Starting phenix.real_space_refine on Sat Jan 18 09:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vv3_43548/01_2025/8vv3_43548.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vv3_43548/01_2025/8vv3_43548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vv3_43548/01_2025/8vv3_43548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vv3_43548/01_2025/8vv3_43548.map" model { file = "/net/cci-nas-00/data/ceres_data/8vv3_43548/01_2025/8vv3_43548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vv3_43548/01_2025/8vv3_43548.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.369 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 7928 2.51 5 N 2028 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12172 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3031 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 6.80, per 1000 atoms: 0.56 Number of scatterers: 12172 At special positions: 0 Unit cell: (111.072, 110.004, 93.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 2084 8.00 N 2028 7.00 C 7928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.4 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 83.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.605A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 26 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 80 removed outlier: 3.753A pdb=" N GLY A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 113 Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 140 through 173 removed outlier: 3.509A pdb=" N GLU A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 227 removed outlier: 3.557A pdb=" N ILE A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 341 removed outlier: 5.157A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix Proline residue: A 331 - end of helix removed outlier: 3.530A pdb=" N SER A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 389 removed outlier: 3.579A pdb=" N LEU A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.882A pdb=" N GLU A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.641A pdb=" N SER A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 423 through 445 removed outlier: 3.504A pdb=" N MET A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.605A pdb=" N ILE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 26 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 80 removed outlier: 3.753A pdb=" N GLY B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 113 Processing helix chain 'B' and resid 113 through 136 Processing helix chain 'B' and resid 140 through 173 removed outlier: 3.510A pdb=" N GLU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 227 removed outlier: 3.557A pdb=" N ILE B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 341 removed outlier: 5.156A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix Proline residue: B 331 - end of helix removed outlier: 3.531A pdb=" N SER B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 389 removed outlier: 3.580A pdb=" N LEU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.883A pdb=" N GLU B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.642A pdb=" N SER B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 423 through 445 removed outlier: 3.504A pdb=" N MET B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.604A pdb=" N ILE C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 26 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 27 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 80 removed outlier: 3.754A pdb=" N GLY C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 113 through 136 Processing helix chain 'C' and resid 140 through 173 removed outlier: 3.510A pdb=" N GLU C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 227 removed outlier: 3.557A pdb=" N ILE C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 341 removed outlier: 5.156A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix Proline residue: C 331 - end of helix removed outlier: 3.531A pdb=" N SER C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 389 removed outlier: 3.579A pdb=" N LEU C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.882A pdb=" N GLU C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 410 removed outlier: 3.642A pdb=" N SER C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 423 through 445 removed outlier: 3.504A pdb=" N MET C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.604A pdb=" N ILE D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 26 " --> pdb=" O HIS D 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 80 removed outlier: 3.754A pdb=" N GLY D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 113 Processing helix chain 'D' and resid 113 through 136 Processing helix chain 'D' and resid 140 through 173 removed outlier: 3.510A pdb=" N GLU D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 227 removed outlier: 3.557A pdb=" N ILE D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 341 removed outlier: 5.156A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Proline residue: D 331 - end of helix removed outlier: 3.531A pdb=" N SER D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 389 removed outlier: 3.580A pdb=" N LEU D 348 " --> pdb=" O ARG D 344 " (cutoff:3.500A) Proline residue: D 368 - end of helix removed outlier: 3.882A pdb=" N GLU D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.641A pdb=" N SER D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 423 through 445 removed outlier: 3.504A pdb=" N MET D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AA4, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'C' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AA7, first strand: chain 'D' and resid 37 through 41 Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 274 1028 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 3.31 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.960 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.860 ------------------------------------------------------------------------------- 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= 0.242 Angle : 0.523 6.136 16836 Z= 0.271 Chirality : 0.037 0.174 2076 Planarity : 0.004 0.025 2024 Dihedral : 14.374 84.801 4564 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.21), residues: 1524 helix: 2.35 (0.14), residues: 1216 sheet: -0.35 (0.86), residues: 40 loop : -2.60 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.002 0.001 HIS A 22 PHE 0.014 0.001 PHE C 203 TYR 0.022 0.001 TYR A 124 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6924 (ttt180) cc_final: 0.6094 (ttm-80) REVERT: A 91 MET cc_start: 0.5187 (tpp) cc_final: 0.4524 (ttt) REVERT: A 118 MET cc_start: 0.8008 (mmp) cc_final: 0.7797 (mmp) REVERT: A 133 ARG cc_start: 0.6573 (ttm110) cc_final: 0.5926 (ttp-110) REVERT: A 171 MET cc_start: 0.6591 (mtm) cc_final: 0.6209 (mmt) REVERT: A 197 MET cc_start: 0.7804 (tpt) cc_final: 0.7594 (tpp) REVERT: A 215 LYS cc_start: 0.8154 (tttm) cc_final: 0.7769 (ttmt) REVERT: A 289 GLU cc_start: 0.7077 (tt0) cc_final: 0.6539 (mm-30) REVERT: A 303 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 310 ASP cc_start: 0.7880 (m-30) cc_final: 0.7573 (m-30) REVERT: B 38 ARG cc_start: 0.6981 (ttt180) cc_final: 0.6170 (ttp-110) REVERT: B 46 TYR cc_start: 0.6974 (m-80) cc_final: 0.6355 (m-80) REVERT: B 52 LYS cc_start: 0.7290 (mttt) cc_final: 0.6998 (mmmt) REVERT: B 91 MET cc_start: 0.5277 (tpp) cc_final: 0.4652 (ttt) REVERT: B 133 ARG cc_start: 0.6975 (ttm110) cc_final: 0.6298 (ttp-110) REVERT: B 167 CYS cc_start: 0.7745 (m) cc_final: 0.7543 (m) REVERT: B 205 PHE cc_start: 0.7160 (m-80) cc_final: 0.6786 (m-80) REVERT: B 219 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7286 (mt-10) REVERT: B 303 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6798 (mt-10) REVERT: B 310 ASP cc_start: 0.7878 (m-30) cc_final: 0.7536 (m-30) REVERT: C 38 ARG cc_start: 0.7256 (ttt180) cc_final: 0.6356 (ttp-110) REVERT: C 91 MET cc_start: 0.5131 (tpp) cc_final: 0.4731 (ttt) REVERT: C 118 MET cc_start: 0.8007 (mmp) cc_final: 0.7757 (mmp) REVERT: C 119 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6907 (mtm-85) REVERT: C 197 MET cc_start: 0.7816 (tpt) cc_final: 0.7522 (tpp) REVERT: C 215 LYS cc_start: 0.8143 (tttm) cc_final: 0.7653 (ttpt) REVERT: C 303 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6960 (mt-10) REVERT: D 38 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6296 (ttp-110) REVERT: D 46 TYR cc_start: 0.6785 (m-80) cc_final: 0.6304 (m-80) REVERT: D 60 ILE cc_start: 0.7859 (pt) cc_final: 0.7561 (mp) REVERT: D 91 MET cc_start: 0.5248 (tpp) cc_final: 0.4821 (ttt) REVERT: D 118 MET cc_start: 0.8186 (mmp) cc_final: 0.7947 (mmp) REVERT: D 119 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6733 (mtm-85) REVERT: D 133 ARG cc_start: 0.6714 (ttm110) cc_final: 0.5997 (ttp-110) REVERT: D 167 CYS cc_start: 0.7713 (m) cc_final: 0.7491 (m) REVERT: D 205 PHE cc_start: 0.7235 (m-80) cc_final: 0.6892 (m-80) REVERT: D 310 ASP cc_start: 0.7968 (m-30) cc_final: 0.7588 (m-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 1.2779 time to fit residues: 398.8487 Evaluate side-chains 217 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4916 r_free = 0.4916 target = 0.262379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.233962 restraints weight = 10255.779| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 1.23 r_work: 0.4375 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.4270 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12408 Z= 0.224 Angle : 0.552 7.394 16836 Z= 0.292 Chirality : 0.038 0.132 2076 Planarity : 0.004 0.029 2024 Dihedral : 3.892 15.349 1784 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.96 % Allowed : 9.25 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.21), residues: 1524 helix: 2.61 (0.14), residues: 1216 sheet: 0.46 (0.80), residues: 40 loop : -2.65 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.004 0.001 HIS B 22 PHE 0.016 0.002 PHE C 203 TYR 0.042 0.002 TYR C 124 ARG 0.005 0.001 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7074 (ttt180) cc_final: 0.6268 (ttm-80) REVERT: A 46 TYR cc_start: 0.6888 (m-80) cc_final: 0.6152 (m-80) REVERT: A 60 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7581 (mt) REVERT: A 91 MET cc_start: 0.5329 (tpp) cc_final: 0.4771 (ttt) REVERT: A 133 ARG cc_start: 0.6966 (ttm110) cc_final: 0.6692 (ttm110) REVERT: A 171 MET cc_start: 0.7244 (mtm) cc_final: 0.6694 (mmt) REVERT: A 179 GLN cc_start: 0.7565 (pm20) cc_final: 0.7200 (pm20) REVERT: A 197 MET cc_start: 0.7925 (tpt) cc_final: 0.7710 (tpp) REVERT: A 215 LYS cc_start: 0.8517 (tttm) cc_final: 0.8302 (tttt) REVERT: A 289 GLU cc_start: 0.7640 (tt0) cc_final: 0.6645 (mm-30) REVERT: A 303 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7233 (mt-10) REVERT: A 310 ASP cc_start: 0.7782 (m-30) cc_final: 0.7473 (m-30) REVERT: A 387 MET cc_start: 0.7568 (mmm) cc_final: 0.7218 (mtp) REVERT: B 38 ARG cc_start: 0.6889 (ttt180) cc_final: 0.6202 (ttp-110) REVERT: B 46 TYR cc_start: 0.6843 (m-80) cc_final: 0.6414 (m-80) REVERT: B 52 LYS cc_start: 0.7468 (mttt) cc_final: 0.6997 (mmmt) REVERT: B 91 MET cc_start: 0.5290 (tpp) cc_final: 0.4818 (ttt) REVERT: B 128 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6154 (mm) REVERT: B 133 ARG cc_start: 0.7160 (ttm110) cc_final: 0.6640 (ttp-110) REVERT: B 164 ASP cc_start: 0.8136 (t70) cc_final: 0.7923 (t70) REVERT: B 167 CYS cc_start: 0.8469 (m) cc_final: 0.8224 (m) REVERT: B 172 GLN cc_start: 0.6908 (mm110) cc_final: 0.6688 (mt0) REVERT: B 179 GLN cc_start: 0.7421 (pm20) cc_final: 0.7082 (pm20) REVERT: B 215 LYS cc_start: 0.8523 (mtpm) cc_final: 0.8277 (mtpt) REVERT: B 219 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 284 GLN cc_start: 0.6074 (mt0) cc_final: 0.5470 (mt0) REVERT: B 303 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7129 (mt-10) REVERT: B 310 ASP cc_start: 0.7782 (m-30) cc_final: 0.7461 (m-30) REVERT: C 38 ARG cc_start: 0.7100 (ttt180) cc_final: 0.6319 (ttp-110) REVERT: C 49 THR cc_start: 0.7029 (t) cc_final: 0.6806 (t) REVERT: C 91 MET cc_start: 0.5100 (tpp) cc_final: 0.4758 (ttt) REVERT: C 119 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6826 (mtm-85) REVERT: C 133 ARG cc_start: 0.6326 (ttm110) cc_final: 0.5803 (ttp-110) REVERT: C 179 GLN cc_start: 0.7399 (pm20) cc_final: 0.7028 (pm20) REVERT: C 197 MET cc_start: 0.7931 (tpt) cc_final: 0.7716 (tpp) REVERT: C 289 GLU cc_start: 0.7693 (tt0) cc_final: 0.6516 (mm-30) REVERT: C 303 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 435 THR cc_start: 0.8051 (p) cc_final: 0.7700 (p) REVERT: D 38 ARG cc_start: 0.6898 (ttt180) cc_final: 0.6218 (ttp-110) REVERT: D 46 TYR cc_start: 0.6783 (m-80) cc_final: 0.6397 (m-80) REVERT: D 60 ILE cc_start: 0.7932 (pt) cc_final: 0.7697 (mp) REVERT: D 91 MET cc_start: 0.5323 (tpp) cc_final: 0.4914 (ttt) REVERT: D 119 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.6706 (mtm-85) REVERT: D 133 ARG cc_start: 0.6796 (ttm110) cc_final: 0.6240 (ttp-110) REVERT: D 167 CYS cc_start: 0.8487 (m) cc_final: 0.8245 (m) REVERT: D 179 GLN cc_start: 0.7431 (pm20) cc_final: 0.7024 (pm20) REVERT: D 289 GLU cc_start: 0.7698 (tt0) cc_final: 0.6526 (mm-30) REVERT: D 310 ASP cc_start: 0.7914 (m-30) cc_final: 0.7552 (m-30) REVERT: D 387 MET cc_start: 0.7866 (mmm) cc_final: 0.7622 (mtt) REVERT: D 401 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7899 (tm-30) REVERT: D 435 THR cc_start: 0.8131 (p) cc_final: 0.7833 (p) outliers start: 40 outliers final: 19 residues processed: 249 average time/residue: 1.3465 time to fit residues: 361.9767 Evaluate side-chains 236 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 151 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 D 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.245151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.216298 restraints weight = 10148.678| |-----------------------------------------------------------------------------| r_work (start): 0.4507 rms_B_bonded: 1.19 r_work: 0.4325 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.4218 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12408 Z= 0.241 Angle : 0.571 8.451 16836 Z= 0.300 Chirality : 0.038 0.134 2076 Planarity : 0.004 0.030 2024 Dihedral : 3.987 15.545 1784 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.62 % Allowed : 11.98 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.21), residues: 1524 helix: 2.63 (0.14), residues: 1220 sheet: 0.22 (0.78), residues: 40 loop : -2.68 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.003 0.001 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.032 0.002 TYR D 124 ARG 0.003 0.000 ARG D 385 *********************** 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 277 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7204 (ttt180) cc_final: 0.6454 (ttm-80) REVERT: A 46 TYR cc_start: 0.6880 (m-80) cc_final: 0.6135 (m-80) REVERT: A 60 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7782 (mt) REVERT: A 133 ARG cc_start: 0.7257 (ttm110) cc_final: 0.6990 (ttm110) REVERT: A 171 MET cc_start: 0.7431 (mtm) cc_final: 0.6843 (mmt) REVERT: A 179 GLN cc_start: 0.7569 (pm20) cc_final: 0.7189 (pm20) REVERT: A 197 MET cc_start: 0.8002 (tpt) cc_final: 0.7796 (tpp) REVERT: A 289 GLU cc_start: 0.7841 (tt0) cc_final: 0.6881 (mm-30) REVERT: A 303 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7307 (mt-10) REVERT: A 310 ASP cc_start: 0.7950 (m-30) cc_final: 0.7648 (m-30) REVERT: A 387 MET cc_start: 0.7698 (mmm) cc_final: 0.7370 (mtp) REVERT: B 38 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6364 (ttm-80) REVERT: B 46 TYR cc_start: 0.6881 (m-80) cc_final: 0.6223 (m-80) REVERT: B 52 LYS cc_start: 0.7561 (mttt) cc_final: 0.7149 (mmmt) REVERT: B 91 MET cc_start: 0.5367 (tpp) cc_final: 0.4890 (ttt) REVERT: B 128 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6421 (mm) REVERT: B 133 ARG cc_start: 0.7359 (ttm110) cc_final: 0.7104 (ttm110) REVERT: B 179 GLN cc_start: 0.7373 (pm20) cc_final: 0.7086 (pm20) REVERT: B 219 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 303 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 310 ASP cc_start: 0.7937 (m-30) cc_final: 0.7606 (m-30) REVERT: B 387 MET cc_start: 0.7858 (mmm) cc_final: 0.7620 (mtt) REVERT: C 38 ARG cc_start: 0.7188 (ttt180) cc_final: 0.6459 (ttp-110) REVERT: C 52 LYS cc_start: 0.7450 (mttt) cc_final: 0.7082 (mmmt) REVERT: C 91 MET cc_start: 0.5291 (tpp) cc_final: 0.4917 (ttt) REVERT: C 119 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.6746 (mtm-85) REVERT: C 133 ARG cc_start: 0.6786 (ttm110) cc_final: 0.6278 (ttp-110) REVERT: C 179 GLN cc_start: 0.7498 (pm20) cc_final: 0.7166 (pm20) REVERT: C 303 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7404 (mt-10) REVERT: C 310 ASP cc_start: 0.7790 (m-30) cc_final: 0.7490 (m-30) REVERT: C 435 THR cc_start: 0.8199 (p) cc_final: 0.7899 (p) REVERT: D 38 ARG cc_start: 0.7053 (ttt180) cc_final: 0.6413 (ttp-110) REVERT: D 46 TYR cc_start: 0.6807 (m-80) cc_final: 0.6294 (m-80) REVERT: D 52 LYS cc_start: 0.7564 (mttt) cc_final: 0.7162 (mmmt) REVERT: D 91 MET cc_start: 0.5463 (tpp) cc_final: 0.5065 (ttt) REVERT: D 118 MET cc_start: 0.8091 (mmp) cc_final: 0.7890 (mmp) REVERT: D 119 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.6744 (mtm-85) REVERT: D 133 ARG cc_start: 0.7030 (ttm110) cc_final: 0.6802 (ttm110) REVERT: D 179 GLN cc_start: 0.7345 (pm20) cc_final: 0.7001 (pm20) REVERT: D 289 GLU cc_start: 0.7879 (tt0) cc_final: 0.7570 (tt0) REVERT: D 310 ASP cc_start: 0.7893 (m-30) cc_final: 0.7557 (m-30) REVERT: D 435 THR cc_start: 0.8193 (p) cc_final: 0.7892 (p) outliers start: 49 outliers final: 26 residues processed: 250 average time/residue: 1.3695 time to fit residues: 370.7917 Evaluate side-chains 246 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain 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 216 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 121 optimal weight: 0.0980 chunk 33 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 134 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN C 172 GLN D 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.257373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.228354 restraints weight = 10366.165| |-----------------------------------------------------------------------------| r_work (start): 0.4505 rms_B_bonded: 1.22 r_work: 0.4307 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4197 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12408 Z= 0.171 Angle : 0.515 6.749 16836 Z= 0.271 Chirality : 0.036 0.136 2076 Planarity : 0.004 0.030 2024 Dihedral : 3.891 15.138 1784 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.25 % Allowed : 14.42 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.21), residues: 1524 helix: 2.83 (0.13), residues: 1220 sheet: 0.34 (0.75), residues: 40 loop : -2.64 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.001 0.000 HIS B 22 PHE 0.016 0.002 PHE A 191 TYR 0.027 0.001 TYR C 124 ARG 0.003 0.000 ARG D 385 *********************** 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: 44 poor density : 225 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7766 (mt) REVERT: A 133 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6774 (ttm110) REVERT: A 171 MET cc_start: 0.7406 (mtm) cc_final: 0.6827 (mmt) REVERT: A 179 GLN cc_start: 0.7555 (pm20) cc_final: 0.7229 (pm20) REVERT: A 197 MET cc_start: 0.8008 (tpt) cc_final: 0.7799 (tpp) REVERT: A 215 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8274 (ttpp) REVERT: A 289 GLU cc_start: 0.7807 (tt0) cc_final: 0.6774 (mm-30) REVERT: A 303 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7223 (mt-10) REVERT: A 310 ASP cc_start: 0.7828 (m-30) cc_final: 0.7502 (m-30) REVERT: A 387 MET cc_start: 0.7661 (mmm) cc_final: 0.7210 (mtp) REVERT: B 38 ARG cc_start: 0.6943 (ttt180) cc_final: 0.6245 (ttm-80) REVERT: B 46 TYR cc_start: 0.6786 (m-80) cc_final: 0.6278 (m-80) REVERT: B 52 LYS cc_start: 0.7492 (mttt) cc_final: 0.7135 (mmmt) REVERT: B 60 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7775 (mt) REVERT: B 91 MET cc_start: 0.5322 (tpp) cc_final: 0.4836 (ttt) REVERT: B 128 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6419 (mm) REVERT: B 133 ARG cc_start: 0.7220 (ttm110) cc_final: 0.6964 (ttm110) REVERT: B 179 GLN cc_start: 0.7415 (pm20) cc_final: 0.7107 (pm20) REVERT: B 219 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7901 (mt-10) REVERT: B 303 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7275 (mt-10) REVERT: B 310 ASP cc_start: 0.7871 (m-30) cc_final: 0.7551 (m-30) REVERT: B 387 MET cc_start: 0.7769 (mmm) cc_final: 0.7484 (mtt) REVERT: C 38 ARG cc_start: 0.7075 (ttt180) cc_final: 0.6405 (ttp-110) REVERT: C 46 TYR cc_start: 0.6977 (m-80) cc_final: 0.6585 (m-80) REVERT: C 52 LYS cc_start: 0.7416 (mttt) cc_final: 0.7105 (mmmt) REVERT: C 91 MET cc_start: 0.5231 (tpp) cc_final: 0.4895 (ttt) REVERT: C 119 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.6709 (mtm-85) REVERT: C 133 ARG cc_start: 0.6681 (ttm110) cc_final: 0.6157 (ttp-110) REVERT: C 179 GLN cc_start: 0.7494 (pm20) cc_final: 0.7161 (pm20) REVERT: C 215 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8139 (ttpp) REVERT: C 303 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 310 ASP cc_start: 0.7764 (m-30) cc_final: 0.7499 (m-30) REVERT: C 435 THR cc_start: 0.8200 (p) cc_final: 0.7902 (p) REVERT: D 38 ARG cc_start: 0.6959 (ttt180) cc_final: 0.6310 (ttp-110) REVERT: D 46 TYR cc_start: 0.6894 (m-80) cc_final: 0.6379 (m-80) REVERT: D 52 LYS cc_start: 0.7652 (mttt) cc_final: 0.7210 (mmmt) REVERT: D 91 MET cc_start: 0.5442 (tpp) cc_final: 0.4993 (ttt) REVERT: D 119 ARG cc_start: 0.7355 (mtm-85) cc_final: 0.6699 (mtm-85) REVERT: D 133 ARG cc_start: 0.6950 (ttm110) cc_final: 0.6704 (ttm110) REVERT: D 179 GLN cc_start: 0.7296 (pm20) cc_final: 0.6981 (pm20) REVERT: D 289 GLU cc_start: 0.7811 (tt0) cc_final: 0.6717 (mm-30) REVERT: D 310 ASP cc_start: 0.7834 (m-30) cc_final: 0.7491 (m-30) REVERT: D 435 THR cc_start: 0.8207 (p) cc_final: 0.7910 (p) outliers start: 44 outliers final: 32 residues processed: 253 average time/residue: 1.3614 time to fit residues: 371.7822 Evaluate side-chains 252 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 215 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 325 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 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 395 VAL Chi-restraints excluded: chain C residue 438 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 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 = 0.4774 r_free = 0.4774 target = 0.244569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.215733 restraints weight = 10021.387| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 1.16 r_work: 0.4312 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4203 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12408 Z= 0.255 Angle : 0.584 7.732 16836 Z= 0.303 Chirality : 0.039 0.184 2076 Planarity : 0.004 0.031 2024 Dihedral : 4.088 15.552 1784 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.51 % Allowed : 15.24 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.21), residues: 1524 helix: 2.67 (0.13), residues: 1220 sheet: 0.57 (0.74), residues: 40 loop : -2.69 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS B 22 PHE 0.018 0.002 PHE A 203 TYR 0.026 0.002 TYR A 124 ARG 0.003 0.001 ARG A 293 *********************** 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 285 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6818 (m-80) cc_final: 0.6076 (m-80) REVERT: A 60 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7738 (mt) REVERT: A 91 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.4744 (ttt) REVERT: A 133 ARG cc_start: 0.7269 (ttm110) cc_final: 0.7018 (ttm110) REVERT: A 171 MET cc_start: 0.7508 (mtm) cc_final: 0.6956 (mmt) REVERT: A 179 GLN cc_start: 0.7669 (pm20) cc_final: 0.7341 (pm20) REVERT: A 197 MET cc_start: 0.8116 (tpt) cc_final: 0.7899 (tpp) REVERT: A 219 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 310 ASP cc_start: 0.7896 (m-30) cc_final: 0.7583 (m-30) REVERT: B 38 ARG cc_start: 0.7154 (ttt180) cc_final: 0.6420 (ttm-80) REVERT: B 46 TYR cc_start: 0.6765 (m-80) cc_final: 0.6162 (m-80) REVERT: B 52 LYS cc_start: 0.7481 (mttt) cc_final: 0.7115 (mmmt) REVERT: B 60 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7753 (mt) REVERT: B 91 MET cc_start: 0.5390 (tpp) cc_final: 0.4936 (ttt) REVERT: B 133 ARG cc_start: 0.7360 (ttm110) cc_final: 0.7096 (ttm110) REVERT: B 179 GLN cc_start: 0.7397 (pm20) cc_final: 0.7101 (pm20) REVERT: B 303 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7298 (mt-10) REVERT: B 310 ASP cc_start: 0.7912 (m-30) cc_final: 0.7592 (m-30) REVERT: C 38 ARG cc_start: 0.7161 (ttt180) cc_final: 0.6430 (ttp-110) REVERT: C 46 TYR cc_start: 0.7023 (m-80) cc_final: 0.6634 (m-80) REVERT: C 52 LYS cc_start: 0.7501 (mttt) cc_final: 0.7124 (mmmt) REVERT: C 91 MET cc_start: 0.5425 (tpp) cc_final: 0.4985 (ttt) REVERT: C 119 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.6746 (mtm-85) REVERT: C 133 ARG cc_start: 0.6992 (ttm110) cc_final: 0.6767 (ttm110) REVERT: C 179 GLN cc_start: 0.7555 (pm20) cc_final: 0.7238 (pm20) REVERT: C 303 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7455 (mt-10) REVERT: C 310 ASP cc_start: 0.7752 (m-30) cc_final: 0.7472 (m-30) REVERT: C 435 THR cc_start: 0.8167 (p) cc_final: 0.7883 (p) REVERT: D 38 ARG cc_start: 0.7020 (ttt180) cc_final: 0.6372 (ttm-80) REVERT: D 46 TYR cc_start: 0.6913 (m-80) cc_final: 0.6409 (m-80) REVERT: D 52 LYS cc_start: 0.7647 (mttt) cc_final: 0.7188 (mmmt) REVERT: D 91 MET cc_start: 0.5507 (tpp) cc_final: 0.5053 (ttt) REVERT: D 119 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.6806 (mtm-85) REVERT: D 133 ARG cc_start: 0.7137 (ttm110) cc_final: 0.6900 (ttm110) REVERT: D 179 GLN cc_start: 0.7388 (pm20) cc_final: 0.7150 (pm20) REVERT: D 289 GLU cc_start: 0.7894 (tt0) cc_final: 0.7600 (tt0) REVERT: D 310 ASP cc_start: 0.7856 (m-30) cc_final: 0.7518 (m-30) REVERT: D 435 THR cc_start: 0.8199 (p) cc_final: 0.7921 (p) outliers start: 61 outliers final: 43 residues processed: 264 average time/residue: 1.2593 time to fit residues: 360.7995 Evaluate side-chains 262 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4779 r_free = 0.4779 target = 0.245037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.216280 restraints weight = 10160.141| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 1.18 r_work: 0.4316 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4204 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12408 Z= 0.239 Angle : 0.589 8.243 16836 Z= 0.304 Chirality : 0.038 0.173 2076 Planarity : 0.004 0.032 2024 Dihedral : 4.140 17.957 1784 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.73 % Allowed : 15.61 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.21), residues: 1524 helix: 2.65 (0.13), residues: 1220 sheet: 0.64 (0.72), residues: 40 loop : -2.65 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.001 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.024 0.002 TYR A 124 ARG 0.003 0.000 ARG A 293 *********************** 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 286 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 222 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6804 (m-80) cc_final: 0.6089 (m-80) REVERT: A 60 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7740 (mt) REVERT: A 91 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.4778 (ttt) REVERT: A 133 ARG cc_start: 0.7261 (ttm110) cc_final: 0.7016 (ttm110) REVERT: A 171 MET cc_start: 0.7617 (mtm) cc_final: 0.7005 (mmt) REVERT: A 179 GLN cc_start: 0.7730 (pm20) cc_final: 0.7481 (pm20) REVERT: A 197 MET cc_start: 0.8103 (tpt) cc_final: 0.7886 (tpp) REVERT: A 310 ASP cc_start: 0.7895 (m-30) cc_final: 0.7572 (m-30) REVERT: B 38 ARG cc_start: 0.7100 (ttt180) cc_final: 0.6394 (ttm-80) REVERT: B 46 TYR cc_start: 0.6731 (m-80) cc_final: 0.6121 (m-80) REVERT: B 52 LYS cc_start: 0.7505 (mttt) cc_final: 0.7108 (mmmt) REVERT: B 60 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7789 (mt) REVERT: B 91 MET cc_start: 0.5394 (tpp) cc_final: 0.4939 (ttt) REVERT: B 133 ARG cc_start: 0.7335 (ttm110) cc_final: 0.7073 (ttm110) REVERT: B 179 GLN cc_start: 0.7456 (pm20) cc_final: 0.7199 (pm20) REVERT: B 303 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 310 ASP cc_start: 0.7920 (m-30) cc_final: 0.7603 (m-30) REVERT: C 38 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6423 (ttp-110) REVERT: C 46 TYR cc_start: 0.7043 (m-80) cc_final: 0.6650 (m-80) REVERT: C 52 LYS cc_start: 0.7492 (mttt) cc_final: 0.7124 (mmmt) REVERT: C 91 MET cc_start: 0.5511 (tpp) cc_final: 0.5108 (ttt) REVERT: C 119 ARG cc_start: 0.7383 (mtm-85) cc_final: 0.6721 (mtm-85) REVERT: C 133 ARG cc_start: 0.7014 (ttm110) cc_final: 0.6777 (ttm110) REVERT: C 179 GLN cc_start: 0.7547 (pm20) cc_final: 0.7316 (pm20) REVERT: C 303 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7442 (mt-10) REVERT: C 310 ASP cc_start: 0.7764 (m-30) cc_final: 0.7488 (m-30) REVERT: C 435 THR cc_start: 0.8149 (p) cc_final: 0.7857 (p) REVERT: D 38 ARG cc_start: 0.6960 (ttt180) cc_final: 0.6369 (ttm-80) REVERT: D 46 TYR cc_start: 0.6876 (m-80) cc_final: 0.6401 (m-80) REVERT: D 52 LYS cc_start: 0.7643 (mttt) cc_final: 0.7183 (mmmt) REVERT: D 91 MET cc_start: 0.5606 (tpp) cc_final: 0.5171 (ttt) REVERT: D 119 ARG cc_start: 0.7408 (mtm-85) cc_final: 0.6747 (mtm-85) REVERT: D 133 ARG cc_start: 0.7096 (ttm110) cc_final: 0.6853 (ttm110) REVERT: D 289 GLU cc_start: 0.7900 (tt0) cc_final: 0.7614 (tt0) REVERT: D 310 ASP cc_start: 0.7854 (m-30) cc_final: 0.7510 (m-30) REVERT: D 435 THR cc_start: 0.8178 (p) cc_final: 0.7899 (p) outliers start: 64 outliers final: 46 residues processed: 263 average time/residue: 1.3000 time to fit residues: 375.6967 Evaluate side-chains 267 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 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 325 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 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 224 THR Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4749 r_free = 0.4749 target = 0.241553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.213255 restraints weight = 10119.085| |-----------------------------------------------------------------------------| r_work (start): 0.4487 rms_B_bonded: 1.14 r_work: 0.4325 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4217 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12408 Z= 0.332 Angle : 0.670 9.941 16836 Z= 0.345 Chirality : 0.042 0.209 2076 Planarity : 0.005 0.034 2024 Dihedral : 4.424 18.719 1784 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 4.44 % Allowed : 16.49 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.21), residues: 1524 helix: 2.29 (0.14), residues: 1228 sheet: 0.49 (0.70), residues: 40 loop : -2.73 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 354 HIS 0.004 0.001 HIS B 22 PHE 0.019 0.003 PHE A 203 TYR 0.025 0.002 TYR A 124 ARG 0.004 0.001 ARG A 293 *********************** 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 278 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 218 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6782 (m-80) cc_final: 0.6126 (m-80) REVERT: A 60 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7772 (mt) REVERT: A 91 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.4791 (ttt) REVERT: A 119 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6551 (mtm-85) REVERT: A 133 ARG cc_start: 0.7345 (ttm110) cc_final: 0.6844 (ttp-110) REVERT: A 171 MET cc_start: 0.7642 (mtm) cc_final: 0.7022 (mmt) REVERT: A 197 MET cc_start: 0.8028 (tpt) cc_final: 0.7817 (tpp) REVERT: A 310 ASP cc_start: 0.7909 (m-30) cc_final: 0.7592 (m-30) REVERT: B 38 ARG cc_start: 0.7187 (ttt180) cc_final: 0.6442 (ttm-80) REVERT: B 46 TYR cc_start: 0.6856 (m-80) cc_final: 0.6264 (m-80) REVERT: B 52 LYS cc_start: 0.7473 (mttt) cc_final: 0.7082 (mmmt) REVERT: B 60 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7761 (mt) REVERT: B 91 MET cc_start: 0.5437 (tpp) cc_final: 0.5028 (ttt) REVERT: B 119 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.6599 (mtm-85) REVERT: B 133 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6859 (ttp-110) REVERT: B 179 GLN cc_start: 0.7531 (pm20) cc_final: 0.7295 (pm20) REVERT: B 297 MET cc_start: 0.8492 (mtm) cc_final: 0.8155 (ttp) REVERT: B 303 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7196 (mt-10) REVERT: B 310 ASP cc_start: 0.7857 (m-30) cc_final: 0.7536 (m-30) REVERT: C 38 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6459 (ttm-80) REVERT: C 46 TYR cc_start: 0.7064 (m-80) cc_final: 0.6655 (m-80) REVERT: C 52 LYS cc_start: 0.7446 (mttt) cc_final: 0.7105 (mmmt) REVERT: C 119 ARG cc_start: 0.7193 (mtm-85) cc_final: 0.6669 (mtm-85) REVERT: C 126 GLU cc_start: 0.6155 (pt0) cc_final: 0.5868 (mm-30) REVERT: C 133 ARG cc_start: 0.7198 (ttm110) cc_final: 0.6747 (ttp-110) REVERT: C 274 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.2256 (ttp) REVERT: C 297 MET cc_start: 0.8484 (mtm) cc_final: 0.8145 (ttp) REVERT: C 303 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7365 (mt-10) REVERT: C 310 ASP cc_start: 0.7821 (m-30) cc_final: 0.7526 (m-30) REVERT: C 387 MET cc_start: 0.7800 (mmm) cc_final: 0.7532 (mtt) REVERT: C 435 THR cc_start: 0.8185 (p) cc_final: 0.7911 (p) REVERT: D 38 ARG cc_start: 0.7086 (ttt180) cc_final: 0.6437 (ttm-80) REVERT: D 46 TYR cc_start: 0.6923 (m-80) cc_final: 0.6492 (m-80) REVERT: D 52 LYS cc_start: 0.7520 (mttt) cc_final: 0.7116 (mmmt) REVERT: D 91 MET cc_start: 0.5566 (tpp) cc_final: 0.5184 (ttt) REVERT: D 119 ARG cc_start: 0.7392 (mtm-85) cc_final: 0.6710 (mtm-85) REVERT: D 133 ARG cc_start: 0.7200 (ttm110) cc_final: 0.6666 (ttp-110) REVERT: D 179 GLN cc_start: 0.7622 (pm20) cc_final: 0.7349 (pm20) REVERT: D 297 MET cc_start: 0.8457 (mtm) cc_final: 0.8179 (ttp) REVERT: D 310 ASP cc_start: 0.7826 (m-30) cc_final: 0.7487 (m-30) REVERT: D 435 THR cc_start: 0.8178 (p) cc_final: 0.7920 (p) outliers start: 60 outliers final: 43 residues processed: 262 average time/residue: 1.2526 time to fit residues: 355.8774 Evaluate side-chains 260 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 215 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 107 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 147 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4772 r_free = 0.4772 target = 0.244432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.215688 restraints weight = 10114.987| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 1.18 r_work: 0.4308 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.4198 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 0.035 12408 Z= 0.235 Angle : 0.595 8.792 16836 Z= 0.307 Chirality : 0.038 0.166 2076 Planarity : 0.004 0.033 2024 Dihedral : 4.275 18.061 1784 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.66 % Allowed : 16.35 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.21), residues: 1524 helix: 2.53 (0.14), residues: 1220 sheet: 0.56 (0.69), residues: 40 loop : -2.60 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.000 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG D 385 *********************** 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 287 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6742 (m-80) cc_final: 0.6104 (m-80) REVERT: A 60 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7805 (mt) REVERT: A 91 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.4776 (ttt) REVERT: A 133 ARG cc_start: 0.7267 (ttm110) cc_final: 0.7012 (ttm110) REVERT: A 171 MET cc_start: 0.7669 (mtm) cc_final: 0.7011 (mmt) REVERT: A 197 MET cc_start: 0.8068 (tpt) cc_final: 0.7857 (tpp) REVERT: A 215 LYS cc_start: 0.8452 (ttpp) cc_final: 0.8245 (ttpp) REVERT: A 310 ASP cc_start: 0.7897 (m-30) cc_final: 0.7581 (m-30) REVERT: B 38 ARG cc_start: 0.7150 (ttt180) cc_final: 0.6472 (ttm-80) REVERT: B 46 TYR cc_start: 0.6760 (m-80) cc_final: 0.6169 (m-80) REVERT: B 52 LYS cc_start: 0.7525 (mttt) cc_final: 0.7124 (mmmt) REVERT: B 60 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7816 (mt) REVERT: B 91 MET cc_start: 0.5483 (tpp) cc_final: 0.5026 (ttt) REVERT: B 133 ARG cc_start: 0.7308 (ttm110) cc_final: 0.6786 (ttp-110) REVERT: B 179 GLN cc_start: 0.7490 (pm20) cc_final: 0.7288 (pm20) REVERT: B 274 MET cc_start: 0.3456 (OUTLIER) cc_final: 0.2584 (pmm) REVERT: B 297 MET cc_start: 0.8563 (mtm) cc_final: 0.8225 (ttp) REVERT: B 303 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7359 (mt-10) REVERT: B 310 ASP cc_start: 0.7928 (m-30) cc_final: 0.7614 (m-30) REVERT: B 435 THR cc_start: 0.8172 (p) cc_final: 0.7919 (p) REVERT: C 38 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6442 (ttm-80) REVERT: C 46 TYR cc_start: 0.6985 (m-80) cc_final: 0.6573 (m-80) REVERT: C 52 LYS cc_start: 0.7507 (mttt) cc_final: 0.7124 (mmmt) REVERT: C 60 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7759 (mt) REVERT: C 91 MET cc_start: 0.7063 (ptt) cc_final: 0.5841 (ttt) REVERT: C 119 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6741 (mtm-85) REVERT: C 126 GLU cc_start: 0.6127 (pt0) cc_final: 0.5816 (mm-30) REVERT: C 133 ARG cc_start: 0.7092 (ttm110) cc_final: 0.6849 (ttm110) REVERT: C 179 GLN cc_start: 0.7751 (pm20) cc_final: 0.7539 (pm20) REVERT: C 274 MET cc_start: 0.4458 (OUTLIER) cc_final: 0.3817 (ttp) REVERT: C 297 MET cc_start: 0.8564 (mtm) cc_final: 0.8225 (ttp) REVERT: C 303 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 310 ASP cc_start: 0.7866 (m-30) cc_final: 0.7561 (m-30) REVERT: C 435 THR cc_start: 0.8136 (p) cc_final: 0.7850 (p) REVERT: D 38 ARG cc_start: 0.7122 (ttt180) cc_final: 0.6443 (ttm-80) REVERT: D 46 TYR cc_start: 0.6884 (m-80) cc_final: 0.6413 (m-80) REVERT: D 52 LYS cc_start: 0.7564 (mttt) cc_final: 0.7173 (mmmt) REVERT: D 60 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7870 (mt) REVERT: D 119 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.6735 (mtm-85) REVERT: D 133 ARG cc_start: 0.7090 (ttm110) cc_final: 0.6846 (ttm110) REVERT: D 179 GLN cc_start: 0.7610 (pm20) cc_final: 0.7324 (pm20) REVERT: D 297 MET cc_start: 0.8474 (mtm) cc_final: 0.8191 (ttp) REVERT: D 310 ASP cc_start: 0.7872 (m-30) cc_final: 0.7549 (m-30) REVERT: D 435 THR cc_start: 0.8173 (p) cc_final: 0.7901 (p) outliers start: 63 outliers final: 46 residues processed: 267 average time/residue: 1.2322 time to fit residues: 357.3053 Evaluate side-chains 274 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU 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 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 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 151 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 146 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4771 r_free = 0.4771 target = 0.244517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.215808 restraints weight = 9997.667| |-----------------------------------------------------------------------------| r_work (start): 0.4510 rms_B_bonded: 1.17 r_work: 0.4310 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12408 Z= 0.244 Angle : 0.619 11.068 16836 Z= 0.318 Chirality : 0.039 0.176 2076 Planarity : 0.004 0.033 2024 Dihedral : 4.357 24.552 1784 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.29 % Allowed : 17.09 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.20), residues: 1524 helix: 2.55 (0.13), residues: 1220 sheet: 0.58 (0.69), residues: 40 loop : -2.61 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.000 HIS D 22 PHE 0.018 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG D 385 *********************** 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 275 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6810 (m-80) cc_final: 0.6201 (m-80) REVERT: A 60 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7804 (mt) REVERT: A 91 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.4840 (ttt) REVERT: A 133 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6953 (ttm110) REVERT: A 171 MET cc_start: 0.7707 (mtm) cc_final: 0.7053 (mmt) REVERT: A 197 MET cc_start: 0.8070 (tpt) cc_final: 0.7861 (tpp) REVERT: A 215 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8213 (ttpp) REVERT: A 310 ASP cc_start: 0.7913 (m-30) cc_final: 0.7604 (m-30) REVERT: B 38 ARG cc_start: 0.7190 (ttt180) cc_final: 0.6456 (ttm-80) REVERT: B 46 TYR cc_start: 0.6848 (m-80) cc_final: 0.6264 (m-80) REVERT: B 52 LYS cc_start: 0.7528 (mttt) cc_final: 0.7136 (mmmt) REVERT: B 60 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7800 (mt) REVERT: B 91 MET cc_start: 0.5485 (tpp) cc_final: 0.5025 (ttt) REVERT: B 133 ARG cc_start: 0.7285 (ttm110) cc_final: 0.7021 (ttm110) REVERT: B 273 MET cc_start: 0.6361 (OUTLIER) cc_final: 0.5532 (mtm) REVERT: B 303 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7306 (mt-10) REVERT: B 310 ASP cc_start: 0.7911 (m-30) cc_final: 0.7594 (m-30) REVERT: B 435 THR cc_start: 0.8178 (p) cc_final: 0.7917 (p) REVERT: C 38 ARG cc_start: 0.7176 (ttt180) cc_final: 0.6474 (ttm-80) REVERT: C 46 TYR cc_start: 0.6972 (m-80) cc_final: 0.6562 (m-80) REVERT: C 52 LYS cc_start: 0.7540 (mttt) cc_final: 0.7148 (mmmt) REVERT: C 60 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7778 (mt) REVERT: C 91 MET cc_start: 0.6958 (ptt) cc_final: 0.5802 (ttt) REVERT: C 119 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6703 (mtm-85) REVERT: C 133 ARG cc_start: 0.7075 (ttm110) cc_final: 0.6852 (ttm110) REVERT: C 297 MET cc_start: 0.8546 (mtm) cc_final: 0.8225 (ttp) REVERT: C 303 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 310 ASP cc_start: 0.7866 (m-30) cc_final: 0.7552 (m-30) REVERT: C 435 THR cc_start: 0.8152 (p) cc_final: 0.7871 (p) REVERT: D 38 ARG cc_start: 0.7149 (ttt180) cc_final: 0.6457 (ttm-80) REVERT: D 46 TYR cc_start: 0.6900 (m-80) cc_final: 0.6436 (m-80) REVERT: D 52 LYS cc_start: 0.7571 (mttt) cc_final: 0.7181 (mmmt) REVERT: D 60 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7866 (mt) REVERT: D 119 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.6714 (mtm-85) REVERT: D 133 ARG cc_start: 0.7120 (ttm110) cc_final: 0.6880 (ttm110) REVERT: D 179 GLN cc_start: 0.7634 (pm20) cc_final: 0.7336 (pm20) REVERT: D 297 MET cc_start: 0.8470 (mtm) cc_final: 0.8188 (ttp) REVERT: D 310 ASP cc_start: 0.7912 (m-30) cc_final: 0.7588 (m-30) REVERT: D 435 THR cc_start: 0.8172 (p) cc_final: 0.7900 (p) outliers start: 58 outliers final: 48 residues processed: 261 average time/residue: 1.2372 time to fit residues: 350.5416 Evaluate side-chains 270 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU 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 B residue 273 MET 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 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.244742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.216260 restraints weight = 10031.915| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 1.16 r_work: 0.4395 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4284 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2462 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= 0.242 Angle : 0.613 9.690 16836 Z= 0.316 Chirality : 0.039 0.180 2076 Planarity : 0.004 0.035 2024 Dihedral : 4.266 18.269 1784 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.66 % Allowed : 17.01 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.20), residues: 1524 helix: 2.55 (0.13), residues: 1220 sheet: 0.58 (0.68), residues: 40 loop : -2.65 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.000 HIS D 22 PHE 0.017 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG D 385 ********************** 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 282 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6724 (m-80) cc_final: 0.6129 (m-80) REVERT: A 60 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7699 (mt) REVERT: A 91 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.4771 (ttt) REVERT: A 133 ARG cc_start: 0.6994 (ttm110) cc_final: 0.6747 (ttm110) REVERT: A 171 MET cc_start: 0.7553 (mtm) cc_final: 0.6884 (mmt) REVERT: A 197 MET cc_start: 0.7943 (tpt) cc_final: 0.7703 (tpp) REVERT: A 215 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8101 (ttpp) REVERT: A 274 MET cc_start: 0.3402 (mmm) cc_final: 0.2612 (ttp) REVERT: A 310 ASP cc_start: 0.7821 (m-30) cc_final: 0.7514 (m-30) REVERT: A 377 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7851 (mtmt) REVERT: A 435 THR cc_start: 0.8025 (p) cc_final: 0.7773 (p) REVERT: B 38 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6276 (ttm-80) REVERT: B 46 TYR cc_start: 0.6755 (m-80) cc_final: 0.6129 (m-80) REVERT: B 52 LYS cc_start: 0.7498 (mttt) cc_final: 0.7026 (mmmt) REVERT: B 60 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7704 (mt) REVERT: B 91 MET cc_start: 0.5491 (tpp) cc_final: 0.5069 (ttt) REVERT: B 133 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6794 (ttm110) REVERT: B 273 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5528 (mtm) REVERT: B 303 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7159 (mt-10) REVERT: B 310 ASP cc_start: 0.7745 (m-30) cc_final: 0.7421 (m-30) REVERT: B 435 THR cc_start: 0.8083 (p) cc_final: 0.7823 (p) REVERT: C 38 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6333 (ttm-80) REVERT: C 46 TYR cc_start: 0.6879 (m-80) cc_final: 0.6443 (m-80) REVERT: C 52 LYS cc_start: 0.7445 (mttt) cc_final: 0.7009 (mmmt) REVERT: C 60 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7686 (mt) REVERT: C 83 LYS cc_start: 0.7554 (mtpt) cc_final: 0.6898 (tppt) REVERT: C 91 MET cc_start: 0.6890 (ptt) cc_final: 0.5752 (ttt) REVERT: C 119 ARG cc_start: 0.7043 (mtm-85) cc_final: 0.6487 (mtm-85) REVERT: C 133 ARG cc_start: 0.6904 (ttm110) cc_final: 0.6670 (ttm110) REVERT: C 297 MET cc_start: 0.8452 (mtm) cc_final: 0.8091 (ttp) REVERT: C 303 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7353 (mt-10) REVERT: C 310 ASP cc_start: 0.7785 (m-30) cc_final: 0.7495 (m-30) REVERT: C 435 THR cc_start: 0.8090 (p) cc_final: 0.7825 (p) REVERT: D 38 ARG cc_start: 0.7076 (ttt180) cc_final: 0.6283 (ttm-80) REVERT: D 46 TYR cc_start: 0.6828 (m-80) cc_final: 0.6329 (m-80) REVERT: D 52 LYS cc_start: 0.7494 (mttt) cc_final: 0.7022 (mmmt) REVERT: D 60 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7760 (mt) REVERT: D 91 MET cc_start: 0.6952 (ptt) cc_final: 0.5644 (ttt) REVERT: D 119 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6510 (mtm-85) REVERT: D 133 ARG cc_start: 0.6929 (ttm110) cc_final: 0.6684 (ttm110) REVERT: D 179 GLN cc_start: 0.7579 (pm20) cc_final: 0.7268 (pm20) REVERT: D 297 MET cc_start: 0.8387 (mtm) cc_final: 0.8077 (ttp) REVERT: D 310 ASP cc_start: 0.7850 (m-30) cc_final: 0.7539 (m-30) REVERT: D 435 THR cc_start: 0.8080 (p) cc_final: 0.7815 (p) outliers start: 63 outliers final: 49 residues processed: 263 average time/residue: 1.2427 time to fit residues: 355.6597 Evaluate side-chains 274 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU 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 102 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 284 GLN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 0.1980 chunk 73 optimal weight: 0.9980 chunk 147 optimal weight: 0.0010 chunk 106 optimal weight: 0.9980 chunk 22 optimal weight: 0.0030 chunk 57 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 351 GLN B 172 GLN B 351 GLN C 351 GLN D 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.248793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.220342 restraints weight = 10046.033| |-----------------------------------------------------------------------------| r_work (start): 0.4543 rms_B_bonded: 1.18 r_work: 0.4390 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.4285 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12408 Z= 0.186 Angle : 0.572 9.243 16836 Z= 0.294 Chirality : 0.037 0.152 2076 Planarity : 0.004 0.036 2024 Dihedral : 4.103 18.405 1784 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.85 % Allowed : 17.97 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.21), residues: 1524 helix: 2.78 (0.14), residues: 1216 sheet: 0.90 (0.69), residues: 40 loop : -2.66 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 354 HIS 0.001 0.000 HIS A 358 PHE 0.015 0.002 PHE A 203 TYR 0.022 0.001 TYR A 124 ARG 0.003 0.000 ARG D 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9573.43 seconds wall clock time: 169 minutes 48.25 seconds (10188.25 seconds total)