Starting phenix.real_space_refine on Thu Sep 26 04:13:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/09_2024/8vv3_43548.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/09_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_43548/09_2024/8vv3_43548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/09_2024/8vv3_43548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/09_2024/8vv3_43548.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vv3_43548/09_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. Time to flip 4 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12172 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3031 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'SOE': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 7.10, per 1000 atoms: 0.58 Number of scatterers: 12172 At special positions: 0 Unit cell: (111.072, 110.004, 93.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 2084 8.00 N 2028 7.00 C 7928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 83.2% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 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: 3.62 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3767 1.34 - 1.46: 2167 1.46 - 1.58: 6274 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 12408 Sorted by residual: bond pdb=" C2 SOE D 501 " pdb=" O6 SOE D 501 " ideal model delta sigma weight residual 1.500 1.426 0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C2 SOE B 501 " pdb=" O6 SOE B 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C2 SOE A 501 " pdb=" O6 SOE A 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C2 SOE C 501 " pdb=" O6 SOE C 501 " ideal model delta sigma weight residual 1.500 1.427 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C2 SOE A 501 " pdb=" O2 SOE A 501 " ideal model delta sigma weight residual 1.358 1.427 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 12403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 16347 1.23 - 2.45: 353 2.45 - 3.68: 83 3.68 - 4.91: 32 4.91 - 6.14: 21 Bond angle restraints: 16836 Sorted by residual: angle pdb=" CA TYR A 124 " pdb=" CB TYR A 124 " pdb=" CG TYR A 124 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.61e+00 angle pdb=" CA TYR B 124 " pdb=" CB TYR B 124 " pdb=" CG TYR B 124 " ideal model delta sigma weight residual 113.90 119.48 -5.58 1.80e+00 3.09e-01 9.60e+00 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 119.46 -5.56 1.80e+00 3.09e-01 9.53e+00 angle pdb=" CA TYR D 124 " pdb=" CB TYR D 124 " pdb=" CG TYR D 124 " ideal model delta sigma weight residual 113.90 119.44 -5.54 1.80e+00 3.09e-01 9.47e+00 angle pdb=" C SER C 123 " pdb=" N TYR C 124 " pdb=" CA TYR C 124 " ideal model delta sigma weight residual 120.72 115.72 5.00 1.67e+00 3.59e-01 8.98e+00 ... (remaining 16831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6680 16.96 - 33.92: 644 33.92 - 50.88: 108 50.88 - 67.84: 32 67.84 - 84.80: 20 Dihedral angle restraints: 7484 sinusoidal: 2968 harmonic: 4516 Sorted by residual: dihedral pdb=" CG ARG B 361 " pdb=" CD ARG B 361 " pdb=" NE ARG B 361 " pdb=" CZ ARG B 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.34 -44.66 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 361 " pdb=" CD ARG A 361 " pdb=" NE ARG A 361 " pdb=" CZ ARG A 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.37 -44.63 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG C 361 " pdb=" CD ARG C 361 " pdb=" NE ARG C 361 " pdb=" CZ ARG C 361 " ideal model delta sinusoidal sigma weight residual -180.00 -135.39 -44.61 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 7481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1509 0.035 - 0.070: 426 0.070 - 0.104: 104 0.104 - 0.139: 29 0.139 - 0.174: 8 Chirality restraints: 2076 Sorted by residual: chirality pdb=" CA TYR D 124 " pdb=" N TYR D 124 " pdb=" C TYR D 124 " pdb=" CB TYR D 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA TYR C 124 " pdb=" N TYR C 124 " pdb=" C TYR C 124 " pdb=" CB TYR C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA TYR A 124 " pdb=" N TYR A 124 " pdb=" C TYR A 124 " pdb=" CB TYR A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 2073 not shown) Planarity restraints: 2024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 124 " -0.002 2.00e-02 2.50e+03 1.20e-02 2.87e+00 pdb=" CG TYR A 124 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 124 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 124 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR A 124 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 124 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 124 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 124 " -0.002 2.00e-02 2.50e+03 1.19e-02 2.83e+00 pdb=" CG TYR B 124 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 124 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 124 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 124 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 124 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 124 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 124 " 0.002 2.00e-02 2.50e+03 1.19e-02 2.82e+00 pdb=" CG TYR C 124 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 124 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 124 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 124 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 124 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR C 124 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 124 " 0.002 2.00e-02 2.50e+03 ... (remaining 2021 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2154 2.77 - 3.30: 12336 3.30 - 3.83: 21645 3.83 - 4.37: 24698 4.37 - 4.90: 42896 Nonbonded interactions: 103729 Sorted by model distance: nonbonded pdb=" OD1 ASN A 222 " pdb=" NH2 ARG A 385 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN C 222 " pdb=" NH2 ARG C 385 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN D 222 " pdb=" NH2 ARG D 385 " model vdw 2.233 3.120 nonbonded pdb=" OD1 ASN B 222 " pdb=" NH2 ARG B 385 " model vdw 2.234 3.120 nonbonded pdb=" OD1 ASP A 99 " pdb=" NE2 HIS A 326 " model vdw 2.249 3.120 ... (remaining 103724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.230 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- 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 : 1.463 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: 1.1917 time to fit residues: 372.4703 Evaluate side-chains 217 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12408 Z= 0.224 Angle : 0.552 7.394 16836 Z= 0.292 Chirality : 0.038 0.132 2076 Planarity : 0.004 0.029 2024 Dihedral : 3.892 15.349 1784 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.96 % Allowed : 9.25 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.21), residues: 1524 helix: 2.61 (0.14), residues: 1216 sheet: 0.46 (0.80), residues: 40 loop : -2.65 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.004 0.001 HIS B 22 PHE 0.016 0.002 PHE C 203 TYR 0.042 0.002 TYR C 124 ARG 0.005 0.001 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 230 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7113 (ttt180) cc_final: 0.6226 (ttm-80) REVERT: A 46 TYR cc_start: 0.6873 (m-80) cc_final: 0.6172 (m-80) REVERT: A 60 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7573 (mt) REVERT: A 91 MET cc_start: 0.5338 (tpp) cc_final: 0.4704 (ttt) REVERT: A 133 ARG cc_start: 0.6616 (ttm110) cc_final: 0.6296 (ttm110) REVERT: A 171 MET cc_start: 0.6662 (mtm) cc_final: 0.6240 (mmt) REVERT: A 179 GLN cc_start: 0.7002 (pm20) cc_final: 0.6485 (pm20) REVERT: A 215 LYS cc_start: 0.8207 (tttm) cc_final: 0.7942 (tttt) REVERT: A 289 GLU cc_start: 0.7260 (tt0) cc_final: 0.6465 (mm-30) REVERT: A 310 ASP cc_start: 0.7877 (m-30) cc_final: 0.7547 (m-30) REVERT: A 387 MET cc_start: 0.7252 (mmm) cc_final: 0.6954 (mtp) REVERT: B 38 ARG cc_start: 0.6952 (ttt180) cc_final: 0.6145 (ttp-110) REVERT: B 46 TYR cc_start: 0.6843 (m-80) cc_final: 0.6437 (m-80) REVERT: B 52 LYS cc_start: 0.7215 (mttt) cc_final: 0.6888 (mmmt) REVERT: B 91 MET cc_start: 0.5381 (tpp) cc_final: 0.4800 (ttt) REVERT: B 128 ILE cc_start: 0.5836 (OUTLIER) cc_final: 0.5378 (mm) REVERT: B 133 ARG cc_start: 0.6884 (ttm110) cc_final: 0.6211 (ttp-110) REVERT: B 164 ASP cc_start: 0.7690 (t70) cc_final: 0.7483 (t70) REVERT: B 167 CYS cc_start: 0.7744 (m) cc_final: 0.7519 (m) REVERT: B 172 GLN cc_start: 0.6530 (mm110) cc_final: 0.6267 (mt0) REVERT: B 179 GLN cc_start: 0.6687 (pm20) cc_final: 0.6234 (pm20) REVERT: B 215 LYS cc_start: 0.8465 (mtpm) cc_final: 0.8178 (mtpt) REVERT: B 219 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7215 (mt-10) REVERT: B 284 GLN cc_start: 0.5322 (mt0) cc_final: 0.4731 (mt0) REVERT: B 303 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6897 (mt-10) REVERT: B 310 ASP cc_start: 0.7888 (m-30) cc_final: 0.7533 (m-30) REVERT: C 38 ARG cc_start: 0.7311 (ttt180) cc_final: 0.6330 (ttp-110) REVERT: C 49 THR cc_start: 0.7134 (t) cc_final: 0.6913 (t) REVERT: C 91 MET cc_start: 0.5080 (tpp) cc_final: 0.4628 (ttt) REVERT: C 119 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6937 (mtm-85) REVERT: C 133 ARG cc_start: 0.6003 (ttm110) cc_final: 0.5332 (ttp-110) REVERT: C 179 GLN cc_start: 0.6721 (pm20) cc_final: 0.6222 (pm20) REVERT: C 289 GLU cc_start: 0.7457 (tt0) cc_final: 0.6426 (mm-30) REVERT: C 303 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7122 (mt-10) REVERT: C 435 THR cc_start: 0.8087 (p) cc_final: 0.7758 (p) REVERT: D 38 ARG cc_start: 0.7041 (ttt180) cc_final: 0.6161 (ttp-110) REVERT: D 46 TYR cc_start: 0.6808 (m-80) cc_final: 0.6443 (m-80) REVERT: D 91 MET cc_start: 0.5254 (tpp) cc_final: 0.4764 (ttt) REVERT: D 119 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6722 (mtm-85) REVERT: D 133 ARG cc_start: 0.6599 (ttm110) cc_final: 0.5888 (ttp-110) REVERT: D 167 CYS cc_start: 0.7740 (m) cc_final: 0.7518 (m) REVERT: D 179 GLN cc_start: 0.6805 (pm20) cc_final: 0.6277 (pm20) REVERT: D 289 GLU cc_start: 0.7351 (tt0) cc_final: 0.6378 (mm-30) REVERT: D 310 ASP cc_start: 0.7990 (m-30) cc_final: 0.7592 (m-30) REVERT: D 387 MET cc_start: 0.7518 (mmm) cc_final: 0.7300 (mtt) REVERT: D 435 THR cc_start: 0.8100 (p) cc_final: 0.7809 (p) outliers start: 40 outliers final: 19 residues processed: 249 average time/residue: 1.2868 time to fit residues: 346.1348 Evaluate side-chains 235 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 214 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 GLN D 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12408 Z= 0.259 Angle : 0.588 8.197 16836 Z= 0.308 Chirality : 0.039 0.134 2076 Planarity : 0.004 0.030 2024 Dihedral : 4.021 15.801 1784 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.55 % Allowed : 12.28 % 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: 2.57 (0.21), residues: 1524 helix: 2.59 (0.14), residues: 1220 sheet: 0.20 (0.78), residues: 40 loop : -2.68 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.004 0.001 HIS B 22 PHE 0.018 0.002 PHE A 203 TYR 0.033 0.002 TYR D 124 ARG 0.004 0.001 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6884 (m-80) cc_final: 0.6150 (m-80) REVERT: A 60 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 133 ARG cc_start: 0.6809 (ttm110) cc_final: 0.6483 (ttm110) REVERT: A 171 MET cc_start: 0.6709 (mtm) cc_final: 0.6250 (mmt) REVERT: A 179 GLN cc_start: 0.6918 (pm20) cc_final: 0.6343 (pm20) REVERT: A 219 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 289 GLU cc_start: 0.7346 (tt0) cc_final: 0.6565 (mm-30) REVERT: A 310 ASP cc_start: 0.7917 (m-30) cc_final: 0.7597 (m-30) REVERT: A 387 MET cc_start: 0.7409 (mmm) cc_final: 0.7075 (mtp) REVERT: B 38 ARG cc_start: 0.7017 (ttt180) cc_final: 0.6158 (ttm-80) REVERT: B 46 TYR cc_start: 0.6854 (m-80) cc_final: 0.6206 (m-80) REVERT: B 52 LYS cc_start: 0.7257 (mttt) cc_final: 0.6934 (mmmt) REVERT: B 91 MET cc_start: 0.5354 (tpp) cc_final: 0.4814 (ttt) REVERT: B 128 ILE cc_start: 0.6082 (OUTLIER) cc_final: 0.5692 (mm) REVERT: B 133 ARG cc_start: 0.6981 (ttm110) cc_final: 0.6656 (ttm110) REVERT: B 179 GLN cc_start: 0.6597 (pm20) cc_final: 0.6195 (pm20) REVERT: B 215 LYS cc_start: 0.8509 (mtpm) cc_final: 0.8254 (mtpt) REVERT: B 219 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7285 (mt-10) REVERT: B 310 ASP cc_start: 0.7923 (m-30) cc_final: 0.7557 (m-30) REVERT: B 387 MET cc_start: 0.7533 (mmm) cc_final: 0.7241 (mtt) REVERT: C 38 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6265 (ttp-110) REVERT: C 52 LYS cc_start: 0.7274 (mttt) cc_final: 0.6977 (mmmt) REVERT: C 91 MET cc_start: 0.5146 (tpp) cc_final: 0.4724 (ttt) REVERT: C 119 ARG cc_start: 0.7172 (mtm-85) cc_final: 0.6697 (mtm-85) REVERT: C 133 ARG cc_start: 0.6357 (ttm110) cc_final: 0.5705 (ttp-110) REVERT: C 179 GLN cc_start: 0.6785 (pm20) cc_final: 0.6283 (pm20) REVERT: C 303 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7067 (mt-10) REVERT: C 310 ASP cc_start: 0.7782 (m-30) cc_final: 0.7471 (m-30) REVERT: C 435 THR cc_start: 0.8114 (p) cc_final: 0.7838 (p) REVERT: D 38 ARG cc_start: 0.7076 (ttt180) cc_final: 0.6199 (ttp-110) REVERT: D 46 TYR cc_start: 0.6794 (m-80) cc_final: 0.6298 (m-80) REVERT: D 52 LYS cc_start: 0.7276 (mttt) cc_final: 0.6962 (mmmt) REVERT: D 91 MET cc_start: 0.5344 (tpp) cc_final: 0.4885 (ttt) REVERT: D 119 ARG cc_start: 0.7076 (mtm-85) cc_final: 0.6587 (mtm-85) REVERT: D 133 ARG cc_start: 0.6770 (ttm110) cc_final: 0.6503 (ttm110) REVERT: D 179 GLN cc_start: 0.6730 (pm20) cc_final: 0.6205 (pm20) REVERT: D 289 GLU cc_start: 0.7402 (tt0) cc_final: 0.7171 (tt0) REVERT: D 310 ASP cc_start: 0.7890 (m-30) cc_final: 0.7527 (m-30) REVERT: D 435 THR cc_start: 0.8110 (p) cc_final: 0.7837 (p) outliers start: 48 outliers final: 26 residues processed: 242 average time/residue: 1.3101 time to fit residues: 342.8798 Evaluate side-chains 244 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12408 Z= 0.209 Angle : 0.547 6.893 16836 Z= 0.286 Chirality : 0.037 0.135 2076 Planarity : 0.004 0.031 2024 Dihedral : 3.991 15.459 1784 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.99 % Allowed : 14.05 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.21), residues: 1524 helix: 2.68 (0.13), residues: 1220 sheet: 0.23 (0.77), residues: 40 loop : -2.62 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.002 0.000 HIS C 22 PHE 0.017 0.002 PHE A 203 TYR 0.027 0.002 TYR B 124 ARG 0.003 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 227 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6889 (m-80) cc_final: 0.6168 (m-80) REVERT: A 60 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7660 (mt) REVERT: A 133 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6420 (ttm110) REVERT: A 171 MET cc_start: 0.6861 (mtm) cc_final: 0.6471 (mmt) REVERT: A 179 GLN cc_start: 0.7007 (pm20) cc_final: 0.6507 (pm20) REVERT: A 215 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8074 (ttpp) REVERT: A 310 ASP cc_start: 0.7926 (m-30) cc_final: 0.7593 (m-30) REVERT: A 387 MET cc_start: 0.7361 (mmm) cc_final: 0.7055 (OUTLIER) REVERT: B 38 ARG cc_start: 0.7048 (ttt180) cc_final: 0.6185 (ttm-80) REVERT: B 46 TYR cc_start: 0.6787 (m-80) cc_final: 0.6184 (m-80) REVERT: B 52 LYS cc_start: 0.7256 (mttt) cc_final: 0.6912 (mmmt) REVERT: B 60 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7659 (mt) REVERT: B 91 MET cc_start: 0.5341 (tpp) cc_final: 0.4812 (ttt) REVERT: B 128 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5683 (mm) REVERT: B 133 ARG cc_start: 0.6923 (ttm110) cc_final: 0.6602 (ttm110) REVERT: B 179 GLN cc_start: 0.6681 (pm20) cc_final: 0.6226 (pm20) REVERT: B 215 LYS cc_start: 0.8480 (mtpm) cc_final: 0.8236 (mtpt) REVERT: B 219 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 310 ASP cc_start: 0.7927 (m-30) cc_final: 0.7565 (m-30) REVERT: B 387 MET cc_start: 0.7402 (mmm) cc_final: 0.7162 (mtt) REVERT: C 38 ARG cc_start: 0.7121 (ttt180) cc_final: 0.6215 (ttp-110) REVERT: C 46 TYR cc_start: 0.7022 (m-80) cc_final: 0.6594 (m-80) REVERT: C 52 LYS cc_start: 0.7195 (mttt) cc_final: 0.6963 (mmmt) REVERT: C 91 MET cc_start: 0.5189 (tpp) cc_final: 0.4740 (ttt) REVERT: C 119 ARG cc_start: 0.7134 (mtm-85) cc_final: 0.6651 (mtm-85) REVERT: C 133 ARG cc_start: 0.6387 (ttm110) cc_final: 0.5708 (ttp-110) REVERT: C 179 GLN cc_start: 0.6849 (pm20) cc_final: 0.6367 (pm20) REVERT: C 303 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7050 (mt-10) REVERT: C 310 ASP cc_start: 0.7747 (m-30) cc_final: 0.7447 (m-30) REVERT: C 435 THR cc_start: 0.8096 (p) cc_final: 0.7825 (p) REVERT: D 38 ARG cc_start: 0.7070 (ttt180) cc_final: 0.6205 (ttp-110) REVERT: D 46 TYR cc_start: 0.6881 (m-80) cc_final: 0.6374 (m-80) REVERT: D 52 LYS cc_start: 0.7288 (mttt) cc_final: 0.6970 (mmmt) REVERT: D 91 MET cc_start: 0.5388 (tpp) cc_final: 0.4900 (ttt) REVERT: D 119 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6644 (mtm-85) REVERT: D 133 ARG cc_start: 0.6703 (ttm110) cc_final: 0.6437 (ttm110) REVERT: D 144 GLU cc_start: 0.5968 (pp20) cc_final: 0.3963 (mm-30) REVERT: D 179 GLN cc_start: 0.6705 (pm20) cc_final: 0.6222 (pm20) REVERT: D 310 ASP cc_start: 0.7892 (m-30) cc_final: 0.7530 (m-30) REVERT: D 435 THR cc_start: 0.8142 (p) cc_final: 0.7869 (p) outliers start: 54 outliers final: 36 residues processed: 261 average time/residue: 1.2115 time to fit residues: 343.1447 Evaluate side-chains 259 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 220 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12408 Z= 0.336 Angle : 0.655 8.249 16836 Z= 0.340 Chirality : 0.042 0.170 2076 Planarity : 0.005 0.037 2024 Dihedral : 4.359 17.200 1784 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 5.33 % Allowed : 14.64 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.21), residues: 1524 helix: 2.37 (0.14), residues: 1220 sheet: 0.14 (0.76), residues: 40 loop : -2.80 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 354 HIS 0.004 0.001 HIS D 22 PHE 0.019 0.003 PHE A 203 TYR 0.027 0.002 TYR C 124 ARG 0.004 0.001 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 226 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6851 (m-80) cc_final: 0.6127 (m-80) REVERT: A 60 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7701 (mt) REVERT: A 119 ARG cc_start: 0.6901 (mtm-85) cc_final: 0.6491 (mtm-85) REVERT: A 133 ARG cc_start: 0.6977 (ttm110) cc_final: 0.6284 (ttp-110) REVERT: A 171 MET cc_start: 0.7057 (mtm) cc_final: 0.6511 (mmt) REVERT: A 179 GLN cc_start: 0.7184 (pm20) cc_final: 0.6717 (pm20) REVERT: A 219 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7226 (mt-10) REVERT: A 310 ASP cc_start: 0.7910 (m-30) cc_final: 0.7567 (m-30) REVERT: B 38 ARG cc_start: 0.7134 (ttt180) cc_final: 0.6262 (ttm-80) REVERT: B 46 TYR cc_start: 0.6774 (m-80) cc_final: 0.6188 (m-80) REVERT: B 52 LYS cc_start: 0.7203 (mttt) cc_final: 0.6916 (mmmt) REVERT: B 60 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7648 (mt) REVERT: B 91 MET cc_start: 0.5307 (tpp) cc_final: 0.4823 (ttt) REVERT: B 119 ARG cc_start: 0.7008 (mtm-85) cc_final: 0.6455 (mtm-85) REVERT: B 133 ARG cc_start: 0.7042 (ttm110) cc_final: 0.6353 (ttp-110) REVERT: B 179 GLN cc_start: 0.6706 (pm20) cc_final: 0.6288 (pm20) REVERT: B 215 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8275 (mtpt) REVERT: B 274 MET cc_start: 0.2619 (OUTLIER) cc_final: 0.2166 (ptp) REVERT: B 310 ASP cc_start: 0.7892 (m-30) cc_final: 0.7531 (m-30) REVERT: C 38 ARG cc_start: 0.7214 (ttt180) cc_final: 0.6280 (ttm-80) REVERT: C 52 LYS cc_start: 0.7214 (mttt) cc_final: 0.6979 (mmmt) REVERT: C 91 MET cc_start: 0.5271 (tpp) cc_final: 0.4892 (ttt) REVERT: C 119 ARG cc_start: 0.7063 (mtm-85) cc_final: 0.6658 (mtm-85) REVERT: C 126 GLU cc_start: 0.4800 (pt0) cc_final: 0.4262 (mm-30) REVERT: C 133 ARG cc_start: 0.6801 (ttm110) cc_final: 0.6091 (ttp-110) REVERT: C 179 GLN cc_start: 0.6848 (pm20) cc_final: 0.6374 (pm20) REVERT: C 310 ASP cc_start: 0.7895 (m-30) cc_final: 0.7568 (m-30) REVERT: C 387 MET cc_start: 0.7441 (mmm) cc_final: 0.7207 (mtt) REVERT: C 435 THR cc_start: 0.8120 (p) cc_final: 0.7851 (p) REVERT: D 38 ARG cc_start: 0.7115 (ttt180) cc_final: 0.6243 (ttm-80) REVERT: D 46 TYR cc_start: 0.6926 (m-80) cc_final: 0.6456 (m-80) REVERT: D 52 LYS cc_start: 0.7303 (mttt) cc_final: 0.6972 (mmmt) REVERT: D 91 MET cc_start: 0.5381 (tpp) cc_final: 0.4975 (ttt) REVERT: D 119 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6610 (mtm-85) REVERT: D 133 ARG cc_start: 0.6975 (ttm110) cc_final: 0.6659 (ttm110) REVERT: D 179 GLN cc_start: 0.6788 (pm20) cc_final: 0.6373 (pm20) REVERT: D 310 ASP cc_start: 0.7890 (m-30) cc_final: 0.7544 (m-30) REVERT: D 435 THR cc_start: 0.8127 (p) cc_final: 0.7865 (p) outliers start: 72 outliers final: 44 residues processed: 269 average time/residue: 1.1665 time to fit residues: 341.0598 Evaluate side-chains 263 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 216 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 chunk 36 optimal weight: 0.2980 chunk 147 optimal weight: 0.1980 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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: 0.7382 moved from start: 0.2208 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= 0.188 Angle : 0.545 8.111 16836 Z= 0.283 Chirality : 0.037 0.167 2076 Planarity : 0.004 0.032 2024 Dihedral : 4.066 17.360 1784 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.07 % Allowed : 16.05 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.21), residues: 1524 helix: 2.68 (0.13), residues: 1220 sheet: 0.49 (0.72), residues: 40 loop : -2.62 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 354 HIS 0.001 0.000 HIS A 326 PHE 0.016 0.002 PHE A 203 TYR 0.023 0.001 TYR C 124 ARG 0.003 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 226 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6823 (m-80) cc_final: 0.6121 (m-80) REVERT: A 60 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7707 (mt) REVERT: A 91 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.4650 (ttt) REVERT: A 133 ARG cc_start: 0.6667 (ttm110) cc_final: 0.6371 (ttm110) REVERT: A 171 MET cc_start: 0.7003 (mtm) cc_final: 0.6513 (mmt) REVERT: A 179 GLN cc_start: 0.7305 (pm20) cc_final: 0.6860 (pm20) REVERT: A 219 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 310 ASP cc_start: 0.7917 (m-30) cc_final: 0.7572 (m-30) REVERT: B 38 ARG cc_start: 0.7048 (ttt180) cc_final: 0.6185 (ttm-80) REVERT: B 46 TYR cc_start: 0.6732 (m-80) cc_final: 0.6229 (m-80) REVERT: B 52 LYS cc_start: 0.7228 (mttt) cc_final: 0.6935 (mmmt) REVERT: B 60 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7669 (mt) REVERT: B 91 MET cc_start: 0.5316 (tpp) cc_final: 0.4801 (ttt) REVERT: B 133 ARG cc_start: 0.6835 (ttm110) cc_final: 0.6537 (ttm110) REVERT: B 179 GLN cc_start: 0.6849 (pm20) cc_final: 0.6408 (pm20) REVERT: B 215 LYS cc_start: 0.8533 (mtpm) cc_final: 0.8232 (mtpt) REVERT: B 274 MET cc_start: 0.2510 (OUTLIER) cc_final: 0.2008 (ttp) REVERT: B 310 ASP cc_start: 0.7903 (m-30) cc_final: 0.7541 (m-30) REVERT: B 435 THR cc_start: 0.8063 (p) cc_final: 0.7823 (p) REVERT: C 38 ARG cc_start: 0.7080 (ttt180) cc_final: 0.6172 (ttm-80) REVERT: C 46 TYR cc_start: 0.7072 (m-80) cc_final: 0.6617 (m-80) REVERT: C 52 LYS cc_start: 0.7223 (mttt) cc_final: 0.6997 (mmmt) REVERT: C 60 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7672 (mt) REVERT: C 91 MET cc_start: 0.5187 (tpp) cc_final: 0.4797 (ttt) REVERT: C 133 ARG cc_start: 0.6507 (ttm110) cc_final: 0.5770 (ttp-110) REVERT: C 179 GLN cc_start: 0.6967 (pm20) cc_final: 0.6556 (pm20) REVERT: C 215 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8177 (ttpp) REVERT: C 310 ASP cc_start: 0.7720 (m-30) cc_final: 0.7418 (m-30) REVERT: C 435 THR cc_start: 0.8072 (p) cc_final: 0.7786 (p) REVERT: D 38 ARG cc_start: 0.7014 (ttt180) cc_final: 0.6153 (ttm-80) REVERT: D 46 TYR cc_start: 0.6858 (m-80) cc_final: 0.6394 (m-80) REVERT: D 52 LYS cc_start: 0.7303 (mttt) cc_final: 0.6984 (mmmt) REVERT: D 60 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7758 (mt) REVERT: D 91 MET cc_start: 0.5405 (tpp) cc_final: 0.4996 (ttt) REVERT: D 133 ARG cc_start: 0.6677 (ttm110) cc_final: 0.6358 (ttm110) REVERT: D 179 GLN cc_start: 0.6793 (pm20) cc_final: 0.6419 (pm20) REVERT: D 215 LYS cc_start: 0.8379 (ttpp) cc_final: 0.8146 (ttpp) REVERT: D 310 ASP cc_start: 0.7897 (m-30) cc_final: 0.7548 (m-30) REVERT: D 435 THR cc_start: 0.8059 (p) cc_final: 0.7780 (p) outliers start: 55 outliers final: 35 residues processed: 262 average time/residue: 1.2582 time to fit residues: 361.0663 Evaluate side-chains 261 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 102 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 395 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 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 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 172 GLN C 172 GLN D 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12408 Z= 0.224 Angle : 0.573 9.097 16836 Z= 0.296 Chirality : 0.038 0.194 2076 Planarity : 0.004 0.033 2024 Dihedral : 4.108 16.561 1784 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.03 % Allowed : 15.90 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.21), residues: 1524 helix: 2.66 (0.13), residues: 1220 sheet: 0.62 (0.71), residues: 40 loop : -2.59 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.000 HIS D 22 PHE 0.018 0.002 PHE A 203 TYR 0.023 0.002 TYR C 124 ARG 0.003 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 291 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 223 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6817 (m-80) cc_final: 0.6104 (m-80) REVERT: A 60 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7682 (mt) REVERT: A 91 MET cc_start: 0.6105 (OUTLIER) cc_final: 0.4642 (ttt) REVERT: A 133 ARG cc_start: 0.6730 (ttm110) cc_final: 0.6442 (ttm110) REVERT: A 171 MET cc_start: 0.7015 (mtm) cc_final: 0.6528 (mmt) REVERT: A 179 GLN cc_start: 0.7300 (pm20) cc_final: 0.6962 (pm20) REVERT: A 219 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7176 (mt-10) REVERT: A 310 ASP cc_start: 0.7913 (m-30) cc_final: 0.7568 (m-30) REVERT: B 38 ARG cc_start: 0.7078 (ttt180) cc_final: 0.6204 (ttm-80) REVERT: B 46 TYR cc_start: 0.6757 (m-80) cc_final: 0.6231 (m-80) REVERT: B 52 LYS cc_start: 0.7201 (mttt) cc_final: 0.6919 (mmmt) REVERT: B 60 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7671 (mt) REVERT: B 91 MET cc_start: 0.5327 (tpp) cc_final: 0.4823 (ttt) REVERT: B 133 ARG cc_start: 0.6846 (ttm110) cc_final: 0.6552 (ttm110) REVERT: B 179 GLN cc_start: 0.6890 (pm20) cc_final: 0.6446 (pm20) REVERT: B 215 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8237 (mtpt) REVERT: B 274 MET cc_start: 0.2503 (OUTLIER) cc_final: 0.2051 (ttp) REVERT: B 310 ASP cc_start: 0.7897 (m-30) cc_final: 0.7545 (m-30) REVERT: B 435 THR cc_start: 0.8085 (p) cc_final: 0.7843 (p) REVERT: C 38 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6210 (ttm-80) REVERT: C 46 TYR cc_start: 0.7053 (m-80) cc_final: 0.6625 (m-80) REVERT: C 52 LYS cc_start: 0.7215 (mttt) cc_final: 0.6992 (mmmt) REVERT: C 60 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7676 (mt) REVERT: C 91 MET cc_start: 0.5265 (tpp) cc_final: 0.4883 (ttt) REVERT: C 119 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6535 (mtm-85) REVERT: C 133 ARG cc_start: 0.6548 (ttm110) cc_final: 0.5806 (ttp-110) REVERT: C 179 GLN cc_start: 0.6979 (pm20) cc_final: 0.6555 (pm20) REVERT: C 215 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8137 (ttpp) REVERT: C 274 MET cc_start: 0.3081 (mtt) cc_final: 0.2440 (ttp) REVERT: C 310 ASP cc_start: 0.7676 (m-30) cc_final: 0.7379 (m-30) REVERT: C 435 THR cc_start: 0.8078 (p) cc_final: 0.7810 (p) REVERT: D 38 ARG cc_start: 0.7048 (ttt180) cc_final: 0.6205 (ttm-80) REVERT: D 46 TYR cc_start: 0.6838 (m-80) cc_final: 0.6376 (m-80) REVERT: D 52 LYS cc_start: 0.7246 (mttt) cc_final: 0.6964 (mmmt) REVERT: D 60 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7764 (mt) REVERT: D 91 MET cc_start: 0.5408 (tpp) cc_final: 0.4996 (ttt) REVERT: D 119 ARG cc_start: 0.7036 (mtm-85) cc_final: 0.6520 (mtm-85) REVERT: D 133 ARG cc_start: 0.6707 (ttm110) cc_final: 0.6405 (ttm110) REVERT: D 179 GLN cc_start: 0.6901 (pm20) cc_final: 0.6566 (pm20) REVERT: D 215 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8164 (ttpp) REVERT: D 310 ASP cc_start: 0.7895 (m-30) cc_final: 0.7542 (m-30) REVERT: D 435 THR cc_start: 0.8071 (p) cc_final: 0.7789 (p) outliers start: 68 outliers final: 48 residues processed: 270 average time/residue: 1.2217 time to fit residues: 358.0349 Evaluate side-chains 275 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 219 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 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 215 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 72 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN C 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12408 Z= 0.225 Angle : 0.576 9.252 16836 Z= 0.296 Chirality : 0.038 0.180 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.121 17.016 1784 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.66 % Allowed : 16.72 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.21), residues: 1524 helix: 2.63 (0.13), residues: 1220 sheet: 0.71 (0.70), residues: 40 loop : -2.58 (0.33), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.002 0.000 HIS D 22 PHE 0.017 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 222 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6766 (m-80) cc_final: 0.6181 (m-80) REVERT: A 60 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7730 (mt) REVERT: A 91 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.4665 (ttt) REVERT: A 133 ARG cc_start: 0.6689 (ttm110) cc_final: 0.6383 (ttm110) REVERT: A 171 MET cc_start: 0.7063 (mtm) cc_final: 0.6557 (mmt) REVERT: A 179 GLN cc_start: 0.7337 (pm20) cc_final: 0.7017 (pm20) REVERT: A 215 LYS cc_start: 0.8309 (tttm) cc_final: 0.7982 (ttpp) REVERT: A 310 ASP cc_start: 0.7909 (m-30) cc_final: 0.7568 (m-30) REVERT: B 38 ARG cc_start: 0.7087 (ttt180) cc_final: 0.6216 (ttm-80) REVERT: B 46 TYR cc_start: 0.6842 (m-80) cc_final: 0.6308 (m-80) REVERT: B 52 LYS cc_start: 0.7209 (mttt) cc_final: 0.6924 (mmmt) REVERT: B 60 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7672 (mt) REVERT: B 91 MET cc_start: 0.5448 (tpp) cc_final: 0.4952 (ttt) REVERT: B 133 ARG cc_start: 0.6840 (ttm110) cc_final: 0.6541 (ttm110) REVERT: B 179 GLN cc_start: 0.6959 (pm20) cc_final: 0.6552 (pm20) REVERT: B 215 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8217 (mtpt) REVERT: B 274 MET cc_start: 0.2559 (OUTLIER) cc_final: 0.2038 (ttp) REVERT: B 310 ASP cc_start: 0.7856 (m-30) cc_final: 0.7490 (m-30) REVERT: B 435 THR cc_start: 0.8075 (p) cc_final: 0.7818 (p) REVERT: C 38 ARG cc_start: 0.7107 (ttt180) cc_final: 0.6192 (ttm-80) REVERT: C 46 TYR cc_start: 0.7004 (m-80) cc_final: 0.6576 (m-80) REVERT: C 52 LYS cc_start: 0.7221 (mttt) cc_final: 0.6997 (mmmt) REVERT: C 60 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7687 (mt) REVERT: C 91 MET cc_start: 0.5298 (tpp) cc_final: 0.4901 (ttt) REVERT: C 119 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6514 (mtm-85) REVERT: C 133 ARG cc_start: 0.6556 (ttm110) cc_final: 0.6254 (ttm110) REVERT: C 179 GLN cc_start: 0.7001 (pm20) cc_final: 0.6604 (pm20) REVERT: C 215 LYS cc_start: 0.8423 (ttpp) cc_final: 0.8138 (ttpp) REVERT: C 274 MET cc_start: 0.3161 (mtt) cc_final: 0.2466 (ttp) REVERT: C 310 ASP cc_start: 0.7749 (m-30) cc_final: 0.7451 (m-30) REVERT: C 435 THR cc_start: 0.8094 (p) cc_final: 0.7830 (p) REVERT: D 38 ARG cc_start: 0.7051 (ttt180) cc_final: 0.6211 (ttm-80) REVERT: D 46 TYR cc_start: 0.6806 (m-80) cc_final: 0.6297 (m-80) REVERT: D 52 LYS cc_start: 0.7245 (mttt) cc_final: 0.6979 (mmmt) REVERT: D 60 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7729 (mt) REVERT: D 91 MET cc_start: 0.5379 (tpp) cc_final: 0.4974 (ttt) REVERT: D 119 ARG cc_start: 0.7031 (mtm-85) cc_final: 0.6488 (mtm-85) REVERT: D 133 ARG cc_start: 0.6694 (ttm110) cc_final: 0.6397 (ttm110) REVERT: D 179 GLN cc_start: 0.6920 (pm20) cc_final: 0.6588 (pm20) REVERT: D 215 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (ttpp) REVERT: D 310 ASP cc_start: 0.7895 (m-30) cc_final: 0.7543 (m-30) REVERT: D 435 THR cc_start: 0.8089 (p) cc_final: 0.7817 (p) outliers start: 63 outliers final: 51 residues processed: 270 average time/residue: 1.1485 time to fit residues: 337.6303 Evaluate side-chains 276 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 217 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 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 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12408 Z= 0.261 Angle : 0.605 9.125 16836 Z= 0.311 Chirality : 0.039 0.171 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.234 17.570 1784 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.44 % Allowed : 17.09 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.21), residues: 1524 helix: 2.50 (0.14), residues: 1224 sheet: 0.60 (0.69), residues: 40 loop : -2.65 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.003 0.001 HIS B 22 PHE 0.019 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 214 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6688 (m-80) cc_final: 0.6056 (m-80) REVERT: A 60 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7718 (mt) REVERT: A 91 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.4662 (ttt) REVERT: A 133 ARG cc_start: 0.6736 (ttm110) cc_final: 0.6067 (ttp-110) REVERT: A 171 MET cc_start: 0.7119 (mtm) cc_final: 0.6562 (mmt) REVERT: A 310 ASP cc_start: 0.7912 (m-30) cc_final: 0.7579 (m-30) REVERT: B 38 ARG cc_start: 0.7121 (ttt180) cc_final: 0.6217 (ttm-80) REVERT: B 46 TYR cc_start: 0.6792 (m-80) cc_final: 0.6232 (m-80) REVERT: B 52 LYS cc_start: 0.7211 (mttt) cc_final: 0.6925 (mmmt) REVERT: B 60 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7696 (mt) REVERT: B 91 MET cc_start: 0.5513 (tpp) cc_final: 0.5000 (ttt) REVERT: B 133 ARG cc_start: 0.6890 (ttm110) cc_final: 0.6579 (ttm110) REVERT: B 179 GLN cc_start: 0.6969 (pm20) cc_final: 0.6627 (pm20) REVERT: B 215 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8245 (mtpt) REVERT: B 274 MET cc_start: 0.2529 (OUTLIER) cc_final: 0.2001 (ttp) REVERT: B 310 ASP cc_start: 0.7890 (m-30) cc_final: 0.7526 (m-30) REVERT: B 435 THR cc_start: 0.8101 (p) cc_final: 0.7855 (p) REVERT: C 38 ARG cc_start: 0.7144 (ttt180) cc_final: 0.6231 (ttm-80) REVERT: C 46 TYR cc_start: 0.6983 (m-80) cc_final: 0.6567 (m-80) REVERT: C 52 LYS cc_start: 0.7222 (mttt) cc_final: 0.7007 (mmmt) REVERT: C 60 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7685 (mt) REVERT: C 119 ARG cc_start: 0.6946 (mtm-85) cc_final: 0.6544 (mtm-85) REVERT: C 133 ARG cc_start: 0.6654 (ttm110) cc_final: 0.6351 (ttm110) REVERT: C 179 GLN cc_start: 0.6936 (pm20) cc_final: 0.6687 (pm20) REVERT: C 215 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8207 (ttpp) REVERT: C 274 MET cc_start: 0.3138 (mtt) cc_final: 0.2421 (ttp) REVERT: C 310 ASP cc_start: 0.7880 (m-30) cc_final: 0.7539 (m-30) REVERT: C 435 THR cc_start: 0.8098 (p) cc_final: 0.7838 (p) REVERT: D 38 ARG cc_start: 0.7106 (ttt180) cc_final: 0.6219 (ttm-80) REVERT: D 46 TYR cc_start: 0.6839 (m-80) cc_final: 0.6382 (m-80) REVERT: D 52 LYS cc_start: 0.7247 (mttt) cc_final: 0.6980 (mmmt) REVERT: D 60 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7714 (mt) REVERT: D 83 LYS cc_start: 0.7425 (mtpt) cc_final: 0.6701 (tppt) REVERT: D 91 MET cc_start: 0.5421 (tpp) cc_final: 0.5010 (ttt) REVERT: D 119 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6501 (mtm-85) REVERT: D 133 ARG cc_start: 0.6789 (ttm110) cc_final: 0.6499 (ttm110) REVERT: D 179 GLN cc_start: 0.6904 (pm20) cc_final: 0.6568 (pm20) REVERT: D 215 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8190 (ttpp) REVERT: D 310 ASP cc_start: 0.7859 (m-30) cc_final: 0.7508 (m-30) REVERT: D 435 THR cc_start: 0.8092 (p) cc_final: 0.7835 (p) outliers start: 60 outliers final: 46 residues processed: 262 average time/residue: 1.1703 time to fit residues: 333.5811 Evaluate side-chains 268 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 213 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12408 Z= 0.250 Angle : 0.603 9.824 16836 Z= 0.310 Chirality : 0.039 0.169 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.245 18.228 1784 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.66 % Allowed : 17.23 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.20), residues: 1524 helix: 2.46 (0.13), residues: 1228 sheet: 0.61 (0.69), residues: 40 loop : -2.53 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 354 HIS 0.002 0.001 HIS D 22 PHE 0.018 0.002 PHE A 203 TYR 0.023 0.002 TYR A 124 ARG 0.003 0.000 ARG D 385 ********************** REFINEMENT MACRO_CYCLE 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 279 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 216 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.6684 (m-80) cc_final: 0.6034 (m-80) REVERT: A 60 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7731 (mt) REVERT: A 91 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.4664 (ttt) REVERT: A 119 ARG cc_start: 0.6940 (mtm-85) cc_final: 0.6453 (mtm-85) REVERT: A 133 ARG cc_start: 0.6747 (ttm110) cc_final: 0.6064 (ttp-110) REVERT: A 215 LYS cc_start: 0.8345 (tttm) cc_final: 0.8041 (ttpp) REVERT: A 310 ASP cc_start: 0.7893 (m-30) cc_final: 0.7551 (m-30) REVERT: A 435 THR cc_start: 0.8059 (p) cc_final: 0.7819 (p) REVERT: B 38 ARG cc_start: 0.7109 (ttt180) cc_final: 0.6215 (ttm-80) REVERT: B 46 TYR cc_start: 0.6787 (m-80) cc_final: 0.6227 (m-80) REVERT: B 52 LYS cc_start: 0.7217 (mttt) cc_final: 0.6929 (mmmt) REVERT: B 60 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7700 (mt) REVERT: B 91 MET cc_start: 0.5507 (tpp) cc_final: 0.4988 (ttt) REVERT: B 133 ARG cc_start: 0.6825 (ttm110) cc_final: 0.6134 (ttp-110) REVERT: B 179 GLN cc_start: 0.6937 (pm20) cc_final: 0.6635 (pm20) REVERT: B 215 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8237 (mtpt) REVERT: B 274 MET cc_start: 0.2551 (OUTLIER) cc_final: 0.2001 (ttp) REVERT: B 310 ASP cc_start: 0.7887 (m-30) cc_final: 0.7525 (m-30) REVERT: B 435 THR cc_start: 0.8073 (p) cc_final: 0.7827 (p) REVERT: C 38 ARG cc_start: 0.7164 (ttt180) cc_final: 0.6288 (ttm-80) REVERT: C 46 TYR cc_start: 0.6945 (m-80) cc_final: 0.6529 (m-80) REVERT: C 52 LYS cc_start: 0.7232 (mttt) cc_final: 0.6987 (mmmt) REVERT: C 60 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7704 (mt) REVERT: C 91 MET cc_start: 0.6852 (ptt) cc_final: 0.5532 (ttt) REVERT: C 119 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6520 (mtm-85) REVERT: C 133 ARG cc_start: 0.6635 (ttm110) cc_final: 0.6327 (ttm110) REVERT: C 179 GLN cc_start: 0.6989 (pm20) cc_final: 0.6699 (pm20) REVERT: C 215 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8143 (ttpp) REVERT: C 274 MET cc_start: 0.3077 (mtt) cc_final: 0.2525 (ttp) REVERT: C 310 ASP cc_start: 0.7874 (m-30) cc_final: 0.7531 (m-30) REVERT: C 435 THR cc_start: 0.8094 (p) cc_final: 0.7827 (p) REVERT: D 38 ARG cc_start: 0.7102 (ttt180) cc_final: 0.6205 (ttm-80) REVERT: D 46 TYR cc_start: 0.6833 (m-80) cc_final: 0.6375 (m-80) REVERT: D 52 LYS cc_start: 0.7248 (mttt) cc_final: 0.6984 (mmmt) REVERT: D 60 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7728 (mt) REVERT: D 119 ARG cc_start: 0.7056 (mtm-85) cc_final: 0.6497 (mtm-85) REVERT: D 133 ARG cc_start: 0.6780 (ttm110) cc_final: 0.6488 (ttm110) REVERT: D 179 GLN cc_start: 0.6912 (pm20) cc_final: 0.6620 (pm20) REVERT: D 215 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8154 (ttpp) REVERT: D 310 ASP cc_start: 0.7882 (m-30) cc_final: 0.7527 (m-30) REVERT: D 435 THR cc_start: 0.8086 (p) cc_final: 0.7832 (p) outliers start: 63 outliers final: 48 residues processed: 263 average time/residue: 1.1703 time to fit residues: 334.8430 Evaluate side-chains 272 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 215 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 224 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 172 GLN C 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.245437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.216974 restraints weight = 9970.262| |-----------------------------------------------------------------------------| r_work (start): 0.4521 rms_B_bonded: 1.17 r_work: 0.4320 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4211 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12408 Z= 0.225 Angle : 0.589 9.526 16836 Z= 0.302 Chirality : 0.038 0.168 2076 Planarity : 0.004 0.034 2024 Dihedral : 4.207 18.644 1784 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.59 % Allowed : 17.38 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.20), residues: 1524 helix: 2.57 (0.13), residues: 1220 sheet: 0.69 (0.69), residues: 40 loop : -2.58 (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 0.003 0.000 ARG A 405 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5400.81 seconds wall clock time: 95 minutes 46.71 seconds (5746.71 seconds total)