Starting phenix.real_space_refine on Sat May 10 11:23:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fkp_50524/05_2025/9fkp_50524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fkp_50524/05_2025/9fkp_50524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fkp_50524/05_2025/9fkp_50524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fkp_50524/05_2025/9fkp_50524.map" model { file = "/net/cci-nas-00/data/ceres_data/9fkp_50524/05_2025/9fkp_50524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fkp_50524/05_2025/9fkp_50524.cif" } resolution = 3.72 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= -0.000 sd= 0.006 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 59 5.16 5 C 3859 2.51 5 N 1037 2.21 5 O 1137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6092 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 896 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "B" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 897 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Chain: "D" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 852 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 868 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2579 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 309} Time building chain proxies: 4.73, per 1000 atoms: 0.78 Number of scatterers: 6092 At special positions: 0 Unit cell: (89.28, 74.88, 143.28, 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 59 16.00 O 1137 8.00 N 1037 7.00 C 3859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 16 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 77 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 16 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 44 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 84 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 71 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 67 " distance=2.03 Simple disulfide: pdb=" SG CYS D 77 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 143 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 84 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 77 " - pdb=" SG CYS E 101 " distance=2.03 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 906.5 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 16 sheets defined 12.1% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.712A pdb=" N CYS A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 69 Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.559A pdb=" N SER B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 69 removed outlier: 3.502A pdb=" N LYS B 60 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 144 No H-bonds generated for 'chain 'E' and resid 142 through 144' Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.867A pdb=" N SER C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.910A pdb=" N SER C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 173 Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 325 through 336 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 80 Processing sheet with id=AA4, first strand: chain 'A' and resid 95 through 106 removed outlier: 6.868A pdb=" N LYS A 97 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 92 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU A 99 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR A 90 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 101 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE A 88 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASN A 103 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 86 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE D 76 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR A 91 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 Processing sheet with id=AA6, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 92 removed outlier: 6.730A pdb=" N SER B 108 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 83 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 106 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N MET B 104 " --> pdb=" O PRO B 85 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N SER B 102 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N VAL B 89 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N GLN B 100 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N TYR B 91 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL B 98 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.788A pdb=" N CYS D 67 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 97 through 102 Processing sheet with id=AB1, first strand: chain 'E' and resid 50 through 52 Processing sheet with id=AB2, first strand: chain 'E' and resid 57 through 58 removed outlier: 4.490A pdb=" N PHE E 133 " --> pdb=" O LYS E 126 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER E 137 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE E 122 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 35 removed outlier: 3.740A pdb=" N LEU C 34 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 236 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR C 345 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE C 238 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR C 347 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU C 240 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C 349 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLN C 242 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 274 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU C 267 " --> pdb=" O MET C 291 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS C 293 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 34 through 35 removed outlier: 3.740A pdb=" N LEU C 34 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 236 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR C 345 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE C 238 " --> pdb=" O THR C 345 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR C 347 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU C 240 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL C 349 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLN C 242 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 274 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN C 313 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY C 292 " --> pdb=" O GLN C 313 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 138 through 141 removed outlier: 6.927A pdb=" N VAL C 87 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG C 119 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU C 89 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ILE C 187 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ALA C 88 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE C 189 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N HIS C 90 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 191 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG C 92 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N PHE C 353 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE C 255 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 355 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASP C 257 " --> pdb=" O LEU C 355 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU C 357 " --> pdb=" O ASP C 257 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ARG C 259 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 252 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL C 284 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL C 254 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LYS C 286 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL C 256 " --> pdb=" O LYS C 286 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N SER C 303 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TRP C 283 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 53 through 56 removed outlier: 5.821A pdb=" N GLU C 66 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE C 107 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N HIS C 68 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE C 130 " --> pdb=" O LEU C 104 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 462 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: 1.81 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1979 1.35 - 1.46: 1392 1.46 - 1.58: 2801 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6244 Sorted by residual: bond pdb=" N CYS A 7 " pdb=" CA CYS A 7 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.33e+00 bond pdb=" N THR C 317 " pdb=" CA THR C 317 " ideal model delta sigma weight residual 1.456 1.483 -0.028 1.22e-02 6.72e+03 5.16e+00 bond pdb=" N GLU C 193 " pdb=" CA GLU C 193 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.14e+00 bond pdb=" N GLU C 240 " pdb=" CA GLU C 240 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.21e-02 6.83e+03 4.84e+00 bond pdb=" N ALA A 1 " pdb=" CA ALA A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 6239 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 7814 0.81 - 1.61: 533 1.61 - 2.42: 63 2.42 - 3.22: 39 3.22 - 4.03: 21 Bond angle restraints: 8470 Sorted by residual: angle pdb=" CA THR C 317 " pdb=" C THR C 317 " pdb=" O THR C 317 " ideal model delta sigma weight residual 121.16 118.36 2.80 1.12e+00 7.97e-01 6.27e+00 angle pdb=" CA CYS A 16 " pdb=" C CYS A 16 " pdb=" O CYS A 16 " ideal model delta sigma weight residual 121.32 118.54 2.78 1.18e+00 7.18e-01 5.55e+00 angle pdb=" CA GLU C 193 " pdb=" C GLU C 193 " pdb=" O GLU C 193 " ideal model delta sigma weight residual 120.58 118.31 2.27 1.07e+00 8.73e-01 4.49e+00 angle pdb=" C CYS A 15 " pdb=" N CYS A 16 " pdb=" CA CYS A 16 " ideal model delta sigma weight residual 122.39 119.07 3.32 1.64e+00 3.72e-01 4.09e+00 angle pdb=" CA THR C 317 " pdb=" CB THR C 317 " pdb=" CG2 THR C 317 " ideal model delta sigma weight residual 110.50 113.89 -3.39 1.70e+00 3.46e-01 3.97e+00 ... (remaining 8465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.93: 3695 14.93 - 29.86: 142 29.86 - 44.79: 24 44.79 - 59.72: 7 59.72 - 74.65: 1 Dihedral angle restraints: 3869 sinusoidal: 1604 harmonic: 2265 Sorted by residual: dihedral pdb=" N CYS A 16 " pdb=" CA CYS A 16 " pdb=" CB CYS A 16 " pdb=" SG CYS A 16 " ideal model delta sinusoidal sigma weight residual 60.00 119.15 -59.15 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS A 37 " pdb=" CG LYS A 37 " pdb=" CD LYS A 37 " pdb=" CE LYS A 37 " ideal model delta sinusoidal sigma weight residual -180.00 -122.71 -57.29 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N CYS B 7 " pdb=" CA CYS B 7 " pdb=" CB CYS B 7 " pdb=" SG CYS B 7 " ideal model delta sinusoidal sigma weight residual -180.00 -124.73 -55.27 3 1.50e+01 4.44e-03 9.34e+00 ... (remaining 3866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 563 0.030 - 0.060: 235 0.060 - 0.089: 40 0.089 - 0.119: 82 0.119 - 0.149: 12 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA THR C 317 " pdb=" N THR C 317 " pdb=" C THR C 317 " pdb=" CB THR C 317 " both_signs ideal model delta sigma weight residual False 2.53 2.67 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE E 76 " pdb=" N ILE E 76 " pdb=" C ILE E 76 " pdb=" CB ILE E 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE B 105 " pdb=" N ILE B 105 " pdb=" C ILE B 105 " pdb=" CB ILE B 105 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 929 not shown) Planarity restraints: 1093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 84 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.41e+00 pdb=" N PRO B 85 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 92 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO C 93 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 95 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 96 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 96 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 96 " 0.016 5.00e-02 4.00e+02 ... (remaining 1090 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 528 2.74 - 3.28: 6306 3.28 - 3.82: 9994 3.82 - 4.36: 12217 4.36 - 4.90: 20681 Nonbonded interactions: 49726 Sorted by model distance: nonbonded pdb=" NZ LYS E 52 " pdb=" OD2 ASP E 145 " model vdw 2.202 3.120 nonbonded pdb=" O HIS C 40 " pdb=" NE2 GLN C 43 " model vdw 2.220 3.120 nonbonded pdb=" ND1 HIS C 237 " pdb=" OG SER C 343 " model vdw 2.222 3.120 nonbonded pdb=" ND2 ASN C 71 " pdb=" OD1 ASN C 161 " model vdw 2.223 3.120 nonbonded pdb=" N GLU E 93 " pdb=" OE1 GLU E 93 " model vdw 2.228 3.120 ... (remaining 49721 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' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB or name OG )))) } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 47 through 153) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 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 : 0.002 0.036 6267 Z= 0.139 Angle : 0.497 4.031 8516 Z= 0.285 Chirality : 0.045 0.149 932 Planarity : 0.004 0.030 1093 Dihedral : 8.233 74.645 2324 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.86 % Allowed : 4.86 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.16 (0.31), residues: 759 helix: 1.01 (0.57), residues: 105 sheet: -0.29 (0.33), residues: 272 loop : -0.14 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 32 HIS 0.001 0.000 HIS C 169 PHE 0.005 0.001 PHE A 24 TYR 0.005 0.001 TYR A 65 ARG 0.002 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.18240 ( 161) hydrogen bonds : angle 6.99608 ( 462) SS BOND : bond 0.00209 ( 23) SS BOND : angle 0.59843 ( 46) covalent geometry : bond 0.00238 ( 6244) covalent geometry : angle 0.49641 ( 8470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 106 LEU cc_start: 0.6692 (mp) cc_final: 0.6457 (tt) REVERT: D 123 MET cc_start: 0.3331 (mmt) cc_final: 0.2361 (mmt) REVERT: E 68 MET cc_start: 0.6230 (ppp) cc_final: 0.5764 (ppp) REVERT: E 78 GLU cc_start: 0.7759 (tp30) cc_final: 0.7408 (tp30) REVERT: E 127 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4638 (pptt) REVERT: C 122 LYS cc_start: 0.9103 (mttt) cc_final: 0.8745 (tttt) REVERT: C 188 TYR cc_start: 0.7735 (m-80) cc_final: 0.7431 (m-80) REVERT: C 205 ASN cc_start: 0.8100 (m-40) cc_final: 0.7128 (t0) REVERT: C 274 LEU cc_start: 0.6989 (mp) cc_final: 0.6766 (mm) outliers start: 13 outliers final: 8 residues processed: 169 average time/residue: 0.2062 time to fit residues: 44.6244 Evaluate side-chains 111 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain E residue 58 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain C residue 201 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 0.2980 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 HIS ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS C 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.136160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.111282 restraints weight = 15507.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.114031 restraints weight = 10065.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.116015 restraints weight = 7343.079| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6267 Z= 0.154 Angle : 0.594 8.868 8516 Z= 0.304 Chirality : 0.046 0.131 932 Planarity : 0.004 0.041 1093 Dihedral : 5.812 49.416 834 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.86 % Allowed : 11.16 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.34 (0.31), residues: 759 helix: 0.39 (0.50), residues: 106 sheet: -0.45 (0.33), residues: 259 loop : -0.08 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 283 HIS 0.003 0.001 HIS C 132 PHE 0.009 0.002 PHE A 43 TYR 0.010 0.001 TYR B 58 ARG 0.007 0.001 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 161) hydrogen bonds : angle 5.88709 ( 462) SS BOND : bond 0.00421 ( 23) SS BOND : angle 1.03327 ( 46) covalent geometry : bond 0.00352 ( 6244) covalent geometry : angle 0.59024 ( 8470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.0710 (mmt) cc_final: 0.0063 (mmt) REVERT: E 78 GLU cc_start: 0.7870 (tp30) cc_final: 0.7278 (pt0) REVERT: E 81 GLN cc_start: 0.8459 (pp30) cc_final: 0.8234 (pp30) REVERT: E 123 MET cc_start: 0.7678 (mmt) cc_final: 0.6979 (tpt) outliers start: 20 outliers final: 18 residues processed: 126 average time/residue: 0.1594 time to fit residues: 28.3090 Evaluate side-chains 110 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 19 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN C 40 HIS ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.134258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.109217 restraints weight = 15780.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.112022 restraints weight = 10226.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.114018 restraints weight = 7422.720| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6267 Z= 0.178 Angle : 0.613 9.231 8516 Z= 0.310 Chirality : 0.045 0.138 932 Planarity : 0.004 0.040 1093 Dihedral : 5.627 48.997 823 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.86 % Allowed : 10.30 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.60 (0.30), residues: 759 helix: -0.01 (0.49), residues: 106 sheet: -0.49 (0.33), residues: 246 loop : -0.32 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 283 HIS 0.009 0.001 HIS D 102 PHE 0.013 0.002 PHE A 24 TYR 0.013 0.001 TYR B 50 ARG 0.004 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 161) hydrogen bonds : angle 5.92251 ( 462) SS BOND : bond 0.00457 ( 23) SS BOND : angle 0.95692 ( 46) covalent geometry : bond 0.00407 ( 6244) covalent geometry : angle 0.61065 ( 8470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7353 (mm-30) REVERT: B 69 ASN cc_start: 0.7967 (t0) cc_final: 0.7685 (t0) REVERT: D 102 HIS cc_start: 0.5384 (m-70) cc_final: 0.4984 (p-80) REVERT: D 123 MET cc_start: 0.0721 (mmt) cc_final: 0.0068 (mmt) outliers start: 27 outliers final: 23 residues processed: 115 average time/residue: 0.1452 time to fit residues: 23.9099 Evaluate side-chains 111 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN C 68 HIS C 100 HIS ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.130125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.105155 restraints weight = 16109.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.107853 restraints weight = 10537.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.109730 restraints weight = 7704.024| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6267 Z= 0.284 Angle : 0.701 8.058 8516 Z= 0.362 Chirality : 0.047 0.157 932 Planarity : 0.005 0.045 1093 Dihedral : 6.266 52.897 823 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.01 % Allowed : 11.73 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.29), residues: 759 helix: -1.03 (0.44), residues: 111 sheet: -0.36 (0.34), residues: 224 loop : -0.65 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 283 HIS 0.006 0.001 HIS C 237 PHE 0.019 0.002 PHE A 24 TYR 0.019 0.002 TYR B 50 ARG 0.003 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 161) hydrogen bonds : angle 6.58507 ( 462) SS BOND : bond 0.00636 ( 23) SS BOND : angle 1.22992 ( 46) covalent geometry : bond 0.00640 ( 6244) covalent geometry : angle 0.69748 ( 8470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 69 ASN cc_start: 0.8028 (t0) cc_final: 0.7712 (t0) REVERT: D 102 HIS cc_start: 0.5551 (m-70) cc_final: 0.5205 (m90) REVERT: D 123 MET cc_start: 0.0844 (mmt) cc_final: 0.0145 (mmt) REVERT: E 68 MET cc_start: 0.5965 (ppp) cc_final: 0.5667 (ppp) REVERT: E 78 GLU cc_start: 0.7908 (tp30) cc_final: 0.7507 (tp30) outliers start: 35 outliers final: 29 residues processed: 112 average time/residue: 0.1393 time to fit residues: 22.3304 Evaluate side-chains 108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.132879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.108163 restraints weight = 15605.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.110896 restraints weight = 10044.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.112846 restraints weight = 7283.712| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6267 Z= 0.150 Angle : 0.577 8.543 8516 Z= 0.294 Chirality : 0.044 0.147 932 Planarity : 0.004 0.039 1093 Dihedral : 5.853 50.433 823 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.15 % Allowed : 12.45 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.29), residues: 759 helix: -0.70 (0.46), residues: 111 sheet: -0.68 (0.33), residues: 249 loop : -0.59 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.004 0.001 HIS C 237 PHE 0.006 0.001 PHE A 43 TYR 0.018 0.001 TYR B 50 ARG 0.004 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 161) hydrogen bonds : angle 6.04976 ( 462) SS BOND : bond 0.00372 ( 23) SS BOND : angle 0.90282 ( 46) covalent geometry : bond 0.00346 ( 6244) covalent geometry : angle 0.57503 ( 8470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASN cc_start: 0.8266 (t0) cc_final: 0.8034 (t0) REVERT: D 102 HIS cc_start: 0.5735 (m-70) cc_final: 0.5493 (m-70) REVERT: D 123 MET cc_start: 0.0703 (mmt) cc_final: 0.0049 (mmt) REVERT: E 68 MET cc_start: 0.5838 (ppp) cc_final: 0.5571 (ppp) REVERT: E 78 GLU cc_start: 0.7891 (tp30) cc_final: 0.7432 (tp30) REVERT: E 123 MET cc_start: 0.7697 (mmt) cc_final: 0.7025 (tpt) REVERT: C 297 MET cc_start: 0.5699 (tpp) cc_final: 0.5217 (tpp) outliers start: 29 outliers final: 28 residues processed: 112 average time/residue: 0.1443 time to fit residues: 22.8625 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 69 optimal weight: 0.0060 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.137356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.111785 restraints weight = 15214.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.114773 restraints weight = 9605.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.116868 restraints weight = 6877.503| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6267 Z= 0.105 Angle : 0.541 8.699 8516 Z= 0.274 Chirality : 0.044 0.137 932 Planarity : 0.004 0.037 1093 Dihedral : 5.632 59.699 823 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 13.59 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.88 (0.30), residues: 759 helix: -0.24 (0.51), residues: 105 sheet: -0.73 (0.31), residues: 251 loop : -0.45 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.004 0.001 HIS C 237 PHE 0.006 0.001 PHE C 49 TYR 0.017 0.001 TYR B 50 ARG 0.004 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 161) hydrogen bonds : angle 5.53867 ( 462) SS BOND : bond 0.00256 ( 23) SS BOND : angle 0.77660 ( 46) covalent geometry : bond 0.00242 ( 6244) covalent geometry : angle 0.53960 ( 8470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASN cc_start: 0.8309 (t0) cc_final: 0.8092 (t0) REVERT: D 123 MET cc_start: 0.0521 (mmt) cc_final: -0.0080 (mmt) REVERT: E 68 MET cc_start: 0.5846 (ppp) cc_final: 0.5537 (ppp) REVERT: E 78 GLU cc_start: 0.7912 (tp30) cc_final: 0.7691 (tp30) REVERT: E 123 MET cc_start: 0.7593 (mmt) cc_final: 0.7168 (tpt) REVERT: C 130 ILE cc_start: 0.7125 (mt) cc_final: 0.6854 (mm) REVERT: C 297 MET cc_start: 0.5744 (tpp) cc_final: 0.5325 (tpp) outliers start: 25 outliers final: 24 residues processed: 110 average time/residue: 0.1445 time to fit residues: 22.9053 Evaluate side-chains 112 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 291 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.135881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.110702 restraints weight = 15350.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.113496 restraints weight = 9801.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.115488 restraints weight = 7117.717| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6267 Z= 0.121 Angle : 0.555 7.378 8516 Z= 0.283 Chirality : 0.044 0.137 932 Planarity : 0.004 0.036 1093 Dihedral : 5.612 59.502 823 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.01 % Allowed : 14.02 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.82 (0.30), residues: 759 helix: -0.31 (0.50), residues: 105 sheet: -0.63 (0.32), residues: 241 loop : -0.44 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 167 HIS 0.003 0.001 HIS D 102 PHE 0.007 0.001 PHE E 111 TYR 0.015 0.001 TYR B 50 ARG 0.003 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.02933 ( 161) hydrogen bonds : angle 5.64337 ( 462) SS BOND : bond 0.00295 ( 23) SS BOND : angle 0.76340 ( 46) covalent geometry : bond 0.00281 ( 6244) covalent geometry : angle 0.55384 ( 8470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 HIS cc_start: 0.5183 (m-70) cc_final: 0.4762 (p90) REVERT: D 123 MET cc_start: 0.0447 (mmt) cc_final: -0.0142 (mmt) REVERT: E 68 MET cc_start: 0.5935 (ppp) cc_final: 0.5638 (ppp) REVERT: E 78 GLU cc_start: 0.7771 (tp30) cc_final: 0.7358 (tp30) REVERT: E 123 MET cc_start: 0.7775 (mmt) cc_final: 0.7365 (tpt) REVERT: C 205 ASN cc_start: 0.7634 (m-40) cc_final: 0.7050 (t0) REVERT: C 297 MET cc_start: 0.5787 (tpp) cc_final: 0.5314 (tpp) outliers start: 28 outliers final: 25 residues processed: 112 average time/residue: 0.1395 time to fit residues: 22.0913 Evaluate side-chains 116 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 291 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.1980 chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 2 optimal weight: 0.3980 chunk 32 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.138209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.112775 restraints weight = 15176.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.115671 restraints weight = 9563.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.117846 restraints weight = 6895.040| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6267 Z= 0.105 Angle : 0.551 7.643 8516 Z= 0.279 Chirality : 0.044 0.174 932 Planarity : 0.004 0.036 1093 Dihedral : 5.501 58.926 823 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.58 % Allowed : 15.02 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.76 (0.30), residues: 759 helix: -0.19 (0.51), residues: 105 sheet: -0.56 (0.34), residues: 219 loop : -0.46 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 167 HIS 0.003 0.000 HIS C 352 PHE 0.009 0.001 PHE E 133 TYR 0.016 0.001 TYR C 216 ARG 0.003 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.02832 ( 161) hydrogen bonds : angle 5.46209 ( 462) SS BOND : bond 0.00239 ( 23) SS BOND : angle 0.73686 ( 46) covalent geometry : bond 0.00244 ( 6244) covalent geometry : angle 0.54990 ( 8470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.0349 (mmt) cc_final: -0.0194 (mmt) REVERT: E 68 MET cc_start: 0.5958 (ppp) cc_final: 0.5614 (ppp) REVERT: E 78 GLU cc_start: 0.7889 (tp30) cc_final: 0.7388 (tp30) REVERT: E 123 MET cc_start: 0.7573 (mmt) cc_final: 0.7362 (tpt) REVERT: C 130 ILE cc_start: 0.7031 (mt) cc_final: 0.6752 (mm) REVERT: C 205 ASN cc_start: 0.7786 (m-40) cc_final: 0.7082 (t0) REVERT: C 297 MET cc_start: 0.5937 (tpp) cc_final: 0.5350 (tpp) outliers start: 25 outliers final: 25 residues processed: 107 average time/residue: 0.1333 time to fit residues: 20.5425 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 291 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.137654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.113242 restraints weight = 15418.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.115093 restraints weight = 9553.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.115910 restraints weight = 8828.634| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6267 Z= 0.124 Angle : 0.569 8.957 8516 Z= 0.289 Chirality : 0.044 0.155 932 Planarity : 0.004 0.037 1093 Dihedral : 5.619 59.953 823 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.86 % Allowed : 15.16 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.73 (0.30), residues: 759 helix: -0.21 (0.51), residues: 105 sheet: -0.63 (0.33), residues: 243 loop : -0.34 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 167 HIS 0.018 0.001 HIS B 34 PHE 0.010 0.001 PHE E 134 TYR 0.015 0.001 TYR A 50 ARG 0.004 0.000 ARG C 269 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 161) hydrogen bonds : angle 5.60795 ( 462) SS BOND : bond 0.00281 ( 23) SS BOND : angle 0.76002 ( 46) covalent geometry : bond 0.00290 ( 6244) covalent geometry : angle 0.56811 ( 8470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 HIS cc_start: 0.5035 (m-70) cc_final: 0.4749 (p90) REVERT: D 123 MET cc_start: 0.0245 (mmt) cc_final: -0.0318 (mmt) REVERT: E 68 MET cc_start: 0.6006 (ppp) cc_final: 0.5638 (ppp) REVERT: E 78 GLU cc_start: 0.7882 (tp30) cc_final: 0.7616 (tp30) REVERT: E 123 MET cc_start: 0.7406 (mmt) cc_final: 0.7068 (tpt) REVERT: C 205 ASN cc_start: 0.7810 (m-40) cc_final: 0.7119 (t0) REVERT: C 297 MET cc_start: 0.5988 (tpp) cc_final: 0.5356 (tpp) outliers start: 27 outliers final: 25 residues processed: 110 average time/residue: 0.1448 time to fit residues: 22.4507 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 291 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.0030 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.0070 chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 0.6810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN C 40 HIS ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.136880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.110753 restraints weight = 15553.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.113808 restraints weight = 9731.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.115937 restraints weight = 6959.128| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6267 Z= 0.130 Angle : 0.569 8.080 8516 Z= 0.294 Chirality : 0.045 0.199 932 Planarity : 0.004 0.037 1093 Dihedral : 5.688 59.854 823 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.15 % Allowed : 14.59 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.75 (0.30), residues: 759 helix: -0.25 (0.50), residues: 105 sheet: -0.65 (0.33), residues: 243 loop : -0.33 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.018 0.001 HIS B 34 PHE 0.014 0.001 PHE E 111 TYR 0.013 0.001 TYR B 50 ARG 0.002 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 161) hydrogen bonds : angle 5.67223 ( 462) SS BOND : bond 0.00289 ( 23) SS BOND : angle 0.75411 ( 46) covalent geometry : bond 0.00299 ( 6244) covalent geometry : angle 0.56817 ( 8470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.0184 (mmt) cc_final: -0.0379 (mmt) REVERT: E 68 MET cc_start: 0.6098 (ppp) cc_final: 0.5732 (ppp) REVERT: E 78 GLU cc_start: 0.7858 (tp30) cc_final: 0.7608 (tp30) REVERT: E 123 MET cc_start: 0.7652 (mmt) cc_final: 0.7258 (tpt) REVERT: C 205 ASN cc_start: 0.7778 (m-40) cc_final: 0.7080 (t0) REVERT: C 276 LYS cc_start: 0.4335 (tttt) cc_final: 0.3973 (tptm) outliers start: 29 outliers final: 28 residues processed: 109 average time/residue: 0.1344 time to fit residues: 20.9035 Evaluate side-chains 117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 121 CYS Chi-restraints excluded: chain C residue 47 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 0.0270 chunk 26 optimal weight: 8.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.137203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.112074 restraints weight = 15735.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.114894 restraints weight = 10341.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.115871 restraints weight = 7817.831| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6267 Z= 0.121 Angle : 0.553 7.895 8516 Z= 0.282 Chirality : 0.045 0.171 932 Planarity : 0.004 0.058 1093 Dihedral : 5.603 59.932 823 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.01 % Allowed : 14.74 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -0.74 (0.30), residues: 759 helix: -0.23 (0.51), residues: 105 sheet: -0.64 (0.33), residues: 247 loop : -0.32 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.019 0.001 HIS B 34 PHE 0.013 0.001 PHE E 133 TYR 0.016 0.001 TYR A 50 ARG 0.003 0.000 ARG C 259 Details of bonding type rmsd hydrogen bonds : bond 0.02894 ( 161) hydrogen bonds : angle 5.61928 ( 462) SS BOND : bond 0.00278 ( 23) SS BOND : angle 0.74635 ( 46) covalent geometry : bond 0.00283 ( 6244) covalent geometry : angle 0.55203 ( 8470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2880.61 seconds wall clock time: 50 minutes 59.88 seconds (3059.88 seconds total)