r_work: 0.4392 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4287 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12408 Z= 0.135 Angle : 0.553 8.834 16836 Z= 0.287 Chirality : 0.037 0.182 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.015 18.828 1784 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.62 % Allowed : 17.60 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.21), residues: 1524 helix: 2.82 (0.13), residues: 1216 sheet: 0.98 (0.68), residues: 40 loop : -2.67 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 405 TYR 0.022 0.001 TYR C 124 PHE 0.016 0.002 PHE A 203 TRP 0.008 0.001 TRP B 193 HIS 0.001 0.000 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00281 (12408) covalent geometry : angle 0.55349 (16836) hydrogen bonds : bond 0.05225 ( 1028) hydrogen bonds : angle 3.54381 ( 3048) ********************** 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 260 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7768 (mt) REVERT: A 91 MET cc_start: 0.5309 (tpp) cc_final: 0.4835 (ttt) REVERT: A 133 ARG cc_start: 0.6873 (ttm110) cc_final: 0.6619 (ttm110) REVERT: A 197 MET cc_start: 0.7981 (tpt) cc_final: 0.7752 (tpp) REVERT: A 215 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8168 (ttpp) REVERT: A 303 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7177 (mt-10) REVERT: A 310 ASP cc_start: 0.7826 (m-30) cc_final: 0.7504 (m-30) REVERT: A 321 MET cc_start: 0.8459 (ttp) cc_final: 0.8193 (ptm) REVERT: A 387 MET cc_start: 0.7765 (mtm) cc_final: 0.7438 (mtp) REVERT: A 435 THR cc_start: 0.8066 (p) cc_final: 0.7805 (p) REVERT: B 38 ARG cc_start: 0.6978 (ttt180) cc_final: 0.6258 (ttm-80) REVERT: B 46 TYR cc_start: 0.6727 (m-80) cc_final: 0.6461 (m-80) REVERT: B 52 LYS cc_start: 0.7493 (mttt) cc_final: 0.7122 (mmmt) REVERT: B 60 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7786 (mt) REVERT: B 91 MET cc_start: 0.5346 (tpp) cc_final: 0.4895 (ttt) REVERT: B 133 ARG cc_start: 0.6958 (ttm110) cc_final: 0.6387 (ttp-110) REVERT: B 310 ASP cc_start: 0.7755 (m-30) cc_final: 0.7422 (m-30) REVERT: B 387 MET cc_start: 0.7741 (mmm) cc_final: 0.7483 (mtt) REVERT: B 435 THR cc_start: 0.8061 (p) cc_final: 0.7809 (p) REVERT: C 38 ARG cc_start: 0.6947 (ttt180) cc_final: 0.6225 (ttm-80) REVERT: C 46 TYR cc_start: 0.6879 (m-80) cc_final: 0.6419 (m-80) REVERT: C 52 LYS cc_start: 0.7431 (mttt) cc_final: 0.7056 (mmmt) REVERT: C 60 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7705 (mt) REVERT: C 83 LYS cc_start: 0.7592 (mtpt) cc_final: 0.6903 (tppt) REVERT: C 91 MET cc_start: 0.5458 (tpp) cc_final: 0.5056 (ttt) REVERT: C 133 ARG cc_start: 0.6849 (ttm110) cc_final: 0.6609 (ttm110) REVERT: C 215 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8201 (ttpp) REVERT: C 274 MET cc_start: 0.3819 (OUTLIER) cc_final: 0.2784 (ttp) REVERT: C 303 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7320 (mt-10) REVERT: C 310 ASP cc_start: 0.7672 (m-30) cc_final: 0.7381 (m-30) REVERT: C 435 THR cc_start: 0.8065 (p) cc_final: 0.7863 (p) REVERT: D 38 ARG cc_start: 0.6918 (ttt180) cc_final: 0.6270 (ttm-80) REVERT: D 46 TYR cc_start: 0.6893 (m-80) cc_final: 0.6375 (m-80) REVERT: D 52 LYS cc_start: 0.7512 (mttt) cc_final: 0.7111 (mmmt) REVERT: D 60 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7808 (mt) REVERT: D 91 MET cc_start: 0.5431 (tpp) cc_final: 0.5061 (ttt) REVERT: D 133 ARG cc_start: 0.6835 (ttm110) cc_final: 0.6592 (ttm110) REVERT: D 310 ASP cc_start: 0.7712 (m-30) cc_final: 0.7355 (m-30) REVERT: D 435 THR cc_start: 0.8079 (p) cc_final: 0.7862 (m) outliers start: 49 outliers final: 39 residues processed: 245 average time/residue: 0.5672 time to fit residues: 150.9361 Evaluate side-chains 256 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 210 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 102 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 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR 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 215 LYS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 395 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 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 42 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.258712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.230583 restraints weight = 10149.055| |-----------------------------------------------------------------------------| r_work (start): 0.4515 rms_B_bonded: 1.18 r_work: 0.4321 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4212 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12408 Z= 0.180 Angle : 0.627 10.082 16836 Z= 0.323 Chirality : 0.040 0.181 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.217 18.514 1784 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.40 % Allowed : 18.12 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.53 (0.21), residues: 1524 helix: 2.57 (0.13), residues: 1220 sheet: 0.85 (0.69), residues: 40 loop : -2.81 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 293 TYR 0.023 0.002 TYR C 124 PHE 0.018 0.002 PHE A 203 TRP 0.013 0.002 TRP B 193 HIS 0.003 0.001 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00416 (12408) covalent geometry : angle 0.62715 (16836) hydrogen bonds : bond 0.06033 ( 1028) hydrogen bonds : angle 3.67936 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4721.12 seconds wall clock time: 81 minutes 16.65 seconds (4876.65 seconds total)