Starting phenix.real_space_refine on Sat Jul 20 20:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/07_2024/8vv3_43548.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/07_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_43548/07_2024/8vv3_43548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/07_2024/8vv3_43548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/07_2024/8vv3_43548.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/07_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.46, per 1000 atoms: 0.61 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: 5.68 Conformation dependent library (CDL) restraints added in 2.4 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 83.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 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: 3.69 Time building geometry restraints manager: 5.20 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 2.520 nonbonded pdb=" OD1 ASN C 222 " pdb=" NH2 ARG C 385 " model vdw 2.233 2.520 nonbonded pdb=" OD1 ASN D 222 " pdb=" NH2 ARG D 385 " model vdw 2.233 2.520 nonbonded pdb=" OD1 ASN B 222 " pdb=" NH2 ARG B 385 " model vdw 2.234 2.520 nonbonded pdb=" OD1 ASP A 99 " pdb=" NE2 HIS A 326 " model vdw 2.249 2.520 ... (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 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.090 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.760 ------------------------------------------------------------------------------- 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 : 1.322 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: 1.2162 time to fit residues: 379.9520 Evaluate side-chains 217 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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: 0.6980 chunk 115 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7380 moved from start: 0.1358 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= 0.225 Angle : 0.548 7.295 16836 Z= 0.289 Chirality : 0.038 0.138 2076 Planarity : 0.004 0.037 2024 Dihedral : 3.741 13.990 1784 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.18 % Allowed : 8.88 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.64 (0.21), residues: 1524 helix: 2.64 (0.14), residues: 1216 sheet: 0.44 (0.80), residues: 40 loop : -2.58 (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 D 22 PHE 0.017 0.002 PHE C 203 TYR 0.038 0.002 TYR C 124 ARG 0.004 0.000 ARG B 293 *********************** 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 262 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6265 (ttm-80) REVERT: A 60 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7595 (mt) REVERT: A 91 MET cc_start: 0.5325 (tpp) cc_final: 0.4730 (ttt) REVERT: A 133 ARG cc_start: 0.6717 (ttm110) cc_final: 0.6402 (ttm110) REVERT: A 171 MET cc_start: 0.6688 (mtm) cc_final: 0.6260 (mmt) REVERT: A 179 GLN cc_start: 0.7007 (pm20) cc_final: 0.6526 (pm20) REVERT: A 215 LYS cc_start: 0.8160 (tttm) cc_final: 0.7830 (ttmt) REVERT: A 289 GLU cc_start: 0.7376 (tt0) cc_final: 0.6496 (mm-30) REVERT: A 303 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6937 (mt-10) REVERT: A 310 ASP cc_start: 0.7935 (m-30) cc_final: 0.7612 (m-30) REVERT: A 387 MET cc_start: 0.7290 (mmm) cc_final: 0.6967 (mtp) REVERT: B 38 ARG cc_start: 0.6975 (ttt180) cc_final: 0.6103 (ttm-80) REVERT: B 46 TYR cc_start: 0.6920 (m-80) cc_final: 0.6297 (m-80) REVERT: B 52 LYS cc_start: 0.7226 (mttt) cc_final: 0.6901 (mmmt) REVERT: B 91 MET cc_start: 0.5377 (tpp) cc_final: 0.4813 (ttt) REVERT: B 128 ILE cc_start: 0.5868 (OUTLIER) cc_final: 0.5406 (mm) REVERT: B 133 ARG cc_start: 0.6945 (ttm110) cc_final: 0.6657 (ttm110) REVERT: B 164 ASP cc_start: 0.7760 (t70) cc_final: 0.7542 (t70) REVERT: B 167 CYS cc_start: 0.7737 (m) cc_final: 0.7518 (m) REVERT: B 172 GLN cc_start: 0.6520 (mm110) cc_final: 0.6238 (mt0) REVERT: B 215 LYS cc_start: 0.8525 (mtpm) cc_final: 0.8312 (mtpt) REVERT: B 303 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6905 (mt-10) REVERT: B 310 ASP cc_start: 0.7862 (m-30) cc_final: 0.7502 (m-30) REVERT: C 38 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6390 (ttp-110) REVERT: C 91 MET cc_start: 0.5132 (tpp) cc_final: 0.4659 (ttt) REVERT: C 119 ARG cc_start: 0.7233 (mtm-85) cc_final: 0.6918 (mtm-85) REVERT: C 133 ARG cc_start: 0.6194 (ttm110) cc_final: 0.5595 (ttp-110) REVERT: C 179 GLN cc_start: 0.6758 (pm20) cc_final: 0.6290 (pm20) REVERT: C 215 LYS cc_start: 0.8139 (tttm) cc_final: 0.7832 (ttpt) REVERT: C 303 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7125 (mt-10) REVERT: C 435 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7704 (p) REVERT: D 38 ARG cc_start: 0.7089 (ttt180) cc_final: 0.6201 (ttp-110) REVERT: D 46 TYR cc_start: 0.6836 (m-80) cc_final: 0.6312 (m-80) REVERT: D 91 MET cc_start: 0.5254 (tpp) cc_final: 0.4757 (ttt) REVERT: D 119 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6711 (mtm-85) REVERT: D 133 ARG cc_start: 0.6747 (ttm110) cc_final: 0.6421 (ttm110) REVERT: D 167 CYS cc_start: 0.7733 (m) cc_final: 0.7514 (m) REVERT: D 179 GLN cc_start: 0.6769 (pm20) cc_final: 0.6330 (pm20) REVERT: D 219 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7248 (mt-10) REVERT: D 289 GLU cc_start: 0.7456 (tt0) cc_final: 0.6481 (mm-30) REVERT: D 310 ASP cc_start: 0.8020 (m-30) cc_final: 0.7635 (m-30) REVERT: D 387 MET cc_start: 0.7528 (mmm) cc_final: 0.7291 (mtt) REVERT: D 435 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7781 (p) outliers start: 43 outliers final: 22 residues processed: 241 average time/residue: 1.2505 time to fit residues: 326.2079 Evaluate side-chains 234 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 153 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 356 THR 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 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 435 THR 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 Chi-restraints excluded: chain D residue 435 THR 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: 0.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN D 172 GLN D 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12408 Z= 0.230 Angle : 0.549 5.310 16836 Z= 0.289 Chirality : 0.037 0.140 2076 Planarity : 0.004 0.034 2024 Dihedral : 3.805 14.096 1784 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.22 % Allowed : 11.61 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.21), residues: 1524 helix: 2.68 (0.14), residues: 1216 sheet: 0.28 (0.77), residues: 40 loop : -2.75 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 354 HIS 0.004 0.001 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.033 0.002 TYR C 124 ARG 0.004 0.000 ARG B 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 269 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 212 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7090 (ttt180) cc_final: 0.6240 (ttm-80) REVERT: A 60 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 133 ARG cc_start: 0.6693 (ttm110) cc_final: 0.6400 (ttm110) REVERT: A 171 MET cc_start: 0.6702 (mtm) cc_final: 0.6239 (mmt) REVERT: A 179 GLN cc_start: 0.6947 (pm20) cc_final: 0.6398 (pm20) REVERT: A 215 LYS cc_start: 0.8175 (tttm) cc_final: 0.7876 (ttpt) REVERT: A 289 GLU cc_start: 0.7420 (tt0) cc_final: 0.6604 (mm-30) REVERT: A 310 ASP cc_start: 0.7922 (m-30) cc_final: 0.7593 (m-30) REVERT: A 387 MET cc_start: 0.7374 (mmm) cc_final: 0.7060 (mtp) REVERT: B 38 ARG cc_start: 0.7051 (ttt180) cc_final: 0.6211 (ttp-110) REVERT: B 46 TYR cc_start: 0.6840 (m-80) cc_final: 0.6150 (m-80) REVERT: B 52 LYS cc_start: 0.7281 (mttt) cc_final: 0.6950 (mmmt) REVERT: B 91 MET cc_start: 0.5350 (tpp) cc_final: 0.4836 (ttt) REVERT: B 128 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5537 (mm) REVERT: B 133 ARG cc_start: 0.6973 (ttm110) cc_final: 0.6672 (ttm110) REVERT: B 215 LYS cc_start: 0.8512 (mtpm) cc_final: 0.8285 (mtpt) REVERT: B 310 ASP cc_start: 0.7886 (m-30) cc_final: 0.7528 (m-30) REVERT: B 387 MET cc_start: 0.7482 (mmm) cc_final: 0.7213 (mtt) REVERT: C 38 ARG cc_start: 0.7225 (ttt180) cc_final: 0.6298 (ttp-110) REVERT: C 52 LYS cc_start: 0.7260 (mttt) cc_final: 0.6967 (mmmt) REVERT: C 91 MET cc_start: 0.5219 (tpp) cc_final: 0.4806 (ttt) REVERT: C 119 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6845 (mtm-85) REVERT: C 133 ARG cc_start: 0.6406 (ttm110) cc_final: 0.5728 (ttp-110) REVERT: C 179 GLN cc_start: 0.6800 (pm20) cc_final: 0.6288 (pm20) REVERT: C 215 LYS cc_start: 0.8191 (tttm) cc_final: 0.7894 (ttmt) REVERT: C 310 ASP cc_start: 0.7942 (m-30) cc_final: 0.7615 (m-30) REVERT: C 435 THR cc_start: 0.8056 (p) cc_final: 0.7771 (p) REVERT: D 38 ARG cc_start: 0.7066 (ttt180) cc_final: 0.6196 (ttp-110) REVERT: D 46 TYR cc_start: 0.6843 (m-80) cc_final: 0.6312 (m-80) REVERT: D 91 MET cc_start: 0.5351 (tpp) cc_final: 0.4874 (ttt) REVERT: D 119 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6629 (mtm-85) REVERT: D 133 ARG cc_start: 0.6778 (ttm110) cc_final: 0.6029 (ttp-110) REVERT: D 179 GLN cc_start: 0.6696 (pm20) cc_final: 0.6266 (pm20) REVERT: D 289 GLU cc_start: 0.7471 (tt0) cc_final: 0.6536 (mm-30) REVERT: D 310 ASP cc_start: 0.8030 (m-30) cc_final: 0.7653 (m-30) REVERT: D 387 MET cc_start: 0.7531 (mmm) cc_final: 0.7290 (mtt) REVERT: D 435 THR cc_start: 0.8128 (p) cc_final: 0.7837 (p) outliers start: 57 outliers final: 39 residues processed: 247 average time/residue: 1.2283 time to fit residues: 329.0171 Evaluate side-chains 245 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 435 THR 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 356 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2028 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= 0.245 Angle : 0.568 7.177 16836 Z= 0.297 Chirality : 0.038 0.128 2076 Planarity : 0.005 0.033 2024 Dihedral : 3.868 14.383 1784 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.33 % Allowed : 13.61 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.21), residues: 1524 helix: 2.66 (0.14), residues: 1216 sheet: 0.17 (0.75), residues: 40 loop : -2.78 (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 D 22 PHE 0.018 0.002 PHE A 203 TYR 0.028 0.002 TYR C 124 ARG 0.003 0.000 ARG A 293 *********************** 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 288 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 216 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7192 (ttt180) cc_final: 0.6317 (ttm-80) REVERT: A 60 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7731 (mt) REVERT: A 133 ARG cc_start: 0.6815 (ttm110) cc_final: 0.6512 (ttm110) REVERT: A 171 MET cc_start: 0.6846 (mtm) cc_final: 0.6378 (mmt) REVERT: A 179 GLN cc_start: 0.7011 (pm20) cc_final: 0.6589 (pm20) REVERT: A 215 LYS cc_start: 0.8244 (tttm) cc_final: 0.7963 (ttpt) REVERT: A 310 ASP cc_start: 0.7921 (m-30) cc_final: 0.7593 (m-30) REVERT: A 387 MET cc_start: 0.7372 (mmm) cc_final: 0.7131 (mtp) REVERT: B 38 ARG cc_start: 0.7164 (ttt180) cc_final: 0.6250 (ttm-80) REVERT: B 46 TYR cc_start: 0.6763 (m-80) cc_final: 0.6106 (m-80) REVERT: B 52 LYS cc_start: 0.7281 (mttt) cc_final: 0.6938 (mmmt) REVERT: B 91 MET cc_start: 0.5324 (tpp) cc_final: 0.4833 (ttt) REVERT: B 133 ARG cc_start: 0.6966 (ttm110) cc_final: 0.6652 (ttm110) REVERT: B 215 LYS cc_start: 0.8544 (mtpm) cc_final: 0.8296 (mtpt) REVERT: B 310 ASP cc_start: 0.7888 (m-30) cc_final: 0.7532 (m-30) REVERT: B 387 MET cc_start: 0.7441 (mmm) cc_final: 0.7226 (mtt) REVERT: C 38 ARG cc_start: 0.7240 (ttt180) cc_final: 0.6304 (ttp-110) REVERT: C 46 TYR cc_start: 0.6966 (m-80) cc_final: 0.6476 (m-80) REVERT: C 52 LYS cc_start: 0.7229 (mttt) cc_final: 0.6995 (mmmt) REVERT: C 91 MET cc_start: 0.5208 (tpp) cc_final: 0.4805 (ttt) REVERT: C 119 ARG cc_start: 0.7101 (mtm-85) cc_final: 0.6791 (mtm-85) REVERT: C 126 GLU cc_start: 0.4874 (pt0) cc_final: 0.4288 (mm-30) REVERT: C 133 ARG cc_start: 0.6522 (ttm110) cc_final: 0.6237 (ttm110) REVERT: C 179 GLN cc_start: 0.6880 (pm20) cc_final: 0.6495 (pm20) REVERT: C 215 LYS cc_start: 0.8261 (tttm) cc_final: 0.7893 (ttmt) REVERT: C 219 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7248 (mt-10) REVERT: C 310 ASP cc_start: 0.7895 (m-30) cc_final: 0.7568 (m-30) REVERT: C 435 THR cc_start: 0.8051 (p) cc_final: 0.7762 (p) REVERT: D 38 ARG cc_start: 0.7118 (ttt180) cc_final: 0.6235 (ttp-110) REVERT: D 46 TYR cc_start: 0.6938 (m-80) cc_final: 0.6428 (m-80) REVERT: D 52 LYS cc_start: 0.7308 (mttt) cc_final: 0.6987 (mmmt) REVERT: D 91 MET cc_start: 0.5429 (tpp) cc_final: 0.4988 (ttt) REVERT: D 119 ARG cc_start: 0.7168 (mtm-85) cc_final: 0.6631 (mtm-85) REVERT: D 133 ARG cc_start: 0.6801 (ttm110) cc_final: 0.6532 (ttm110) REVERT: D 179 GLN cc_start: 0.6803 (pm20) cc_final: 0.6447 (pm20) REVERT: D 310 ASP cc_start: 0.7890 (m-30) cc_final: 0.7532 (m-30) REVERT: D 435 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7794 (p) outliers start: 72 outliers final: 49 residues processed: 260 average time/residue: 1.1882 time to fit residues: 335.5885 Evaluate side-chains 261 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 435 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.0030 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12408 Z= 0.260 Angle : 0.585 7.962 16836 Z= 0.304 Chirality : 0.038 0.153 2076 Planarity : 0.005 0.035 2024 Dihedral : 3.932 15.124 1784 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.92 % Allowed : 14.57 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.21), residues: 1524 helix: 2.58 (0.14), residues: 1220 sheet: 0.26 (0.72), residues: 40 loop : -2.86 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.004 0.001 HIS B 22 PHE 0.018 0.002 PHE A 203 TYR 0.026 0.002 TYR B 124 ARG 0.003 0.000 ARG D 296 *********************** 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 301 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 221 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7245 (ttt180) cc_final: 0.6356 (ttm-80) REVERT: A 60 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7709 (mt) REVERT: A 119 ARG cc_start: 0.6834 (mtm-85) cc_final: 0.6382 (mtm-85) REVERT: A 133 ARG cc_start: 0.6849 (ttm110) cc_final: 0.6531 (ttm110) REVERT: A 171 MET cc_start: 0.7021 (mtm) cc_final: 0.6502 (mmt) REVERT: A 179 GLN cc_start: 0.7260 (pm20) cc_final: 0.6884 (pm20) REVERT: A 215 LYS cc_start: 0.8250 (tttm) cc_final: 0.7965 (ttpt) REVERT: A 289 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 310 ASP cc_start: 0.7914 (m-30) cc_final: 0.7567 (m-30) REVERT: B 38 ARG cc_start: 0.7210 (ttt180) cc_final: 0.6296 (ttm-80) REVERT: B 46 TYR cc_start: 0.6763 (m-80) cc_final: 0.6150 (m-80) REVERT: B 52 LYS cc_start: 0.7228 (mttt) cc_final: 0.6944 (mmmt) REVERT: B 60 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7736 (mt) REVERT: B 91 MET cc_start: 0.5304 (tpp) cc_final: 0.4845 (ttt) REVERT: B 119 ARG cc_start: 0.6983 (mtm-85) cc_final: 0.6423 (mtm-85) REVERT: B 133 ARG cc_start: 0.6978 (ttm110) cc_final: 0.6661 (ttm110) REVERT: B 215 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8286 (mtpt) REVERT: B 310 ASP cc_start: 0.7885 (m-30) cc_final: 0.7533 (m-30) REVERT: B 387 MET cc_start: 0.7441 (mmm) cc_final: 0.7194 (mtt) REVERT: C 38 ARG cc_start: 0.7259 (ttt180) cc_final: 0.6311 (ttp-110) REVERT: C 46 TYR cc_start: 0.7100 (m-80) cc_final: 0.6621 (m-80) REVERT: C 52 LYS cc_start: 0.7237 (mttt) cc_final: 0.7013 (mmmt) REVERT: C 91 MET cc_start: 0.5255 (tpp) cc_final: 0.4886 (ttt) REVERT: C 119 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6781 (mtm-85) REVERT: C 126 GLU cc_start: 0.4739 (pt0) cc_final: 0.4204 (mm-30) REVERT: C 133 ARG cc_start: 0.6610 (ttm110) cc_final: 0.6334 (ttm110) REVERT: C 179 GLN cc_start: 0.6958 (pm20) cc_final: 0.6638 (pm20) REVERT: C 215 LYS cc_start: 0.8288 (tttm) cc_final: 0.7881 (ttpt) REVERT: C 219 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7303 (mt-10) REVERT: C 310 ASP cc_start: 0.7880 (m-30) cc_final: 0.7550 (m-30) REVERT: C 435 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7740 (p) REVERT: D 38 ARG cc_start: 0.7114 (ttt180) cc_final: 0.6221 (ttm-80) REVERT: D 46 TYR cc_start: 0.6944 (m-80) cc_final: 0.6469 (m-80) REVERT: D 52 LYS cc_start: 0.7312 (mttt) cc_final: 0.6982 (mmmt) REVERT: D 91 MET cc_start: 0.5387 (tpp) cc_final: 0.4985 (ttt) REVERT: D 119 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6595 (mtm-85) REVERT: D 133 ARG cc_start: 0.6795 (ttm110) cc_final: 0.6523 (ttm110) REVERT: D 179 GLN cc_start: 0.6865 (pm20) cc_final: 0.6387 (pm20) REVERT: D 289 GLU cc_start: 0.7457 (tt0) cc_final: 0.6917 (tt0) REVERT: D 310 ASP cc_start: 0.7883 (m-30) cc_final: 0.7531 (m-30) REVERT: D 435 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7773 (m) outliers start: 80 outliers final: 53 residues processed: 275 average time/residue: 1.1747 time to fit residues: 351.1502 Evaluate side-chains 274 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 215 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 435 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 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 356 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 435 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 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 Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 435 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 147 optimal weight: 0.0270 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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: 0.7399 moved from start: 0.2162 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= 0.193 Angle : 0.539 8.549 16836 Z= 0.280 Chirality : 0.036 0.162 2076 Planarity : 0.004 0.034 2024 Dihedral : 3.796 16.570 1784 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.66 % Allowed : 16.79 % Favored : 78.55 % 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: 2.79 (0.21), residues: 1524 helix: 2.76 (0.13), residues: 1220 sheet: 0.54 (0.68), residues: 40 loop : -2.70 (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 0.016 0.002 PHE A 203 TYR 0.023 0.001 TYR A 124 ARG 0.002 0.000 ARG D 296 *********************** 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 283 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 220 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7223 (ttt180) cc_final: 0.6364 (ttm-80) REVERT: A 60 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7739 (mt) REVERT: A 91 MET cc_start: 0.6158 (mmm) cc_final: 0.4637 (ttt) REVERT: A 133 ARG cc_start: 0.6669 (ttm110) cc_final: 0.6374 (ttm110) REVERT: A 171 MET cc_start: 0.6983 (mtm) cc_final: 0.6531 (mmt) REVERT: A 179 GLN cc_start: 0.7289 (pm20) cc_final: 0.6876 (pm20) REVERT: A 215 LYS cc_start: 0.8180 (tttm) cc_final: 0.7844 (ttmt) REVERT: A 289 GLU cc_start: 0.7543 (tt0) cc_final: 0.7025 (tt0) REVERT: A 310 ASP cc_start: 0.7886 (m-30) cc_final: 0.7553 (m-30) REVERT: B 38 ARG cc_start: 0.7179 (ttt180) cc_final: 0.6293 (ttm-80) REVERT: B 52 LYS cc_start: 0.7261 (mttt) cc_final: 0.6992 (mmmt) REVERT: B 60 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7719 (mt) REVERT: B 91 MET cc_start: 0.5345 (tpp) cc_final: 0.4872 (ttt) REVERT: B 133 ARG cc_start: 0.6881 (ttm110) cc_final: 0.6586 (ttm110) REVERT: B 215 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8269 (mtpt) REVERT: B 310 ASP cc_start: 0.7910 (m-30) cc_final: 0.7545 (m-30) REVERT: B 387 MET cc_start: 0.7348 (mmm) cc_final: 0.7131 (mtt) REVERT: C 38 ARG cc_start: 0.7232 (ttt180) cc_final: 0.6290 (ttp-110) REVERT: C 46 TYR cc_start: 0.7135 (m-80) cc_final: 0.6629 (m-80) REVERT: C 52 LYS cc_start: 0.7245 (mttt) cc_final: 0.6996 (mmmt) REVERT: C 91 MET cc_start: 0.5283 (tpp) cc_final: 0.4903 (ttt) REVERT: C 119 ARG cc_start: 0.6942 (mtm-85) cc_final: 0.6504 (mtm-85) REVERT: C 133 ARG cc_start: 0.6530 (ttm110) cc_final: 0.6218 (ttm110) REVERT: C 179 GLN cc_start: 0.6986 (pm20) cc_final: 0.6570 (pm20) REVERT: C 215 LYS cc_start: 0.8167 (tttm) cc_final: 0.7817 (ttmt) REVERT: C 310 ASP cc_start: 0.7730 (m-30) cc_final: 0.7425 (m-30) REVERT: C 435 THR cc_start: 0.7995 (p) cc_final: 0.7716 (m) REVERT: D 38 ARG cc_start: 0.7107 (ttt180) cc_final: 0.6215 (ttp-110) REVERT: D 46 TYR cc_start: 0.6969 (m-80) cc_final: 0.6457 (m-80) REVERT: D 52 LYS cc_start: 0.7312 (mttt) cc_final: 0.6986 (mmmt) REVERT: D 60 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7777 (mt) REVERT: D 91 MET cc_start: 0.5379 (tpp) cc_final: 0.4982 (ttt) REVERT: D 119 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.6449 (mtm-85) REVERT: D 133 ARG cc_start: 0.6702 (ttm110) cc_final: 0.6415 (ttm110) REVERT: D 179 GLN cc_start: 0.6931 (pm20) cc_final: 0.6494 (pm20) REVERT: D 289 GLU cc_start: 0.7446 (tt0) cc_final: 0.6983 (tt0) REVERT: D 310 ASP cc_start: 0.7884 (m-30) cc_final: 0.7525 (m-30) REVERT: D 435 THR cc_start: 0.8010 (p) cc_final: 0.7761 (m) outliers start: 63 outliers final: 46 residues processed: 266 average time/residue: 1.2133 time to fit residues: 350.2944 Evaluate side-chains 262 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 210 LEU 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 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 435 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 356 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 83 optimal weight: 0.0670 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2216 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= 0.194 Angle : 0.540 8.317 16836 Z= 0.279 Chirality : 0.036 0.188 2076 Planarity : 0.004 0.034 2024 Dihedral : 3.774 17.304 1784 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.88 % Allowed : 16.94 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.21), residues: 1524 helix: 2.79 (0.13), residues: 1220 sheet: 0.74 (0.68), residues: 40 loop : -2.71 (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 0.022 0.001 TYR C 124 ARG 0.002 0.000 ARG D 385 *********************** 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 285 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 219 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7239 (ttt180) cc_final: 0.6376 (ttm-80) REVERT: A 60 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7743 (mt) REVERT: A 91 MET cc_start: 0.6201 (mmm) cc_final: 0.4691 (ttt) REVERT: A 133 ARG cc_start: 0.6583 (ttm110) cc_final: 0.6260 (ttm110) REVERT: A 171 MET cc_start: 0.6983 (mtm) cc_final: 0.6530 (mmt) REVERT: A 179 GLN cc_start: 0.7293 (pm20) cc_final: 0.6957 (pm20) REVERT: A 310 ASP cc_start: 0.7874 (m-30) cc_final: 0.7528 (m-30) REVERT: B 38 ARG cc_start: 0.7182 (ttt180) cc_final: 0.6285 (ttm-80) REVERT: B 52 LYS cc_start: 0.7246 (mttt) cc_final: 0.6984 (mmmt) REVERT: B 60 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7724 (mt) REVERT: B 91 MET cc_start: 0.5351 (tpp) cc_final: 0.4881 (ttt) REVERT: B 133 ARG cc_start: 0.6861 (ttm110) cc_final: 0.6571 (ttm110) REVERT: B 215 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8277 (mtpt) REVERT: B 219 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7192 (mt-10) REVERT: B 310 ASP cc_start: 0.7856 (m-30) cc_final: 0.7471 (m-30) REVERT: C 38 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6282 (ttp-110) REVERT: C 46 TYR cc_start: 0.7073 (m-80) cc_final: 0.6620 (m-80) REVERT: C 52 LYS cc_start: 0.7236 (mttt) cc_final: 0.6994 (mmmt) REVERT: C 60 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7726 (mt) REVERT: C 91 MET cc_start: 0.5271 (tpp) cc_final: 0.4898 (ttt) REVERT: C 119 ARG cc_start: 0.6890 (mtm-85) cc_final: 0.6460 (mtm-85) REVERT: C 133 ARG cc_start: 0.6523 (ttm110) cc_final: 0.6215 (ttm110) REVERT: C 179 GLN cc_start: 0.6994 (pm20) cc_final: 0.6588 (pm20) REVERT: C 310 ASP cc_start: 0.7819 (m-30) cc_final: 0.7507 (m-30) REVERT: C 435 THR cc_start: 0.7984 (p) cc_final: 0.7708 (m) REVERT: D 38 ARG cc_start: 0.7131 (ttt180) cc_final: 0.6194 (ttm-80) REVERT: D 46 TYR cc_start: 0.6945 (m-80) cc_final: 0.6390 (m-80) REVERT: D 52 LYS cc_start: 0.7250 (mttt) cc_final: 0.6978 (mmmt) REVERT: D 60 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7765 (mt) REVERT: D 91 MET cc_start: 0.5392 (tpp) cc_final: 0.4983 (ttt) REVERT: D 119 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6434 (mtm-85) REVERT: D 133 ARG cc_start: 0.6604 (ttm110) cc_final: 0.6309 (ttm110) REVERT: D 179 GLN cc_start: 0.6943 (pm20) cc_final: 0.6501 (pm20) REVERT: D 310 ASP cc_start: 0.7853 (m-30) cc_final: 0.7496 (m-30) REVERT: D 435 THR cc_start: 0.7998 (p) cc_final: 0.7755 (m) outliers start: 66 outliers final: 56 residues processed: 271 average time/residue: 1.1952 time to fit residues: 351.6198 Evaluate side-chains 269 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 208 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 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 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 435 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 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 356 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain D residue 356 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: 1.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7424 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12408 Z= 0.243 Angle : 0.583 9.068 16836 Z= 0.300 Chirality : 0.038 0.174 2076 Planarity : 0.004 0.035 2024 Dihedral : 3.884 18.087 1784 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 5.03 % Allowed : 17.90 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.21), residues: 1524 helix: 2.62 (0.14), residues: 1224 sheet: 0.73 (0.68), residues: 40 loop : -2.78 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.001 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 B 293 *********************** 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 280 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 212 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7284 (ttt180) cc_final: 0.6387 (ttm-80) REVERT: A 60 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7746 (mt) REVERT: A 91 MET cc_start: 0.6133 (mmm) cc_final: 0.4657 (ttt) REVERT: A 133 ARG cc_start: 0.6667 (ttm110) cc_final: 0.6375 (ttm110) REVERT: A 171 MET cc_start: 0.7058 (mtm) cc_final: 0.6529 (mmt) REVERT: A 179 GLN cc_start: 0.7297 (pm20) cc_final: 0.7073 (pm20) REVERT: A 310 ASP cc_start: 0.7831 (m-30) cc_final: 0.7491 (m-30) REVERT: B 38 ARG cc_start: 0.7249 (ttt180) cc_final: 0.6335 (ttm-80) REVERT: B 52 LYS cc_start: 0.7249 (mttt) cc_final: 0.6987 (mmmt) REVERT: B 60 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7767 (mt) REVERT: B 91 MET cc_start: 0.5377 (tpp) cc_final: 0.4906 (ttt) REVERT: B 133 ARG cc_start: 0.6894 (ttm110) cc_final: 0.6594 (ttm110) REVERT: B 215 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8268 (mtpt) REVERT: B 310 ASP cc_start: 0.7859 (m-30) cc_final: 0.7505 (m-30) REVERT: C 38 ARG cc_start: 0.7254 (ttt180) cc_final: 0.6307 (ttp-110) REVERT: C 46 TYR cc_start: 0.6985 (m-80) cc_final: 0.6525 (m-80) REVERT: C 52 LYS cc_start: 0.7240 (mttt) cc_final: 0.7001 (mmmt) REVERT: C 60 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7739 (mt) REVERT: C 119 ARG cc_start: 0.6881 (mtm-85) cc_final: 0.6449 (mtm-85) REVERT: C 133 ARG cc_start: 0.6627 (ttm110) cc_final: 0.6388 (ttm110) REVERT: C 179 GLN cc_start: 0.7003 (pm20) cc_final: 0.6676 (pm20) REVERT: C 297 MET cc_start: 0.7835 (mtm) cc_final: 0.7494 (ttp) REVERT: C 310 ASP cc_start: 0.7856 (m-30) cc_final: 0.7519 (m-30) REVERT: C 435 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7738 (p) REVERT: D 38 ARG cc_start: 0.7149 (ttt180) cc_final: 0.6266 (ttp-110) REVERT: D 46 TYR cc_start: 0.6988 (m-80) cc_final: 0.6471 (m-80) REVERT: D 52 LYS cc_start: 0.7254 (mttt) cc_final: 0.6989 (mmmt) REVERT: D 60 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7777 (mt) REVERT: D 91 MET cc_start: 0.5383 (tpp) cc_final: 0.4988 (ttt) REVERT: D 119 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6440 (mtm-85) REVERT: D 133 ARG cc_start: 0.6752 (ttm110) cc_final: 0.6478 (ttm110) REVERT: D 179 GLN cc_start: 0.6941 (pm20) cc_final: 0.6502 (pm20) REVERT: D 310 ASP cc_start: 0.7853 (m-30) cc_final: 0.7503 (m-30) REVERT: D 435 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7795 (m) outliers start: 68 outliers final: 55 residues processed: 263 average time/residue: 1.2039 time to fit residues: 344.0043 Evaluate side-chains 271 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 209 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 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 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 435 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 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 356 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 435 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 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 Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 435 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 0.3980 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 129 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12408 Z= 0.202 Angle : 0.556 8.731 16836 Z= 0.286 Chirality : 0.037 0.177 2076 Planarity : 0.004 0.035 2024 Dihedral : 3.804 17.427 1784 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.59 % Allowed : 18.42 % Favored : 77.00 % 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: 2.76 (0.21), residues: 1524 helix: 2.73 (0.14), residues: 1220 sheet: 0.72 (0.68), residues: 40 loop : -2.69 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.000 HIS D 22 PHE 0.017 0.002 PHE A 203 TYR 0.022 0.001 TYR C 124 ARG 0.003 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 210 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7264 (ttt180) cc_final: 0.6345 (ttm-80) REVERT: A 60 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 91 MET cc_start: 0.6134 (mmm) cc_final: 0.4655 (ttt) REVERT: A 133 ARG cc_start: 0.6594 (ttm110) cc_final: 0.6312 (ttm110) REVERT: A 171 MET cc_start: 0.7056 (mtm) cc_final: 0.6521 (mmt) REVERT: A 179 GLN cc_start: 0.7322 (pm20) cc_final: 0.7045 (pm20) REVERT: A 310 ASP cc_start: 0.7866 (m-30) cc_final: 0.7524 (m-30) REVERT: B 38 ARG cc_start: 0.7186 (ttt180) cc_final: 0.6266 (ttm-80) REVERT: B 52 LYS cc_start: 0.7254 (mttt) cc_final: 0.6989 (mmmt) REVERT: B 60 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 91 MET cc_start: 0.5372 (tpp) cc_final: 0.4904 (ttt) REVERT: B 133 ARG cc_start: 0.6724 (ttm110) cc_final: 0.6442 (ttm110) REVERT: B 215 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8260 (mtpt) REVERT: B 310 ASP cc_start: 0.7894 (m-30) cc_final: 0.7536 (m-30) REVERT: C 38 ARG cc_start: 0.7237 (ttt180) cc_final: 0.6306 (ttp-110) REVERT: C 46 TYR cc_start: 0.7019 (m-80) cc_final: 0.6511 (m-80) REVERT: C 52 LYS cc_start: 0.7241 (mttt) cc_final: 0.7001 (mmmt) REVERT: C 60 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7762 (mt) REVERT: C 91 MET cc_start: 0.6903 (ptt) cc_final: 0.5696 (ttt) REVERT: C 119 ARG cc_start: 0.6883 (mtm-85) cc_final: 0.6445 (mtm-85) REVERT: C 133 ARG cc_start: 0.6551 (ttm110) cc_final: 0.6288 (ttm110) REVERT: C 179 GLN cc_start: 0.7030 (pm20) cc_final: 0.6658 (pm20) REVERT: C 297 MET cc_start: 0.7841 (mtm) cc_final: 0.7496 (ttp) REVERT: C 310 ASP cc_start: 0.7747 (m-30) cc_final: 0.7441 (m-30) REVERT: C 435 THR cc_start: 0.8015 (p) cc_final: 0.7750 (m) REVERT: D 38 ARG cc_start: 0.7132 (ttt180) cc_final: 0.6242 (ttm-80) REVERT: D 46 TYR cc_start: 0.6962 (m-80) cc_final: 0.6409 (m-80) REVERT: D 52 LYS cc_start: 0.7255 (mttt) cc_final: 0.6991 (mmmt) REVERT: D 60 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7821 (mt) REVERT: D 91 MET cc_start: 0.5392 (tpp) cc_final: 0.4981 (ttt) REVERT: D 119 ARG cc_start: 0.6994 (mtm-85) cc_final: 0.6419 (mtm-85) REVERT: D 133 ARG cc_start: 0.6650 (ttm110) cc_final: 0.6351 (ttm110) REVERT: D 179 GLN cc_start: 0.6937 (pm20) cc_final: 0.6621 (pm20) REVERT: D 310 ASP cc_start: 0.7888 (m-30) cc_final: 0.7539 (m-30) REVERT: D 435 THR cc_start: 0.8029 (p) cc_final: 0.7798 (m) outliers start: 62 outliers final: 55 residues processed: 259 average time/residue: 1.2052 time to fit residues: 339.6296 Evaluate side-chains 267 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 207 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 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 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 435 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 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 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain D residue 356 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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: 0.7396 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12408 Z= 0.201 Angle : 0.556 8.720 16836 Z= 0.285 Chirality : 0.037 0.165 2076 Planarity : 0.004 0.035 2024 Dihedral : 3.791 17.286 1784 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.59 % Allowed : 18.49 % Favored : 76.92 % 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: 2.77 (0.21), residues: 1524 helix: 2.73 (0.14), residues: 1220 sheet: 0.75 (0.68), residues: 40 loop : -2.69 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.000 HIS B 22 PHE 0.017 0.002 PHE A 203 TYR 0.022 0.002 TYR A 124 ARG 0.002 0.000 ARG C 86 ********************** 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 271 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 209 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6343 (ttm-80) REVERT: A 60 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7748 (mt) REVERT: A 91 MET cc_start: 0.6143 (mmm) cc_final: 0.4691 (ttt) REVERT: A 133 ARG cc_start: 0.6594 (ttm110) cc_final: 0.6312 (ttm110) REVERT: A 171 MET cc_start: 0.7065 (mtm) cc_final: 0.6521 (mmt) REVERT: A 179 GLN cc_start: 0.7329 (pm20) cc_final: 0.7052 (pm20) REVERT: A 310 ASP cc_start: 0.7861 (m-30) cc_final: 0.7514 (m-30) REVERT: B 38 ARG cc_start: 0.7193 (ttt180) cc_final: 0.6272 (ttm-80) REVERT: B 52 LYS cc_start: 0.7253 (mttt) cc_final: 0.6986 (mmmt) REVERT: B 60 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7750 (mt) REVERT: B 91 MET cc_start: 0.5480 (tpp) cc_final: 0.4993 (ttt) REVERT: B 133 ARG cc_start: 0.6690 (ttm110) cc_final: 0.6415 (ttm110) REVERT: B 215 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8260 (mtpt) REVERT: B 310 ASP cc_start: 0.7891 (m-30) cc_final: 0.7513 (m-30) REVERT: C 38 ARG cc_start: 0.7234 (ttt180) cc_final: 0.6303 (ttp-110) REVERT: C 46 TYR cc_start: 0.7015 (m-80) cc_final: 0.6510 (m-80) REVERT: C 52 LYS cc_start: 0.7239 (mttt) cc_final: 0.6999 (mmmt) REVERT: C 60 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7779 (mt) REVERT: C 91 MET cc_start: 0.6876 (ptt) cc_final: 0.5679 (ttt) REVERT: C 133 ARG cc_start: 0.6557 (ttm110) cc_final: 0.6297 (ttm110) REVERT: C 179 GLN cc_start: 0.7024 (pm20) cc_final: 0.6815 (pm20) REVERT: C 274 MET cc_start: 0.2421 (mmm) cc_final: 0.1112 (ttp) REVERT: C 297 MET cc_start: 0.7833 (mtm) cc_final: 0.7487 (ttp) REVERT: C 310 ASP cc_start: 0.7748 (m-30) cc_final: 0.7435 (m-30) REVERT: C 435 THR cc_start: 0.8002 (p) cc_final: 0.7739 (m) REVERT: D 38 ARG cc_start: 0.7165 (ttt180) cc_final: 0.6292 (ttp-110) REVERT: D 46 TYR cc_start: 0.6907 (m-80) cc_final: 0.6361 (m-80) REVERT: D 52 LYS cc_start: 0.7254 (mttt) cc_final: 0.6987 (mmmt) REVERT: D 60 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7775 (mt) REVERT: D 91 MET cc_start: 0.5422 (tpp) cc_final: 0.5012 (ttt) REVERT: D 119 ARG cc_start: 0.6934 (mtm-85) cc_final: 0.6383 (mtm-85) REVERT: D 133 ARG cc_start: 0.6648 (ttm110) cc_final: 0.6348 (ttm110) REVERT: D 179 GLN cc_start: 0.6983 (pm20) cc_final: 0.6616 (pm20) REVERT: D 310 ASP cc_start: 0.7904 (m-30) cc_final: 0.7557 (m-30) REVERT: D 435 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7799 (m) outliers start: 62 outliers final: 52 residues processed: 257 average time/residue: 1.1839 time to fit residues: 330.6737 Evaluate side-chains 265 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 207 time to evaluate : 1.397 ------------------------------------------------------------------------------- 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 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 435 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 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 356 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain D residue 356 THR Chi-restraints excluded: chain D residue 435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.253276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.223392 restraints weight = 10251.001| |-----------------------------------------------------------------------------| r_work (start): 0.4493 rms_B_bonded: 1.22 r_work: 0.4315 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.4204 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12408 Z= 0.256 Angle : 0.608 8.654 16836 Z= 0.310 Chirality : 0.039 0.171 2076 Planarity : 0.004 0.035 2024 Dihedral : 3.952 17.136 1784 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.81 % Allowed : 18.34 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.21), residues: 1524 helix: 2.60 (0.14), residues: 1220 sheet: 0.73 (0.68), residues: 40 loop : -2.78 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.001 HIS B 22 PHE 0.018 0.002 PHE A 203 TYR 0.023 0.002 TYR C 124 ARG 0.002 0.000 ARG A 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5313.41 seconds wall clock time: 93 minutes 46.69 seconds (5626.69 seconds total)