Starting phenix.real_space_refine on Wed Sep 17 06:27:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fkp_50524/09_2025/9fkp_50524.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fkp_50524/09_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_50524/09_2025/9fkp_50524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fkp_50524/09_2025/9fkp_50524.map" model { file = "/net/cci-nas-00/data/ceres_data/9fkp_50524/09_2025/9fkp_50524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fkp_50524/09_2025/9fkp_50524.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.72, per 1000 atoms: 0.28 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: 0.43 Conformation dependent library (CDL) restraints added in 373.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.26 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: 0.93 Time building geometry restraints manager: 0.61 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: 3.740 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.670 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 25 TYR 0.005 0.001 TYR A 65 PHE 0.005 0.001 PHE A 24 TRP 0.004 0.001 TRP B 32 HIS 0.001 0.000 HIS C 169 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6244) covalent geometry : angle 0.49641 ( 8470) SS BOND : bond 0.00209 ( 23) SS BOND : angle 0.59843 ( 46) hydrogen bonds : bond 0.18240 ( 161) hydrogen bonds : angle 6.99608 ( 462) *********************** 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 : 0.182 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: 0.2360 (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: 0.0981 time to fit residues: 21.2721 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 : 0.209 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4529 r_free = 0.4529 target = 0.135709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.110705 restraints weight = 15647.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.113504 restraints weight = 10121.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.115434 restraints weight = 7370.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.116770 restraints weight = 5827.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.117804 restraints weight = 4882.038| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.2220 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= 0.160 Angle : 0.599 8.822 8516 Z= 0.307 Chirality : 0.046 0.133 932 Planarity : 0.005 0.042 1093 Dihedral : 5.910 49.506 834 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.00 % Allowed : 11.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.31), residues: 759 helix: 0.32 (0.50), residues: 106 sheet: -0.51 (0.33), residues: 267 loop : -0.07 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 259 TYR 0.010 0.001 TYR B 58 PHE 0.011 0.002 PHE A 24 TRP 0.015 0.001 TRP C 283 HIS 0.004 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6244) covalent geometry : angle 0.59527 ( 8470) SS BOND : bond 0.00406 ( 23) SS BOND : angle 1.05644 ( 46) hydrogen bonds : bond 0.03599 ( 161) hydrogen bonds : angle 5.95610 ( 462) *********************** 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 131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.0696 (mmt) cc_final: 0.0032 (mmt) REVERT: E 78 GLU cc_start: 0.7867 (tp30) cc_final: 0.7282 (pt0) REVERT: E 81 GLN cc_start: 0.8456 (pp30) cc_final: 0.8240 (pp30) REVERT: E 123 MET cc_start: 0.7708 (mmt) cc_final: 0.6993 (tpt) outliers start: 21 outliers final: 18 residues processed: 122 average time/residue: 0.0701 time to fit residues: 12.0185 Evaluate side-chains 108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 66 ASN C 40 HIS C 100 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.135867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.110943 restraints weight = 15619.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.113837 restraints weight = 10015.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.115858 restraints weight = 7213.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.117289 restraints weight = 5640.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.118101 restraints weight = 4679.604| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6267 Z= 0.134 Angle : 0.582 9.328 8516 Z= 0.292 Chirality : 0.045 0.135 932 Planarity : 0.004 0.037 1093 Dihedral : 5.419 47.508 823 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.58 % Allowed : 10.87 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.30), residues: 759 helix: 0.09 (0.49), residues: 106 sheet: -0.55 (0.31), residues: 284 loop : -0.18 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 259 TYR 0.013 0.001 TYR B 50 PHE 0.011 0.001 PHE D 133 TRP 0.010 0.001 TRP C 283 HIS 0.008 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6244) covalent geometry : angle 0.57924 ( 8470) SS BOND : bond 0.00392 ( 23) SS BOND : angle 0.91698 ( 46) hydrogen bonds : bond 0.03103 ( 161) hydrogen bonds : angle 5.68191 ( 462) *********************** 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 127 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASN cc_start: 0.8011 (t0) cc_final: 0.7710 (t0) REVERT: D 102 HIS cc_start: 0.5430 (m-70) cc_final: 0.5096 (p-80) REVERT: D 123 MET cc_start: 0.0804 (mmt) cc_final: 0.0155 (mmt) REVERT: E 78 GLU cc_start: 0.7886 (tp30) cc_final: 0.7279 (pt0) REVERT: E 123 MET cc_start: 0.7790 (mmt) cc_final: 0.7286 (tpt) outliers start: 25 outliers final: 21 residues processed: 117 average time/residue: 0.0710 time to fit residues: 11.6509 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 59 SER Chi-restraints excluded: chain B residue 77 CYS 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 74 THR Chi-restraints excluded: chain E residue 77 CYS 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 6 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.135143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.110230 restraints weight = 15818.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.113000 restraints weight = 10191.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.114990 restraints weight = 7396.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.116205 restraints weight = 5821.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.117257 restraints weight = 4932.183| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.3159 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= 0.139 Angle : 0.558 7.796 8516 Z= 0.283 Chirality : 0.044 0.171 932 Planarity : 0.004 0.037 1093 Dihedral : 5.432 47.026 823 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.29 % Allowed : 12.16 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.29), residues: 759 helix: 0.01 (0.49), residues: 106 sheet: -0.39 (0.35), residues: 218 loop : -0.26 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.018 0.001 TYR B 50 PHE 0.009 0.001 PHE D 133 TRP 0.009 0.001 TRP C 283 HIS 0.004 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6244) covalent geometry : angle 0.55431 ( 8470) SS BOND : bond 0.00372 ( 23) SS BOND : angle 1.00382 ( 46) hydrogen bonds : bond 0.03071 ( 161) hydrogen bonds : angle 5.55967 ( 462) *********************** 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 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.258 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: 0.7992 (t0) cc_final: 0.7725 (t0) REVERT: D 102 HIS cc_start: 0.5568 (m-70) cc_final: 0.5254 (m90) REVERT: D 123 MET cc_start: 0.0625 (mmt) cc_final: -0.0024 (mmt) REVERT: E 68 MET cc_start: 0.5712 (ppp) cc_final: 0.5451 (ppp) REVERT: E 123 MET cc_start: 0.7779 (mmt) cc_final: 0.7417 (tpt) outliers start: 30 outliers final: 26 residues processed: 117 average time/residue: 0.0667 time to fit residues: 11.0831 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 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 201 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 240 GLU 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 65 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 26 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.136099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.110645 restraints weight = 15926.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.113660 restraints weight = 10047.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.115823 restraints weight = 7202.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.117143 restraints weight = 5594.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.118319 restraints weight = 4695.905| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6047 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6267 Z= 0.126 Angle : 0.551 7.688 8516 Z= 0.279 Chirality : 0.044 0.137 932 Planarity : 0.004 0.035 1093 Dihedral : 5.335 46.359 823 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.58 % Allowed : 11.44 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.29), residues: 759 helix: -0.15 (0.48), residues: 105 sheet: -0.26 (0.36), residues: 209 loop : -0.29 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.017 0.001 TYR B 50 PHE 0.011 0.001 PHE E 111 TRP 0.011 0.001 TRP C 167 HIS 0.003 0.000 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6244) covalent geometry : angle 0.54852 ( 8470) SS BOND : bond 0.00356 ( 23) SS BOND : angle 0.84069 ( 46) hydrogen bonds : bond 0.02868 ( 161) hydrogen bonds : angle 5.43826 ( 462) *********************** 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 130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 LYS cc_start: 0.8654 (mppt) cc_final: 0.8249 (mppt) REVERT: B 69 ASN cc_start: 0.8166 (t0) cc_final: 0.7954 (t0) REVERT: D 102 HIS cc_start: 0.5565 (m-70) cc_final: 0.5223 (m90) REVERT: D 123 MET cc_start: 0.0488 (mmt) cc_final: -0.0121 (mmt) REVERT: E 68 MET cc_start: 0.5763 (ppp) cc_final: 0.5477 (ppp) REVERT: E 78 GLU cc_start: 0.7818 (tp30) cc_final: 0.7335 (tp30) REVERT: E 111 PHE cc_start: 0.4419 (OUTLIER) cc_final: 0.4019 (t80) outliers start: 32 outliers final: 25 residues processed: 118 average time/residue: 0.0584 time to fit residues: 10.1781 Evaluate side-chains 119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 111 PHE Chi-restraints excluded: chain C residue 99 VAL 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 240 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 6 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 30 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.138110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.111921 restraints weight = 15562.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.114925 restraints weight = 9831.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.117061 restraints weight = 7092.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.118474 restraints weight = 5549.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.119659 restraints weight = 4662.507| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5999 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6267 Z= 0.102 Angle : 0.529 7.655 8516 Z= 0.267 Chirality : 0.044 0.130 932 Planarity : 0.004 0.035 1093 Dihedral : 5.188 45.929 823 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.29 % Allowed : 13.02 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.29), residues: 759 helix: -0.13 (0.49), residues: 105 sheet: -0.29 (0.34), residues: 228 loop : -0.27 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.017 0.001 TYR B 50 PHE 0.009 0.001 PHE E 133 TRP 0.013 0.001 TRP C 167 HIS 0.004 0.000 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6244) covalent geometry : angle 0.52767 ( 8470) SS BOND : bond 0.00270 ( 23) SS BOND : angle 0.74658 ( 46) hydrogen bonds : bond 0.02704 ( 161) hydrogen bonds : angle 5.28090 ( 462) *********************** 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 131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 TYR cc_start: 0.6194 (t80) cc_final: 0.5990 (t80) REVERT: B 26 LYS cc_start: 0.8624 (mppt) cc_final: 0.8260 (mppt) REVERT: B 65 TYR cc_start: 0.7525 (t80) cc_final: 0.7316 (t80) REVERT: B 69 ASN cc_start: 0.8306 (t0) cc_final: 0.8092 (t0) REVERT: D 102 HIS cc_start: 0.5648 (m-70) cc_final: 0.5296 (m90) REVERT: D 123 MET cc_start: 0.0476 (mmt) cc_final: -0.0105 (mmt) REVERT: E 68 MET cc_start: 0.5842 (ppp) cc_final: 0.5497 (ppp) REVERT: E 78 GLU cc_start: 0.7829 (tp30) cc_final: 0.7306 (tp30) outliers start: 30 outliers final: 26 residues processed: 116 average time/residue: 0.0624 time to fit residues: 10.5502 Evaluate side-chains 117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 77 CYS Chi-restraints excluded: chain B residue 79 VAL 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 181 LEU 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 240 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 285 ILE 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 6 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 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 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN C 251 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.137600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.111710 restraints weight = 15458.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.114781 restraints weight = 9649.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.116894 restraints weight = 6831.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.118385 restraints weight = 5317.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.119468 restraints weight = 4411.624| |-----------------------------------------------------------------------------| r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6017 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6267 Z= 0.113 Angle : 0.541 7.356 8516 Z= 0.271 Chirality : 0.044 0.146 932 Planarity : 0.004 0.036 1093 Dihedral : 5.189 46.063 823 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.29 % Allowed : 13.45 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.30), residues: 759 helix: -0.13 (0.49), residues: 105 sheet: -0.39 (0.33), residues: 248 loop : -0.27 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 269 TYR 0.015 0.001 TYR B 50 PHE 0.005 0.001 PHE A 43 TRP 0.028 0.001 TRP C 332 HIS 0.003 0.001 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6244) covalent geometry : angle 0.53960 ( 8470) SS BOND : bond 0.00274 ( 23) SS BOND : angle 0.74625 ( 46) hydrogen bonds : bond 0.02702 ( 161) hydrogen bonds : angle 5.32940 ( 462) *********************** 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 125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.4492 (mt) cc_final: 0.4130 (mt) REVERT: B 65 TYR cc_start: 0.7463 (t80) cc_final: 0.7252 (t80) REVERT: D 102 HIS cc_start: 0.5666 (m-70) cc_final: 0.5313 (m90) REVERT: D 123 MET cc_start: 0.0390 (mmt) cc_final: -0.0168 (mmt) REVERT: E 68 MET cc_start: 0.5881 (ppp) cc_final: 0.5542 (ppp) REVERT: E 78 GLU cc_start: 0.7817 (tp30) cc_final: 0.7303 (tp30) REVERT: C 297 MET cc_start: 0.6012 (ttm) cc_final: 0.5663 (ttt) outliers start: 30 outliers final: 26 residues processed: 113 average time/residue: 0.0568 time to fit residues: 9.5476 Evaluate side-chains 118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 77 CYS Chi-restraints excluded: chain B residue 79 VAL 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 181 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** C 40 HIS ** 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 = 0.4474 r_free = 0.4474 target = 0.131956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.106778 restraints weight = 15698.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.109514 restraints weight = 10130.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.111337 restraints weight = 7364.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.112792 restraints weight = 5860.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.113740 restraints weight = 4887.172| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6267 Z= 0.260 Angle : 0.680 8.127 8516 Z= 0.349 Chirality : 0.047 0.158 932 Planarity : 0.005 0.044 1093 Dihedral : 5.959 50.322 823 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.86 % Allowed : 14.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.29), residues: 759 helix: -0.80 (0.45), residues: 111 sheet: -0.65 (0.31), residues: 258 loop : -0.65 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 94 TYR 0.015 0.002 TYR B 50 PHE 0.016 0.002 PHE A 24 TRP 0.018 0.002 TRP C 332 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 6244) covalent geometry : angle 0.67721 ( 8470) SS BOND : bond 0.00583 ( 23) SS BOND : angle 1.08314 ( 46) hydrogen bonds : bond 0.03711 ( 161) hydrogen bonds : angle 6.39631 ( 462) *********************** 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 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 HIS cc_start: 0.5810 (m-70) cc_final: 0.5607 (m-70) REVERT: D 123 MET cc_start: 0.0187 (mmt) cc_final: -0.0377 (mmt) REVERT: E 68 MET cc_start: 0.5986 (ppp) cc_final: 0.5655 (ppp) REVERT: C 205 ASN cc_start: 0.7731 (m-40) cc_final: 0.7008 (t0) REVERT: C 276 LYS cc_start: 0.4431 (tptt) cc_final: 0.4033 (tptm) outliers start: 27 outliers final: 26 residues processed: 112 average time/residue: 0.0557 time to fit residues: 9.3973 Evaluate side-chains 110 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 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 355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.134856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.109177 restraints weight = 15561.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.112136 restraints weight = 9817.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.114234 restraints weight = 7019.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.115668 restraints weight = 5464.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.116447 restraints weight = 4541.676| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.4057 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= 0.148 Angle : 0.594 7.828 8516 Z= 0.303 Chirality : 0.045 0.173 932 Planarity : 0.004 0.040 1093 Dihedral : 5.674 47.215 823 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.15 % Allowed : 14.16 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.29), residues: 759 helix: -0.45 (0.49), residues: 105 sheet: -0.62 (0.33), residues: 245 loop : -0.53 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 259 TYR 0.018 0.001 TYR B 50 PHE 0.012 0.001 PHE E 111 TRP 0.022 0.001 TRP C 332 HIS 0.003 0.001 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 6244) covalent geometry : angle 0.59248 ( 8470) SS BOND : bond 0.00329 ( 23) SS BOND : angle 0.86069 ( 46) hydrogen bonds : bond 0.03157 ( 161) hydrogen bonds : angle 5.97426 ( 462) *********************** 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 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 HIS cc_start: 0.5870 (m-70) cc_final: 0.5636 (m-70) REVERT: D 123 MET cc_start: 0.0363 (mmt) cc_final: -0.0189 (mmt) REVERT: E 68 MET cc_start: 0.5864 (ppp) cc_final: 0.5544 (ppp) REVERT: E 78 GLU cc_start: 0.7839 (tp30) cc_final: 0.7490 (tp30) REVERT: C 205 ASN cc_start: 0.7814 (m-40) cc_final: 0.7045 (t0) REVERT: C 253 ASP cc_start: 0.4347 (t0) cc_final: 0.4007 (t0) REVERT: C 276 LYS cc_start: 0.4386 (tptt) cc_final: 0.4006 (tptm) REVERT: C 297 MET cc_start: 0.5748 (ttm) cc_final: 0.5539 (ttt) outliers start: 29 outliers final: 26 residues processed: 114 average time/residue: 0.0603 time to fit residues: 10.1391 Evaluate side-chains 119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 105 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 29 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 67 GLN C 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.135811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.110254 restraints weight = 15496.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.113301 restraints weight = 9667.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.115418 restraints weight = 6861.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.116859 restraints weight = 5329.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.117978 restraints weight = 4421.952| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6267 Z= 0.127 Angle : 0.583 7.810 8516 Z= 0.296 Chirality : 0.045 0.184 932 Planarity : 0.004 0.059 1093 Dihedral : 5.666 59.622 823 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.58 % Allowed : 15.74 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.29), residues: 759 helix: -0.43 (0.49), residues: 105 sheet: -0.64 (0.32), residues: 245 loop : -0.43 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 107 TYR 0.018 0.001 TYR B 50 PHE 0.012 0.001 PHE E 111 TRP 0.033 0.002 TRP C 167 HIS 0.003 0.001 HIS C 237 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6244) covalent geometry : angle 0.58214 ( 8470) SS BOND : bond 0.00320 ( 23) SS BOND : angle 0.76678 ( 46) hydrogen bonds : bond 0.02941 ( 161) hydrogen bonds : angle 5.77307 ( 462) ********************** 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 124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 102 HIS cc_start: 0.5898 (m-70) cc_final: 0.5667 (m-70) REVERT: D 123 MET cc_start: 0.0115 (mmt) cc_final: -0.0420 (mmt) REVERT: E 68 MET cc_start: 0.5904 (ppp) cc_final: 0.5578 (ppp) REVERT: E 78 GLU cc_start: 0.7846 (tp30) cc_final: 0.7501 (tp30) REVERT: C 205 ASN cc_start: 0.7803 (m-40) cc_final: 0.7080 (t0) REVERT: C 206 LYS cc_start: 0.6681 (mttt) cc_final: 0.6384 (mttm) REVERT: C 253 ASP cc_start: 0.4368 (t0) cc_final: 0.3958 (t0) REVERT: C 276 LYS cc_start: 0.4138 (tptt) cc_final: 0.3801 (tptm) REVERT: C 297 MET cc_start: 0.5815 (ttm) cc_final: 0.5589 (ttt) outliers start: 25 outliers final: 25 residues processed: 114 average time/residue: 0.0613 time to fit residues: 10.2733 Evaluate side-chains 120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 105 ILE 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 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 355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 29 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 67 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.135818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.110091 restraints weight = 15527.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.113134 restraints weight = 9604.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.115271 restraints weight = 6810.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.116747 restraints weight = 5286.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.117955 restraints weight = 4379.050| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.4265 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= 0.126 Angle : 0.577 7.709 8516 Z= 0.292 Chirality : 0.045 0.173 932 Planarity : 0.004 0.054 1093 Dihedral : 5.635 59.963 823 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.86 % Allowed : 15.74 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.29), residues: 759 helix: -0.44 (0.48), residues: 105 sheet: -0.66 (0.33), residues: 245 loop : -0.41 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.016 0.001 TYR B 50 PHE 0.008 0.001 PHE E 111 TRP 0.033 0.002 TRP C 167 HIS 0.016 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6244) covalent geometry : angle 0.57570 ( 8470) SS BOND : bond 0.00276 ( 23) SS BOND : angle 0.73601 ( 46) hydrogen bonds : bond 0.02813 ( 161) hydrogen bonds : angle 5.72070 ( 462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1566.66 seconds wall clock time: 27 minutes 49.54 seconds (1669.54 seconds total)