Starting phenix.real_space_refine on Mon Aug 5 02:01:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/08_2024/8vv3_43548.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/08_2024/8vv3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/08_2024/8vv3_43548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/08_2024/8vv3_43548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/08_2024/8vv3_43548.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/08_2024/8vv3_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 Residue "A TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12172 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.85, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 2.0 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: 0.98 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: 3.56 Time building geometry restraints manager: 5.06 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: 99.72 - 106.57: 324 106.57 - 113.42: 7128 113.42 - 120.27: 4261 120.27 - 127.13: 5007 127.13 - 133.98: 116 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.770 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.330 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.365 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: 1.2236 time to fit residues: 382.5378 Evaluate side-chains 217 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 fitting. rotamer outliers: 40 poor density : 230 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7113 (ttt180) cc_final: 0.6226 (ttm-80) REVERT: A 46 TYR cc_start: 0.6873 (m-80) cc_final: 0.6172 (m-80) REVERT: A 60 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7573 (mt) REVERT: A 91 MET cc_start: 0.5338 (tpp) cc_final: 0.4704 (ttt) REVERT: A 133 ARG cc_start: 0.6616 (ttm110) cc_final: 0.6296 (ttm110) REVERT: A 171 MET cc_start: 0.6662 (mtm) cc_final: 0.6240 (mmt) REVERT: A 179 GLN cc_start: 0.7002 (pm20) cc_final: 0.6485 (pm20) REVERT: A 215 LYS cc_start: 0.8207 (tttm) cc_final: 0.7942 (tttt) REVERT: A 289 GLU cc_start: 0.7260 (tt0) cc_final: 0.6465 (mm-30) REVERT: A 310 ASP cc_start: 0.7877 (m-30) cc_final: 0.7547 (m-30) REVERT: A 387 MET cc_start: 0.7252 (mmm) cc_final: 0.6954 (mtp) REVERT: B 38 ARG cc_start: 0.6952 (ttt180) cc_final: 0.6145 (ttp-110) REVERT: B 46 TYR cc_start: 0.6843 (m-80) cc_final: 0.6437 (m-80) REVERT: B 52 LYS cc_start: 0.7215 (mttt) cc_final: 0.6888 (mmmt) REVERT: B 91 MET cc_start: 0.5381 (tpp) cc_final: 0.4800 (ttt) REVERT: B 128 ILE cc_start: 0.5836 (OUTLIER) cc_final: 0.5378 (mm) REVERT: B 133 ARG cc_start: 0.6884 (ttm110) cc_final: 0.6211 (ttp-110) REVERT: B 164 ASP cc_start: 0.7690 (t70) cc_final: 0.7483 (t70) REVERT: B 167 CYS cc_start: 0.7744 (m) cc_final: 0.7519 (m) REVERT: B 172 GLN cc_start: 0.6530 (mm110) cc_final: 0.6267 (mt0) REVERT: B 179 GLN cc_start: 0.6687 (pm20) cc_final: 0.6234 (pm20) REVERT: B 215 LYS cc_start: 0.8465 (mtpm) cc_final: 0.8178 (mtpt) REVERT: B 219 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7215 (mt-10) REVERT: B 284 GLN cc_start: 0.5322 (mt0) cc_final: 0.4731 (mt0) REVERT: B 303 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6897 (mt-10) REVERT: B 310 ASP cc_start: 0.7888 (m-30) cc_final: 0.7533 (m-30) REVERT: C 38 ARG cc_start: 0.7311 (ttt180) cc_final: 0.6330 (ttp-110) REVERT: C 49 THR cc_start: 0.7134 (t) cc_final: 0.6913 (t) REVERT: C 91 MET cc_start: 0.5080 (tpp) cc_final: 0.4628 (ttt) REVERT: C 119 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6937 (mtm-85) REVERT: C 133 ARG cc_start: 0.6003 (ttm110) cc_final: 0.5332 (ttp-110) REVERT: C 179 GLN cc_start: 0.6721 (pm20) cc_final: 0.6222 (pm20) REVERT: C 289 GLU cc_start: 0.7457 (tt0) cc_final: 0.6426 (mm-30) REVERT: C 303 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7122 (mt-10) REVERT: C 435 THR cc_start: 0.8087 (p) cc_final: 0.7758 (p) REVERT: D 38 ARG cc_start: 0.7041 (ttt180) cc_final: 0.6161 (ttp-110) REVERT: D 46 TYR cc_start: 0.6808 (m-80) cc_final: 0.6443 (m-80) REVERT: D 91 MET cc_start: 0.5254 (tpp) cc_final: 0.4764 (ttt) REVERT: D 119 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6722 (mtm-85) REVERT: D 133 ARG cc_start: 0.6599 (ttm110) cc_final: 0.5888 (ttp-110) REVERT: D 167 CYS cc_start: 0.7740 (m) cc_final: 0.7518 (m) REVERT: D 179 GLN cc_start: 0.6805 (pm20) cc_final: 0.6277 (pm20) REVERT: D 289 GLU cc_start: 0.7351 (tt0) cc_final: 0.6378 (mm-30) REVERT: D 310 ASP cc_start: 0.7990 (m-30) cc_final: 0.7592 (m-30) REVERT: D 387 MET cc_start: 0.7518 (mmm) cc_final: 0.7300 (mtt) REVERT: D 435 THR cc_start: 0.8100 (p) cc_final: 0.7809 (p) outliers start: 40 outliers final: 19 residues processed: 249 average time/residue: 1.2708 time to fit residues: 342.0345 Evaluate side-chains 235 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN D 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1797 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= 0.260 Angle : 0.584 6.503 16836 Z= 0.306 Chirality : 0.039 0.134 2076 Planarity : 0.004 0.030 2024 Dihedral : 4.011 15.758 1784 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.55 % Allowed : 12.06 % 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: 2.57 (0.21), residues: 1524 helix: 2.62 (0.14), residues: 1216 sheet: 0.23 (0.79), residues: 40 loop : -2.72 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS C 22 PHE 0.018 0.002 PHE A 203 TYR 0.033 0.002 TYR D 124 ARG 0.004 0.001 ARG A 293 *********************** 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 267 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6870 (m-80) cc_final: 0.6124 (m-80) REVERT: A 60 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7639 (mt) REVERT: A 133 ARG cc_start: 0.6803 (ttm110) cc_final: 0.6479 (ttm110) REVERT: A 171 MET cc_start: 0.6706 (mtm) cc_final: 0.6247 (mmt) REVERT: A 179 GLN cc_start: 0.6899 (pm20) cc_final: 0.6341 (pm20) REVERT: A 289 GLU cc_start: 0.7338 (tt0) cc_final: 0.6558 (mm-30) REVERT: A 310 ASP cc_start: 0.7919 (m-30) cc_final: 0.7578 (m-30) REVERT: A 387 MET cc_start: 0.7391 (mmm) cc_final: 0.7037 (mtp) REVERT: B 38 ARG cc_start: 0.7008 (ttt180) cc_final: 0.6150 (ttm-80) REVERT: B 46 TYR cc_start: 0.6850 (m-80) cc_final: 0.6206 (m-80) REVERT: B 52 LYS cc_start: 0.7258 (mttt) cc_final: 0.6935 (mmmt) REVERT: B 91 MET cc_start: 0.5356 (tpp) cc_final: 0.4813 (ttt) REVERT: B 128 ILE cc_start: 0.5945 (OUTLIER) cc_final: 0.5546 (mm) REVERT: B 133 ARG cc_start: 0.6978 (ttm110) cc_final: 0.6652 (ttm110) REVERT: B 179 GLN cc_start: 0.6595 (pm20) cc_final: 0.6195 (pm20) REVERT: B 215 LYS cc_start: 0.8508 (mtpm) cc_final: 0.8303 (mtpt) REVERT: B 303 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6922 (mt-10) REVERT: B 310 ASP cc_start: 0.7922 (m-30) cc_final: 0.7561 (m-30) REVERT: B 377 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7855 (mtmt) REVERT: C 38 ARG cc_start: 0.7227 (ttt180) cc_final: 0.6288 (ttp-110) REVERT: C 52 LYS cc_start: 0.7274 (mttt) cc_final: 0.6977 (mmmt) REVERT: C 91 MET cc_start: 0.5148 (tpp) cc_final: 0.4721 (ttt) REVERT: C 119 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6731 (mtm-85) REVERT: C 133 ARG cc_start: 0.6341 (ttm110) cc_final: 0.5696 (ttp-110) REVERT: C 179 GLN cc_start: 0.6785 (pm20) cc_final: 0.6283 (pm20) REVERT: C 303 GLU cc_start: 0.7315 (mt-10) cc_final: 0.7068 (mt-10) REVERT: C 310 ASP cc_start: 0.7765 (m-30) cc_final: 0.7463 (m-30) REVERT: C 435 THR cc_start: 0.8143 (p) cc_final: 0.7868 (p) REVERT: D 38 ARG cc_start: 0.7071 (ttt180) cc_final: 0.6197 (ttp-110) REVERT: D 46 TYR cc_start: 0.6789 (m-80) cc_final: 0.6301 (m-80) REVERT: D 52 LYS cc_start: 0.7277 (mttt) cc_final: 0.6961 (mmmt) REVERT: D 91 MET cc_start: 0.5306 (tpp) cc_final: 0.4855 (ttt) REVERT: D 119 ARG cc_start: 0.7120 (mtm-85) cc_final: 0.6639 (mtm-85) REVERT: D 133 ARG cc_start: 0.6722 (ttm110) cc_final: 0.6451 (ttm110) REVERT: D 179 GLN cc_start: 0.6738 (pm20) cc_final: 0.6219 (pm20) REVERT: D 289 GLU cc_start: 0.7398 (tt0) cc_final: 0.6447 (mm-30) REVERT: D 310 ASP cc_start: 0.8023 (m-30) cc_final: 0.7636 (m-30) REVERT: D 387 MET cc_start: 0.7542 (mmm) cc_final: 0.7329 (mtt) REVERT: D 435 THR cc_start: 0.8115 (p) cc_final: 0.7834 (p) outliers start: 48 outliers final: 27 residues processed: 239 average time/residue: 1.2671 time to fit residues: 327.3963 Evaluate side-chains 242 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 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 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 136 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 72 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12408 Z= 0.208 Angle : 0.543 6.882 16836 Z= 0.285 Chirality : 0.037 0.135 2076 Planarity : 0.004 0.031 2024 Dihedral : 3.971 15.363 1784 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.85 % Allowed : 13.83 % 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: 2.71 (0.21), residues: 1524 helix: 2.70 (0.13), residues: 1220 sheet: 0.24 (0.77), residues: 40 loop : -2.66 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.002 0.000 HIS C 22 PHE 0.017 0.002 PHE A 191 TYR 0.027 0.002 TYR B 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 277 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 225 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6885 (m-80) cc_final: 0.6155 (m-80) REVERT: A 60 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7690 (mt) REVERT: A 91 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.4596 (ttt) REVERT: A 133 ARG cc_start: 0.6709 (ttm110) cc_final: 0.6394 (ttm110) REVERT: A 171 MET cc_start: 0.6858 (mtm) cc_final: 0.6469 (mmt) REVERT: A 179 GLN cc_start: 0.7006 (pm20) cc_final: 0.6510 (pm20) REVERT: A 310 ASP cc_start: 0.7913 (m-30) cc_final: 0.7579 (m-30) REVERT: A 387 MET cc_start: 0.7344 (mmm) cc_final: 0.6981 (mtp) REVERT: B 38 ARG cc_start: 0.7037 (ttt180) cc_final: 0.6182 (ttm-80) REVERT: B 46 TYR cc_start: 0.6786 (m-80) cc_final: 0.6183 (m-80) REVERT: B 52 LYS cc_start: 0.7199 (mttt) cc_final: 0.6918 (mmmt) REVERT: B 60 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7662 (mt) REVERT: B 91 MET cc_start: 0.5352 (tpp) cc_final: 0.4815 (ttt) REVERT: B 128 ILE cc_start: 0.5922 (OUTLIER) cc_final: 0.5553 (mm) REVERT: B 133 ARG cc_start: 0.6900 (ttm110) cc_final: 0.6598 (ttm110) REVERT: B 179 GLN cc_start: 0.6725 (pm20) cc_final: 0.6274 (pm20) REVERT: B 215 LYS cc_start: 0.8484 (mtpm) cc_final: 0.8259 (mtpt) REVERT: B 219 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7290 (mt-10) REVERT: B 310 ASP cc_start: 0.7948 (m-30) cc_final: 0.7588 (m-30) REVERT: B 435 THR cc_start: 0.8042 (p) cc_final: 0.7798 (p) REVERT: C 38 ARG cc_start: 0.7104 (ttt180) cc_final: 0.6212 (ttp-110) REVERT: C 46 TYR cc_start: 0.7018 (m-80) cc_final: 0.6598 (m-80) REVERT: C 52 LYS cc_start: 0.7193 (mttt) cc_final: 0.6964 (mmmt) REVERT: C 91 MET cc_start: 0.5197 (tpp) cc_final: 0.4741 (ttt) REVERT: C 119 ARG cc_start: 0.7126 (mtm-85) cc_final: 0.6654 (mtm-85) REVERT: C 133 ARG cc_start: 0.6381 (ttm110) cc_final: 0.5704 (ttp-110) REVERT: C 179 GLN cc_start: 0.6849 (pm20) cc_final: 0.6369 (pm20) REVERT: C 215 LYS cc_start: 0.8300 (ttpp) cc_final: 0.8097 (ttpp) REVERT: C 303 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7052 (mt-10) REVERT: C 310 ASP cc_start: 0.7771 (m-30) cc_final: 0.7460 (m-30) REVERT: C 435 THR cc_start: 0.8101 (p) cc_final: 0.7823 (p) REVERT: D 38 ARG cc_start: 0.7038 (ttt180) cc_final: 0.6153 (ttp-110) REVERT: D 46 TYR cc_start: 0.6875 (m-80) cc_final: 0.6375 (m-80) REVERT: D 52 LYS cc_start: 0.7289 (mttt) cc_final: 0.6970 (mmmt) REVERT: D 91 MET cc_start: 0.5384 (tpp) cc_final: 0.4902 (ttt) REVERT: D 119 ARG cc_start: 0.7073 (mtm-85) cc_final: 0.6554 (mtm-85) REVERT: D 133 ARG cc_start: 0.6694 (ttm110) cc_final: 0.6389 (ttm110) REVERT: D 144 GLU cc_start: 0.5962 (pp20) cc_final: 0.3956 (mm-30) REVERT: D 179 GLN cc_start: 0.6666 (pm20) cc_final: 0.6187 (pm20) REVERT: D 215 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8176 (ttpp) REVERT: D 310 ASP cc_start: 0.7908 (m-30) cc_final: 0.7557 (m-30) REVERT: D 377 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7849 (mtmt) REVERT: D 387 MET cc_start: 0.7447 (mmm) cc_final: 0.7198 (mtt) REVERT: D 435 THR cc_start: 0.8142 (p) cc_final: 0.7865 (p) outliers start: 52 outliers final: 35 residues processed: 258 average time/residue: 1.3291 time to fit residues: 371.7289 Evaluate side-chains 258 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.0270 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12408 Z= 0.399 Angle : 0.704 9.028 16836 Z= 0.364 Chirality : 0.044 0.186 2076 Planarity : 0.006 0.048 2024 Dihedral : 4.496 17.912 1784 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.27 % Favored : 95.60 % Rotamer: Outliers : 5.18 % Allowed : 15.16 % 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: 1.98 (0.21), residues: 1524 helix: 2.13 (0.14), residues: 1228 sheet: 0.05 (0.74), residues: 40 loop : -2.73 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 354 HIS 0.006 0.001 HIS B 22 PHE 0.020 0.003 PHE A 205 TYR 0.028 0.003 TYR A 124 ARG 0.005 0.001 ARG B 211 *********************** 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 295 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 225 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6860 (m-80) cc_final: 0.6163 (m-80) REVERT: A 60 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7686 (mt) REVERT: A 91 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.4642 (ttt) REVERT: A 119 ARG cc_start: 0.7043 (mtm-85) cc_final: 0.6574 (mtm-85) REVERT: A 133 ARG cc_start: 0.7023 (ttm110) cc_final: 0.6330 (ttp-110) REVERT: A 171 MET cc_start: 0.7086 (mtm) cc_final: 0.6515 (mmt) REVERT: A 179 GLN cc_start: 0.7258 (pm20) cc_final: 0.6957 (pm20) REVERT: A 310 ASP cc_start: 0.7964 (m-30) cc_final: 0.7626 (m-30) REVERT: B 38 ARG cc_start: 0.7123 (ttt180) cc_final: 0.6279 (ttm-80) REVERT: B 46 TYR cc_start: 0.6813 (m-80) cc_final: 0.6189 (m-80) REVERT: B 52 LYS cc_start: 0.7207 (mttt) cc_final: 0.6934 (mmmt) REVERT: B 91 MET cc_start: 0.5355 (tpp) cc_final: 0.4862 (ttt) REVERT: B 119 ARG cc_start: 0.7136 (mtm-85) cc_final: 0.6588 (mtm-85) REVERT: B 133 ARG cc_start: 0.6974 (ttm110) cc_final: 0.6281 (ttp-110) REVERT: B 179 GLN cc_start: 0.6739 (pm20) cc_final: 0.6323 (pm20) REVERT: B 215 LYS cc_start: 0.8568 (mtpm) cc_final: 0.8297 (mtpt) REVERT: B 310 ASP cc_start: 0.7905 (m-30) cc_final: 0.7543 (m-30) REVERT: B 427 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7881 (ttt) REVERT: B 435 THR cc_start: 0.8112 (p) cc_final: 0.7859 (p) REVERT: C 38 ARG cc_start: 0.7272 (ttt180) cc_final: 0.6353 (ttm-80) REVERT: C 52 LYS cc_start: 0.7252 (mttt) cc_final: 0.7002 (mmmt) REVERT: C 91 MET cc_start: 0.5280 (tpp) cc_final: 0.4898 (ttt) REVERT: C 119 ARG cc_start: 0.7118 (mtm-85) cc_final: 0.6707 (mtm-85) REVERT: C 126 GLU cc_start: 0.4767 (pt0) cc_final: 0.4281 (mm-30) REVERT: C 133 ARG cc_start: 0.6932 (ttm110) cc_final: 0.6290 (ttp-110) REVERT: C 179 GLN cc_start: 0.6865 (pm20) cc_final: 0.6404 (pm20) REVERT: C 274 MET cc_start: 0.3354 (mtt) cc_final: 0.2756 (ttp) REVERT: C 297 MET cc_start: 0.7993 (mtm) cc_final: 0.7643 (ttp) REVERT: C 310 ASP cc_start: 0.7900 (m-30) cc_final: 0.7576 (m-30) REVERT: C 387 MET cc_start: 0.7452 (mmm) cc_final: 0.7244 (mtt) REVERT: C 435 THR cc_start: 0.8118 (p) cc_final: 0.7852 (p) REVERT: D 38 ARG cc_start: 0.7162 (ttt180) cc_final: 0.6265 (ttm-80) REVERT: D 46 TYR cc_start: 0.7013 (m-80) cc_final: 0.6571 (m-80) REVERT: D 52 LYS cc_start: 0.7306 (mttt) cc_final: 0.6976 (mmmt) REVERT: D 91 MET cc_start: 0.5404 (tpp) cc_final: 0.4965 (ttt) REVERT: D 119 ARG cc_start: 0.7150 (mtm-85) cc_final: 0.6634 (mtm-85) REVERT: D 133 ARG cc_start: 0.7024 (ttm110) cc_final: 0.6394 (ttp-110) REVERT: D 144 GLU cc_start: 0.5872 (pp20) cc_final: 0.4101 (tp30) REVERT: D 179 GLN cc_start: 0.6836 (pm20) cc_final: 0.6407 (pm20) REVERT: D 215 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8164 (mtpt) REVERT: D 219 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7207 (mt-10) REVERT: D 310 ASP cc_start: 0.7899 (m-30) cc_final: 0.7550 (m-30) REVERT: D 435 THR cc_start: 0.8147 (p) cc_final: 0.7871 (p) outliers start: 70 outliers final: 44 residues processed: 269 average time/residue: 1.1927 time to fit residues: 349.6702 Evaluate side-chains 263 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 215 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 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 B residue 427 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 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 153 LEU 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 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 153 LEU Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 215 LYS 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 49 optimal weight: 0.8980 chunk 132 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2276 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= 0.226 Angle : 0.584 8.723 16836 Z= 0.302 Chirality : 0.038 0.162 2076 Planarity : 0.004 0.035 2024 Dihedral : 4.232 17.485 1784 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.73 % Allowed : 15.90 % Favored : 79.36 % 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: 2.43 (0.21), residues: 1524 helix: 2.48 (0.14), residues: 1220 sheet: 0.22 (0.72), residues: 40 loop : -2.60 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.002 0.000 HIS D 22 PHE 0.017 0.002 PHE A 203 TYR 0.024 0.002 TYR A 124 ARG 0.003 0.000 ARG D 385 *********************** 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 292 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 228 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6817 (m-80) cc_final: 0.6084 (m-80) REVERT: A 60 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7713 (mt) REVERT: A 91 MET cc_start: 0.6120 (OUTLIER) cc_final: 0.4664 (ttt) REVERT: A 133 ARG cc_start: 0.6821 (ttm110) cc_final: 0.6104 (ttp-110) REVERT: A 171 MET cc_start: 0.7008 (mtm) cc_final: 0.6462 (mmt) REVERT: A 179 GLN cc_start: 0.7279 (pm20) cc_final: 0.6952 (pm20) REVERT: A 215 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8154 (ttpp) REVERT: A 310 ASP cc_start: 0.7889 (m-30) cc_final: 0.7551 (m-30) REVERT: B 38 ARG cc_start: 0.7124 (ttt180) cc_final: 0.6261 (ttm-80) REVERT: B 46 TYR cc_start: 0.6739 (m-80) cc_final: 0.6154 (m-80) REVERT: B 52 LYS cc_start: 0.7221 (mttt) cc_final: 0.6934 (mmmt) REVERT: B 60 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7658 (mt) REVERT: B 91 MET cc_start: 0.5293 (tpp) cc_final: 0.4836 (ttt) REVERT: B 133 ARG cc_start: 0.6941 (ttm110) cc_final: 0.6257 (ttp-110) REVERT: B 179 GLN cc_start: 0.6852 (pm20) cc_final: 0.6398 (pm20) REVERT: B 215 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8236 (mtpt) REVERT: B 274 MET cc_start: 0.2800 (OUTLIER) cc_final: 0.2319 (ptp) REVERT: B 310 ASP cc_start: 0.7921 (m-30) cc_final: 0.7574 (m-30) REVERT: B 435 THR cc_start: 0.8059 (p) cc_final: 0.7788 (p) REVERT: C 38 ARG cc_start: 0.7203 (ttt180) cc_final: 0.6277 (ttm-80) REVERT: C 46 TYR cc_start: 0.7102 (m-80) cc_final: 0.6692 (m-80) REVERT: C 52 LYS cc_start: 0.7233 (mttt) cc_final: 0.7002 (mmmt) REVERT: C 91 MET cc_start: 0.5251 (tpp) cc_final: 0.4899 (ttt) REVERT: C 119 ARG cc_start: 0.7061 (mtm-85) cc_final: 0.6671 (mtm-85) REVERT: C 126 GLU cc_start: 0.4693 (pt0) cc_final: 0.4199 (mm-30) REVERT: C 133 ARG cc_start: 0.6631 (ttm110) cc_final: 0.6376 (ttm110) REVERT: C 179 GLN cc_start: 0.6921 (pm20) cc_final: 0.6497 (pm20) REVERT: C 274 MET cc_start: 0.3319 (mtt) cc_final: 0.2672 (ttp) REVERT: C 297 MET cc_start: 0.7936 (mtm) cc_final: 0.7565 (ttp) REVERT: C 310 ASP cc_start: 0.7862 (m-30) cc_final: 0.7544 (m-30) REVERT: C 435 THR cc_start: 0.8085 (p) cc_final: 0.7800 (p) REVERT: D 38 ARG cc_start: 0.7084 (ttt180) cc_final: 0.6218 (ttm-80) REVERT: D 46 TYR cc_start: 0.6876 (m-80) cc_final: 0.6405 (m-80) REVERT: D 52 LYS cc_start: 0.7311 (mttt) cc_final: 0.6974 (mmmt) REVERT: D 60 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7719 (mt) REVERT: D 91 MET cc_start: 0.5389 (tpp) cc_final: 0.4956 (ttt) REVERT: D 119 ARG cc_start: 0.7039 (mtm-85) cc_final: 0.6523 (mtm-85) REVERT: D 133 ARG cc_start: 0.6792 (ttm110) cc_final: 0.6496 (ttm110) REVERT: D 179 GLN cc_start: 0.6872 (pm20) cc_final: 0.6519 (pm20) REVERT: D 215 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8035 (ttpp) REVERT: D 310 ASP cc_start: 0.7919 (m-30) cc_final: 0.7576 (m-30) REVERT: D 435 THR cc_start: 0.8092 (p) cc_final: 0.7816 (p) outliers start: 64 outliers final: 41 residues processed: 268 average time/residue: 1.2271 time to fit residues: 357.3015 Evaluate side-chains 270 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 222 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 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 216 LEU 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 215 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 273 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12408 Z= 0.223 Angle : 0.578 9.118 16836 Z= 0.298 Chirality : 0.038 0.186 2076 Planarity : 0.004 0.035 2024 Dihedral : 4.203 17.762 1784 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.10 % Allowed : 16.42 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.59 (0.21), residues: 1524 helix: 2.58 (0.13), residues: 1220 sheet: 0.40 (0.70), residues: 40 loop : -2.55 (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 0.017 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.004 0.000 ARG C 405 *********************** 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 294 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 225 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6856 (m-80) cc_final: 0.6209 (m-80) REVERT: A 60 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7723 (mt) REVERT: A 91 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.4660 (ttt) REVERT: A 133 ARG cc_start: 0.6766 (ttm110) cc_final: 0.6461 (ttm110) REVERT: A 171 MET cc_start: 0.7070 (mtm) cc_final: 0.6553 (mmt) REVERT: A 179 GLN cc_start: 0.7292 (pm20) cc_final: 0.6962 (pm20) REVERT: A 215 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8063 (ttpp) REVERT: A 310 ASP cc_start: 0.7924 (m-30) cc_final: 0.7578 (m-30) REVERT: A 377 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7756 (mtmt) REVERT: B 38 ARG cc_start: 0.7096 (ttt180) cc_final: 0.6249 (ttm-80) REVERT: B 46 TYR cc_start: 0.6828 (m-80) cc_final: 0.6220 (m-80) REVERT: B 52 LYS cc_start: 0.7230 (mttt) cc_final: 0.6932 (mmmt) REVERT: B 60 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7666 (mt) REVERT: B 91 MET cc_start: 0.5340 (tpp) cc_final: 0.4863 (ttt) REVERT: B 133 ARG cc_start: 0.6847 (ttm110) cc_final: 0.6546 (ttm110) REVERT: B 179 GLN cc_start: 0.6960 (pm20) cc_final: 0.6556 (pm20) REVERT: B 215 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8257 (mtpt) REVERT: B 274 MET cc_start: 0.2774 (OUTLIER) cc_final: 0.2141 (ttp) REVERT: B 310 ASP cc_start: 0.7905 (m-30) cc_final: 0.7543 (m-30) REVERT: B 435 THR cc_start: 0.8060 (p) cc_final: 0.7798 (p) REVERT: C 38 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6204 (ttm-80) REVERT: C 46 TYR cc_start: 0.7053 (m-80) cc_final: 0.6611 (m-80) REVERT: C 52 LYS cc_start: 0.7230 (mttt) cc_final: 0.7007 (mmmt) REVERT: C 60 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7679 (mt) REVERT: C 119 ARG cc_start: 0.6939 (mtm-85) cc_final: 0.6550 (mtm-85) REVERT: C 126 GLU cc_start: 0.4702 (pt0) cc_final: 0.4185 (mm-30) REVERT: C 133 ARG cc_start: 0.6576 (ttm110) cc_final: 0.6253 (ttm110) REVERT: C 179 GLN cc_start: 0.7012 (pm20) cc_final: 0.6624 (pm20) REVERT: C 215 LYS cc_start: 0.8316 (tttm) cc_final: 0.8004 (ttpp) REVERT: C 274 MET cc_start: 0.3390 (mtt) cc_final: 0.2750 (ttp) REVERT: C 310 ASP cc_start: 0.7713 (m-30) cc_final: 0.7419 (m-30) REVERT: C 387 MET cc_start: 0.7349 (mmm) cc_final: 0.7013 (mtt) REVERT: C 435 THR cc_start: 0.8074 (p) cc_final: 0.7788 (p) REVERT: D 38 ARG cc_start: 0.7084 (ttt180) cc_final: 0.6187 (ttm-80) REVERT: D 46 TYR cc_start: 0.6839 (m-80) cc_final: 0.6374 (m-80) REVERT: D 52 LYS cc_start: 0.7251 (mttt) cc_final: 0.6985 (mmmt) REVERT: D 60 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7757 (mt) REVERT: D 91 MET cc_start: 0.5362 (tpp) cc_final: 0.4980 (ttt) REVERT: D 119 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.6523 (mtm-85) REVERT: D 133 ARG cc_start: 0.6743 (ttm110) cc_final: 0.6452 (ttm110) REVERT: D 179 GLN cc_start: 0.6888 (pm20) cc_final: 0.6546 (pm20) REVERT: D 215 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8054 (ttpp) REVERT: D 310 ASP cc_start: 0.7926 (m-30) cc_final: 0.7575 (m-30) REVERT: D 435 THR cc_start: 0.8070 (p) cc_final: 0.7791 (p) outliers start: 69 outliers final: 49 residues processed: 271 average time/residue: 1.1799 time to fit residues: 347.3958 Evaluate side-chains 279 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 221 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 210 LEU Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 274 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 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 215 LYS 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 58 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN C 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12408 Z= 0.216 Angle : 0.574 9.184 16836 Z= 0.296 Chirality : 0.038 0.185 2076 Planarity : 0.004 0.035 2024 Dihedral : 4.165 17.778 1784 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.62 % Allowed : 16.05 % 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: 2.63 (0.20), residues: 1524 helix: 2.64 (0.13), residues: 1216 sheet: 0.58 (0.70), residues: 40 loop : -2.61 (0.32), residues: 268 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 0.001 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 300 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 224 time to evaluate : 1.354 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6834 (m-80) cc_final: 0.6186 (m-80) REVERT: A 60 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7727 (mt) REVERT: A 91 MET cc_start: 0.6077 (OUTLIER) cc_final: 0.4655 (ttt) REVERT: A 133 ARG cc_start: 0.6626 (ttm110) cc_final: 0.6315 (ttm110) REVERT: A 171 MET cc_start: 0.7080 (mtm) cc_final: 0.6551 (mmt) REVERT: A 179 GLN cc_start: 0.7296 (pm20) cc_final: 0.6974 (pm20) REVERT: A 215 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8118 (ttpp) REVERT: A 274 MET cc_start: 0.2394 (mmm) cc_final: 0.1756 (ttp) REVERT: A 310 ASP cc_start: 0.7905 (m-30) cc_final: 0.7563 (m-30) REVERT: A 435 THR cc_start: 0.8023 (p) cc_final: 0.7783 (p) REVERT: B 38 ARG cc_start: 0.7090 (ttt180) cc_final: 0.6198 (ttm-80) REVERT: B 46 TYR cc_start: 0.6823 (m-80) cc_final: 0.6228 (m-80) REVERT: B 52 LYS cc_start: 0.7214 (mttt) cc_final: 0.6927 (mmmt) REVERT: B 60 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7672 (mt) REVERT: B 91 MET cc_start: 0.5352 (tpp) cc_final: 0.4865 (ttt) REVERT: B 133 ARG cc_start: 0.6827 (ttm110) cc_final: 0.6537 (ttm110) REVERT: B 179 GLN cc_start: 0.6943 (pm20) cc_final: 0.6624 (pm20) REVERT: B 215 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8247 (mtpt) REVERT: B 274 MET cc_start: 0.2808 (OUTLIER) cc_final: 0.2180 (ttp) REVERT: B 310 ASP cc_start: 0.7898 (m-30) cc_final: 0.7538 (m-30) REVERT: B 435 THR cc_start: 0.8072 (p) cc_final: 0.7816 (p) REVERT: C 38 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6250 (ttm-80) REVERT: C 46 TYR cc_start: 0.6970 (m-80) cc_final: 0.6570 (m-80) REVERT: C 52 LYS cc_start: 0.7229 (mttt) cc_final: 0.6989 (mmmt) REVERT: C 60 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7687 (mt) REVERT: C 119 ARG cc_start: 0.6915 (mtm-85) cc_final: 0.6511 (mtm-85) REVERT: C 133 ARG cc_start: 0.6553 (ttm110) cc_final: 0.5803 (ttp-110) REVERT: C 179 GLN cc_start: 0.6973 (pm20) cc_final: 0.6731 (pm20) REVERT: C 274 MET cc_start: 0.3022 (mtt) cc_final: 0.2355 (ttp) REVERT: C 310 ASP cc_start: 0.7787 (m-30) cc_final: 0.7477 (m-30) REVERT: C 387 MET cc_start: 0.7341 (mmm) cc_final: 0.6984 (mtt) REVERT: C 435 THR cc_start: 0.8080 (p) cc_final: 0.7812 (p) REVERT: D 38 ARG cc_start: 0.7081 (ttt180) cc_final: 0.6186 (ttm-80) REVERT: D 46 TYR cc_start: 0.6806 (m-80) cc_final: 0.6293 (m-80) REVERT: D 52 LYS cc_start: 0.7250 (mttt) cc_final: 0.6975 (mmmt) REVERT: D 60 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7726 (mt) REVERT: D 91 MET cc_start: 0.5406 (tpp) cc_final: 0.4991 (ttt) REVERT: D 133 ARG cc_start: 0.6682 (ttm110) cc_final: 0.6391 (ttm110) REVERT: D 179 GLN cc_start: 0.6905 (pm20) cc_final: 0.6579 (pm20) REVERT: D 215 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8115 (ttpp) REVERT: D 310 ASP cc_start: 0.7895 (m-30) cc_final: 0.7548 (m-30) REVERT: D 435 THR cc_start: 0.8084 (p) cc_final: 0.7812 (p) outliers start: 76 outliers final: 55 residues processed: 278 average time/residue: 1.1554 time to fit residues: 349.4591 Evaluate side-chains 286 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 222 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 85 VAL 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 210 LEU Chi-restraints excluded: chain A residue 215 LYS 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 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 274 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 102 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 288 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 144 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 C 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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= 0.234 Angle : 0.586 8.907 16836 Z= 0.301 Chirality : 0.038 0.174 2076 Planarity : 0.004 0.035 2024 Dihedral : 4.200 17.837 1784 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.81 % Allowed : 16.86 % 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: 2.58 (0.20), residues: 1524 helix: 2.61 (0.13), residues: 1212 sheet: 0.67 (0.70), residues: 40 loop : -2.63 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.002 0.000 HIS C 22 PHE 0.018 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG A 405 *********************** 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 285 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 220 time to evaluate : 1.314 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6716 (m-80) cc_final: 0.6078 (m-80) REVERT: A 60 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7733 (mt) REVERT: A 91 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.4683 (ttt) REVERT: A 133 ARG cc_start: 0.6731 (ttm110) cc_final: 0.6423 (ttm110) REVERT: A 179 GLN cc_start: 0.7328 (pm20) cc_final: 0.7020 (pm20) REVERT: A 215 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8173 (ttpp) REVERT: A 310 ASP cc_start: 0.7908 (m-30) cc_final: 0.7564 (m-30) REVERT: A 435 THR cc_start: 0.8051 (p) cc_final: 0.7785 (p) REVERT: B 38 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6207 (ttm-80) REVERT: B 46 TYR cc_start: 0.6825 (m-80) cc_final: 0.6265 (m-80) REVERT: B 52 LYS cc_start: 0.7249 (mttt) cc_final: 0.6967 (mmmt) REVERT: B 60 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7672 (mt) REVERT: B 91 MET cc_start: 0.5382 (tpp) cc_final: 0.4887 (ttt) REVERT: B 133 ARG cc_start: 0.6801 (ttm110) cc_final: 0.6131 (ttp-110) REVERT: B 179 GLN cc_start: 0.6961 (pm20) cc_final: 0.6652 (pm20) REVERT: B 215 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8259 (mtpt) REVERT: B 274 MET cc_start: 0.2799 (OUTLIER) cc_final: 0.2091 (ttp) REVERT: B 310 ASP cc_start: 0.7857 (m-30) cc_final: 0.7496 (m-30) REVERT: B 435 THR cc_start: 0.8077 (p) cc_final: 0.7821 (p) REVERT: C 38 ARG cc_start: 0.7105 (ttt180) cc_final: 0.6207 (ttm-80) REVERT: C 46 TYR cc_start: 0.6942 (m-80) cc_final: 0.6521 (m-80) REVERT: C 52 LYS cc_start: 0.7230 (mttt) cc_final: 0.6984 (mmmt) REVERT: C 60 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7692 (mt) REVERT: C 91 MET cc_start: 0.6875 (ptt) cc_final: 0.5538 (ttt) REVERT: C 119 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6527 (mtm-85) REVERT: C 133 ARG cc_start: 0.6577 (ttm110) cc_final: 0.6259 (ttm110) REVERT: C 179 GLN cc_start: 0.7010 (pm20) cc_final: 0.6720 (pm20) REVERT: C 215 LYS cc_start: 0.8338 (tttm) cc_final: 0.8091 (ttpp) REVERT: C 274 MET cc_start: 0.3044 (mtt) cc_final: 0.2385 (ttp) REVERT: C 310 ASP cc_start: 0.7747 (m-30) cc_final: 0.7437 (m-30) REVERT: C 387 MET cc_start: 0.7386 (mmm) cc_final: 0.7093 (mtt) REVERT: C 435 THR cc_start: 0.8081 (p) cc_final: 0.7819 (p) REVERT: D 38 ARG cc_start: 0.7090 (ttt180) cc_final: 0.6191 (ttm-80) REVERT: D 46 TYR cc_start: 0.6831 (m-80) cc_final: 0.6311 (m-80) REVERT: D 52 LYS cc_start: 0.7246 (mttt) cc_final: 0.6982 (mmmt) REVERT: D 60 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7727 (mt) REVERT: D 119 ARG cc_start: 0.7037 (mtm-85) cc_final: 0.6503 (mtm-85) REVERT: D 133 ARG cc_start: 0.6747 (ttm110) cc_final: 0.6457 (ttm110) REVERT: D 179 GLN cc_start: 0.6931 (pm20) cc_final: 0.6609 (pm20) REVERT: D 215 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8110 (ttpp) REVERT: D 310 ASP cc_start: 0.7903 (m-30) cc_final: 0.7549 (m-30) REVERT: D 435 THR cc_start: 0.8076 (p) cc_final: 0.7813 (p) outliers start: 65 outliers final: 51 residues processed: 268 average time/residue: 1.1202 time to fit residues: 326.5514 Evaluate side-chains 277 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 217 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 215 LYS 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 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 274 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 102 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 215 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 288 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 120 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN C 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12408 Z= 0.246 Angle : 0.604 9.911 16836 Z= 0.309 Chirality : 0.039 0.174 2076 Planarity : 0.004 0.035 2024 Dihedral : 4.255 17.979 1784 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.81 % Allowed : 17.16 % Favored : 78.03 % 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 (0.20), residues: 1524 helix: 2.57 (0.13), residues: 1212 sheet: 0.63 (0.69), residues: 40 loop : -2.65 (0.32), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.002 0.000 HIS B 22 PHE 0.018 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.002 0.000 ARG D 296 ********************** 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 fitting. rotamer outliers: 65 poor density : 217 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6828 (m-80) cc_final: 0.6190 (m-80) REVERT: A 60 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7732 (mt) REVERT: A 91 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.4667 (ttt) REVERT: A 133 ARG cc_start: 0.6740 (ttm110) cc_final: 0.6058 (ttp-110) REVERT: A 215 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8151 (ttpp) REVERT: A 274 MET cc_start: 0.2257 (mtt) cc_final: 0.1867 (ttp) REVERT: A 310 ASP cc_start: 0.7889 (m-30) cc_final: 0.7542 (m-30) REVERT: A 435 THR cc_start: 0.8041 (p) cc_final: 0.7779 (p) REVERT: B 38 ARG cc_start: 0.7111 (ttt180) cc_final: 0.6214 (ttm-80) REVERT: B 46 TYR cc_start: 0.6826 (m-80) cc_final: 0.6257 (m-80) REVERT: B 52 LYS cc_start: 0.7252 (mttt) cc_final: 0.6970 (mmmt) REVERT: B 60 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7693 (mt) REVERT: B 91 MET cc_start: 0.5490 (tpp) cc_final: 0.4987 (ttt) REVERT: B 133 ARG cc_start: 0.6812 (ttm110) cc_final: 0.6137 (ttp-110) REVERT: B 179 GLN cc_start: 0.6950 (pm20) cc_final: 0.6644 (pm20) REVERT: B 215 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8254 (mtpt) REVERT: B 274 MET cc_start: 0.2833 (OUTLIER) cc_final: 0.2108 (ttp) REVERT: B 310 ASP cc_start: 0.7883 (m-30) cc_final: 0.7522 (m-30) REVERT: B 377 LYS cc_start: 0.7933 (mtmt) cc_final: 0.7682 (mttt) REVERT: B 435 THR cc_start: 0.8067 (p) cc_final: 0.7814 (p) REVERT: C 38 ARG cc_start: 0.7146 (ttt180) cc_final: 0.6280 (ttm-80) REVERT: C 46 TYR cc_start: 0.6944 (m-80) cc_final: 0.6524 (m-80) REVERT: C 52 LYS cc_start: 0.7236 (mttt) cc_final: 0.6989 (mmmt) REVERT: C 60 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7709 (mt) REVERT: C 91 MET cc_start: 0.6853 (ptt) cc_final: 0.5537 (ttt) REVERT: C 119 ARG cc_start: 0.6937 (mtm-85) cc_final: 0.6522 (mtm-85) REVERT: C 133 ARG cc_start: 0.6628 (ttm110) cc_final: 0.6314 (ttm110) REVERT: C 179 GLN cc_start: 0.7020 (pm20) cc_final: 0.6732 (pm20) REVERT: C 215 LYS cc_start: 0.8334 (tttm) cc_final: 0.8000 (ttpp) REVERT: C 274 MET cc_start: 0.3025 (mtt) cc_final: 0.2346 (ttp) REVERT: C 310 ASP cc_start: 0.7865 (m-30) cc_final: 0.7520 (m-30) REVERT: C 387 MET cc_start: 0.7407 (mmm) cc_final: 0.7105 (mtt) REVERT: C 435 THR cc_start: 0.8076 (p) cc_final: 0.7813 (p) REVERT: D 38 ARG cc_start: 0.7095 (ttt180) cc_final: 0.6197 (ttm-80) REVERT: D 46 TYR cc_start: 0.6843 (m-80) cc_final: 0.6378 (m-80) REVERT: D 52 LYS cc_start: 0.7248 (mttt) cc_final: 0.6986 (mmmt) REVERT: D 60 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7729 (mt) REVERT: D 119 ARG cc_start: 0.7049 (mtm-85) cc_final: 0.6498 (mtm-85) REVERT: D 133 ARG cc_start: 0.6760 (ttm110) cc_final: 0.6469 (ttm110) REVERT: D 179 GLN cc_start: 0.6941 (pm20) cc_final: 0.6644 (pm20) REVERT: D 215 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8142 (ttpp) REVERT: D 310 ASP cc_start: 0.7883 (m-30) cc_final: 0.7528 (m-30) REVERT: D 435 THR cc_start: 0.8082 (p) cc_final: 0.7820 (p) outliers start: 65 outliers final: 51 residues processed: 266 average time/residue: 1.0660 time to fit residues: 308.9400 Evaluate side-chains 277 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 217 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 215 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR 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 274 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 102 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 102 VAL 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 215 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 223 VAL 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 36 optimal weight: 0.3980 chunk 111 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN C 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.244366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.215791 restraints weight = 9972.457| |-----------------------------------------------------------------------------| r_work (start): 0.4578 rms_B_bonded: 1.16 r_work: 0.4389 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4277 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2477 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= 0.249 Angle : 0.605 9.662 16836 Z= 0.310 Chirality : 0.039 0.175 2076 Planarity : 0.004 0.035 2024 Dihedral : 4.275 18.493 1784 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.73 % Allowed : 17.31 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.44 (0.20), residues: 1524 helix: 2.47 (0.14), residues: 1224 sheet: 0.60 (0.69), residues: 40 loop : -2.70 (0.32), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.000 HIS B 22 PHE 0.018 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5419.24 seconds wall clock time: 95 minutes 52.21 seconds (5752.21 seconds total)