Starting phenix.real_space_refine on Sun Apr 27 15:43:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fdy_50333/04_2025/9fdy_50333.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fdy_50333/04_2025/9fdy_50333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fdy_50333/04_2025/9fdy_50333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fdy_50333/04_2025/9fdy_50333.map" model { file = "/net/cci-nas-00/data/ceres_data/9fdy_50333/04_2025/9fdy_50333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fdy_50333/04_2025/9fdy_50333.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 60 5.16 5 C 3881 2.51 5 N 1037 2.21 5 O 1141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6119 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: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2606 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 305} 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} Time building chain proxies: 4.60, per 1000 atoms: 0.75 Number of scatterers: 6119 At special positions: 0 Unit cell: (76.443, 86.574, 145.518, 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 60 16.00 O 1141 8.00 N 1037 7.00 C 3881 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 C 4 " - pdb=" SG CYS C 197 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 17 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 34 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 64 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 101 " - pdb=" SG CYS E 106 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 879.1 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 14 sheets defined 12.1% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.762A pdb=" N SER A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 69 removed outlier: 3.580A pdb=" N LYS A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 56 through 69 Processing helix chain 'C' and resid 117 through 120 Processing helix chain 'C' and resid 132 through 145 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 299 through 311 removed outlier: 3.905A pdb=" N MET C 304 " --> pdb=" O GLN C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 removed outlier: 4.543A pdb=" N ALA D 80 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 4.304A pdb=" N ASP E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' 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 95 through 112 removed outlier: 7.102A pdb=" N LYS A 97 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 92 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU A 99 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR A 90 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 101 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE A 88 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN A 103 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 86 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA A 82 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N CYS A 109 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS A 111 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS A 78 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 15.446A pdb=" N THR D 37 " --> pdb=" O PRO A 87 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N VAL A 89 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N ILE D 39 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N TYR A 91 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.394A pdb=" N LEU B 2 " --> pdb=" O CYS B 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 109 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS B 97 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 92 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU B 99 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 90 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 101 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 88 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASN B 103 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 86 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 82 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS B 109 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS B 111 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS B 78 " --> pdb=" O CYS B 111 " (cutoff:3.500A) removed outlier: 15.246A pdb=" N THR E 37 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N VAL B 89 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ILE E 39 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR B 91 " --> pdb=" O ILE E 39 " (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 'C' and resid 7 through 8 removed outlier: 6.855A pdb=" N VAL C 323 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL C 241 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ASN C 267 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS C 243 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LYS C 269 " --> pdb=" O LYS C 243 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU C 245 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE C 271 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 247 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR C 287 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N GLY C 266 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR C 289 " --> pdb=" O GLY C 266 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU C 268 " --> pdb=" O THR C 289 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU C 291 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL C 270 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 92 removed outlier: 8.396A pdb=" N ILE C 159 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N THR C 60 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE C 161 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS C 62 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 163 " --> pdb=" O HIS C 62 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN C 64 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN C 158 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 186 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR C 23 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C 192 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA C 17 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 18 " --> pdb=" O ARG C 326 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE C 229 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU C 329 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP C 231 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C 331 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG C 233 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP C 257 " --> pdb=" O GLY C 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.186A pdb=" N GLU C 39 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C 79 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS C 41 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 81 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 43 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE C 76 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 104 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE C 78 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N SER C 106 " --> pdb=" O PHE C 78 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU C 80 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG C 101 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU C 125 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 103 " --> pdb=" O GLU C 125 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG C 127 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 105 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 17 through 20 removed outlier: 4.981A pdb=" N ASP D 18 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR D 62 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 29 through 31 Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 21 removed outlier: 4.629A pdb=" N PHE E 96 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 31 162 hydrogen bonds defined for protein. 405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1981 1.34 - 1.46: 1342 1.46 - 1.58: 2877 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 6273 Sorted by residual: bond pdb=" N ASP E 66 " pdb=" CA ASP E 66 " ideal model delta sigma weight residual 1.458 1.483 -0.026 1.64e-02 3.72e+03 2.46e+00 bond pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta sigma weight residual 1.474 1.457 0.018 1.57e-02 4.06e+03 1.29e+00 bond pdb=" C ASP E 66 " pdb=" N PRO E 67 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.26e+00 bond pdb=" N ILE B 51 " pdb=" CA ILE B 51 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.19e+00 bond pdb=" CA ASN E 107 " pdb=" C ASN E 107 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.41e-02 5.03e+03 1.08e+00 ... (remaining 6268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 8053 1.05 - 2.09: 366 2.09 - 3.14: 86 3.14 - 4.19: 8 4.19 - 5.23: 2 Bond angle restraints: 8515 Sorted by residual: angle pdb=" N ASN E 26 " pdb=" CA ASN E 26 " pdb=" CB ASN E 26 " ideal model delta sigma weight residual 113.65 110.50 3.15 1.47e+00 4.63e-01 4.59e+00 angle pdb=" CA ILE B 51 " pdb=" C ILE B 51 " pdb=" O ILE B 51 " ideal model delta sigma weight residual 122.63 120.82 1.81 8.70e-01 1.32e+00 4.35e+00 angle pdb=" N ILE A 51 " pdb=" CA ILE A 51 " pdb=" C ILE A 51 " ideal model delta sigma weight residual 106.21 108.43 -2.22 1.07e+00 8.73e-01 4.30e+00 angle pdb=" C ALA C 186 " pdb=" N GLU C 187 " pdb=" CA GLU C 187 " ideal model delta sigma weight residual 123.00 120.11 2.89 1.41e+00 5.03e-01 4.19e+00 angle pdb=" CA ILE A 51 " pdb=" C ILE A 51 " pdb=" O ILE A 51 " ideal model delta sigma weight residual 122.63 120.86 1.77 8.70e-01 1.32e+00 4.13e+00 ... (remaining 8510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 3645 16.10 - 32.19: 209 32.19 - 48.29: 33 48.29 - 64.38: 14 64.38 - 80.48: 1 Dihedral angle restraints: 3902 sinusoidal: 1626 harmonic: 2276 Sorted by residual: dihedral pdb=" CA VAL E 63 " pdb=" C VAL E 63 " pdb=" N CYS E 64 " pdb=" CA CYS E 64 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" N CYS B 16 " pdb=" CA CYS B 16 " pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " ideal model delta sinusoidal sigma weight residual -60.00 -119.83 59.83 3 1.50e+01 4.44e-03 9.48e+00 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 -118.88 58.88 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 492 0.026 - 0.052: 260 0.052 - 0.078: 75 0.078 - 0.103: 74 0.103 - 0.129: 33 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA ILE C 159 " pdb=" N ILE C 159 " pdb=" C ILE C 159 " pdb=" CB ILE C 159 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE E 58 " pdb=" N ILE E 58 " pdb=" C ILE E 58 " pdb=" CB ILE E 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL E 48 " pdb=" N VAL E 48 " pdb=" C VAL E 48 " pdb=" CB VAL E 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 931 not shown) Planarity restraints: 1103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 86 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO B 87 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 48 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO B 49 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 190 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO C 191 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.017 5.00e-02 4.00e+02 ... (remaining 1100 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 180 2.71 - 3.26: 5864 3.26 - 3.80: 9575 3.80 - 4.35: 12041 4.35 - 4.90: 20820 Nonbonded interactions: 48480 Sorted by model distance: nonbonded pdb=" OD1 ASP A 3 " pdb=" OG SER A 108 " model vdw 2.162 3.040 nonbonded pdb=" O ALA A 72 " pdb=" OG SER A 73 " model vdw 2.240 3.040 nonbonded pdb=" O LEU E 13 " pdb=" N GLU E 105 " model vdw 2.252 3.120 nonbonded pdb=" NE2 HIS C 13 " pdb=" OG1 THR C 319 " model vdw 2.264 3.120 nonbonded pdb=" NZ LYS C 74 " pdb=" OE2 GLU C 165 " model vdw 2.316 3.120 ... (remaining 48475 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 10 through 116) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.270 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6296 Z= 0.167 Angle : 0.535 5.232 8561 Z= 0.300 Chirality : 0.044 0.129 934 Planarity : 0.004 0.046 1103 Dihedral : 10.682 80.477 2349 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.56 % Allowed : 7.68 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.31), residues: 760 helix: 1.26 (0.61), residues: 79 sheet: -0.58 (0.30), residues: 304 loop : -0.32 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 257 HIS 0.003 0.001 HIS C 62 PHE 0.009 0.001 PHE B 43 TYR 0.006 0.001 TYR A 39 ARG 0.002 0.000 ARG B 107 Details of bonding type rmsd hydrogen bonds : bond 0.14181 ( 160) hydrogen bonds : angle 6.29593 ( 405) SS BOND : bond 0.00275 ( 23) SS BOND : angle 0.59920 ( 46) covalent geometry : bond 0.00360 ( 6273) covalent geometry : angle 0.53493 ( 8515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8668 (mmm) cc_final: 0.8032 (tpp) REVERT: A 105 ILE cc_start: 0.8903 (mt) cc_final: 0.8593 (mp) REVERT: B 60 LYS cc_start: 0.8656 (mtpm) cc_final: 0.8370 (mttt) REVERT: C 113 PHE cc_start: 0.8195 (m-80) cc_final: 0.7947 (m-80) REVERT: C 132 GLU cc_start: 0.8777 (tp30) cc_final: 0.8417 (tt0) REVERT: C 195 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7654 (mm-30) REVERT: C 231 ASP cc_start: 0.8010 (m-30) cc_final: 0.7406 (m-30) REVERT: C 251 CYS cc_start: 0.8309 (t) cc_final: 0.8057 (t) REVERT: C 263 ASP cc_start: 0.8211 (m-30) cc_final: 0.7926 (t0) REVERT: E 21 PHE cc_start: 0.7822 (m-80) cc_final: 0.7470 (m-80) REVERT: E 45 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6704 (mp0) REVERT: E 63 VAL cc_start: 0.8939 (m) cc_final: 0.8737 (m) REVERT: E 91 LYS cc_start: 0.7592 (tppt) cc_final: 0.7178 (tptt) REVERT: E 97 PHE cc_start: 0.7633 (m-80) cc_final: 0.6844 (m-80) outliers start: 18 outliers final: 8 residues processed: 221 average time/residue: 0.2069 time to fit residues: 57.6079 Evaluate side-chains 168 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 77 CYS Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 84 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.0020 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS C 302 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.182147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116676 restraints weight = 7900.816| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.80 r_work: 0.3246 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6296 Z= 0.156 Angle : 0.589 7.918 8561 Z= 0.297 Chirality : 0.046 0.139 934 Planarity : 0.004 0.063 1103 Dihedral : 6.395 57.878 835 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.12 % Allowed : 14.37 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.31), residues: 760 helix: 1.22 (0.62), residues: 81 sheet: -0.78 (0.31), residues: 278 loop : -0.15 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 52 HIS 0.002 0.001 HIS A 40 PHE 0.014 0.001 PHE A 8 TYR 0.009 0.001 TYR A 50 ARG 0.003 0.000 ARG C 284 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 160) hydrogen bonds : angle 5.76850 ( 405) SS BOND : bond 0.00448 ( 23) SS BOND : angle 1.25645 ( 46) covalent geometry : bond 0.00362 ( 6273) covalent geometry : angle 0.58287 ( 8515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7836 (tp30) cc_final: 0.7435 (mm-30) REVERT: A 104 MET cc_start: 0.8874 (mmm) cc_final: 0.7849 (mmm) REVERT: A 105 ILE cc_start: 0.8792 (mt) cc_final: 0.8444 (mp) REVERT: B 60 LYS cc_start: 0.8391 (mtpm) cc_final: 0.8083 (mttt) REVERT: B 102 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8775 (m) REVERT: C 132 GLU cc_start: 0.8936 (tp30) cc_final: 0.8317 (tt0) REVERT: C 195 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7797 (mm-30) REVERT: C 231 ASP cc_start: 0.8330 (m-30) cc_final: 0.7627 (m-30) REVERT: C 251 CYS cc_start: 0.8727 (t) cc_final: 0.8380 (t) REVERT: C 263 ASP cc_start: 0.8706 (m-30) cc_final: 0.8090 (t0) REVERT: C 283 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: E 18 ASP cc_start: 0.7753 (m-30) cc_final: 0.7536 (m-30) REVERT: E 21 PHE cc_start: 0.8425 (m-80) cc_final: 0.8106 (m-80) REVERT: E 28 LYS cc_start: 0.8723 (ptmm) cc_final: 0.8057 (ttpt) REVERT: E 87 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7458 (mtmm) REVERT: E 91 LYS cc_start: 0.7388 (tppt) cc_final: 0.6837 (tptt) REVERT: E 96 PHE cc_start: 0.7230 (t80) cc_final: 0.6581 (t80) REVERT: E 97 PHE cc_start: 0.7721 (m-80) cc_final: 0.6591 (m-80) outliers start: 36 outliers final: 20 residues processed: 175 average time/residue: 0.1823 time to fit residues: 41.6240 Evaluate side-chains 169 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 67 optimal weight: 0.0070 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.0270 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 42 ASN B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 204 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.181974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118076 restraints weight = 7911.821| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.73 r_work: 0.3270 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6296 Z= 0.117 Angle : 0.553 10.861 8561 Z= 0.274 Chirality : 0.045 0.137 934 Planarity : 0.004 0.041 1103 Dihedral : 6.078 58.647 834 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.98 % Allowed : 15.22 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.31), residues: 760 helix: 1.18 (0.62), residues: 81 sheet: -0.75 (0.31), residues: 279 loop : -0.18 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 257 HIS 0.008 0.001 HIS A 34 PHE 0.020 0.001 PHE C 113 TYR 0.011 0.001 TYR A 50 ARG 0.002 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 160) hydrogen bonds : angle 5.45881 ( 405) SS BOND : bond 0.00450 ( 23) SS BOND : angle 1.06968 ( 46) covalent geometry : bond 0.00274 ( 6273) covalent geometry : angle 0.54857 ( 8515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ASP cc_start: 0.7726 (p0) cc_final: 0.7221 (p0) REVERT: A 5 ASN cc_start: 0.9438 (m-40) cc_final: 0.9031 (p0) REVERT: A 99 GLU cc_start: 0.7821 (tp30) cc_final: 0.7408 (mm-30) REVERT: A 105 ILE cc_start: 0.8843 (mt) cc_final: 0.8524 (mp) REVERT: B 13 LYS cc_start: 0.8008 (tppt) cc_final: 0.7701 (mttp) REVERT: B 60 LYS cc_start: 0.8383 (mtpm) cc_final: 0.8076 (mttt) REVERT: C 23 THR cc_start: 0.8801 (m) cc_final: 0.8460 (p) REVERT: C 77 VAL cc_start: 0.9157 (t) cc_final: 0.8815 (m) REVERT: C 132 GLU cc_start: 0.8950 (tp30) cc_final: 0.8362 (tt0) REVERT: C 195 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7810 (mm-30) REVERT: C 231 ASP cc_start: 0.8291 (m-30) cc_final: 0.7575 (m-30) REVERT: C 251 CYS cc_start: 0.8706 (t) cc_final: 0.8362 (t) REVERT: C 263 ASP cc_start: 0.8679 (m-30) cc_final: 0.8071 (t0) REVERT: C 283 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: D 31 MET cc_start: 0.8117 (tpp) cc_final: 0.7668 (tpt) REVERT: E 18 ASP cc_start: 0.7647 (m-30) cc_final: 0.7429 (m-30) REVERT: E 21 PHE cc_start: 0.8431 (m-80) cc_final: 0.8189 (m-80) REVERT: E 28 LYS cc_start: 0.8740 (ptmm) cc_final: 0.8137 (ttpt) REVERT: E 78 ASP cc_start: 0.7291 (t0) cc_final: 0.6956 (t0) REVERT: E 97 PHE cc_start: 0.7834 (m-80) cc_final: 0.6476 (m-80) outliers start: 35 outliers final: 20 residues processed: 175 average time/residue: 0.1750 time to fit residues: 40.0162 Evaluate side-chains 163 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** D 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.181263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116014 restraints weight = 8096.697| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.87 r_work: 0.3257 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6296 Z= 0.129 Angle : 0.541 6.908 8561 Z= 0.271 Chirality : 0.044 0.132 934 Planarity : 0.004 0.036 1103 Dihedral : 6.121 59.554 834 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.69 % Allowed : 17.07 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.31), residues: 760 helix: 1.03 (0.62), residues: 81 sheet: -0.83 (0.31), residues: 292 loop : -0.17 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 257 HIS 0.007 0.001 HIS A 34 PHE 0.025 0.001 PHE C 113 TYR 0.009 0.001 TYR B 58 ARG 0.003 0.000 ARG C 330 Details of bonding type rmsd hydrogen bonds : bond 0.02880 ( 160) hydrogen bonds : angle 5.36439 ( 405) SS BOND : bond 0.00311 ( 23) SS BOND : angle 1.02845 ( 46) covalent geometry : bond 0.00306 ( 6273) covalent geometry : angle 0.53754 ( 8515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.683 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: A 39 TYR cc_start: 0.8736 (p90) cc_final: 0.8222 (p90) REVERT: A 99 GLU cc_start: 0.7721 (tp30) cc_final: 0.7167 (mm-30) REVERT: A 104 MET cc_start: 0.8207 (tpp) cc_final: 0.7777 (tpp) REVERT: A 105 ILE cc_start: 0.8837 (mt) cc_final: 0.8517 (mp) REVERT: B 13 LYS cc_start: 0.8045 (tppt) cc_final: 0.7780 (mttp) REVERT: B 15 CYS cc_start: 0.6842 (OUTLIER) cc_final: 0.6001 (t) REVERT: B 60 LYS cc_start: 0.8300 (mtpm) cc_final: 0.7909 (mttt) REVERT: C 77 VAL cc_start: 0.9160 (t) cc_final: 0.8820 (m) REVERT: C 132 GLU cc_start: 0.8953 (tp30) cc_final: 0.8321 (tt0) REVERT: C 195 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7805 (mm-30) REVERT: C 231 ASP cc_start: 0.8351 (m-30) cc_final: 0.7641 (m-30) REVERT: C 263 ASP cc_start: 0.8693 (m-30) cc_final: 0.8075 (t0) REVERT: C 283 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: E 18 ASP cc_start: 0.7546 (m-30) cc_final: 0.7331 (m-30) REVERT: E 28 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8171 (ttpp) REVERT: E 78 ASP cc_start: 0.7449 (t0) cc_final: 0.7233 (t0) REVERT: E 97 PHE cc_start: 0.7629 (m-80) cc_final: 0.6984 (m-80) REVERT: E 98 MET cc_start: 0.8620 (ttp) cc_final: 0.8056 (ttt) outliers start: 33 outliers final: 25 residues processed: 167 average time/residue: 0.1702 time to fit residues: 37.3148 Evaluate side-chains 167 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 204 HIS C 333 ASN E 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.177312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.110983 restraints weight = 8058.143| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.88 r_work: 0.3196 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6296 Z= 0.221 Angle : 0.602 6.800 8561 Z= 0.306 Chirality : 0.046 0.139 934 Planarity : 0.004 0.048 1103 Dihedral : 6.277 58.586 834 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.41 % Allowed : 16.50 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.31), residues: 760 helix: 0.63 (0.60), residues: 87 sheet: -0.86 (0.31), residues: 299 loop : -0.30 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 52 HIS 0.011 0.001 HIS A 34 PHE 0.025 0.002 PHE C 113 TYR 0.011 0.001 TYR B 58 ARG 0.004 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 160) hydrogen bonds : angle 5.54408 ( 405) SS BOND : bond 0.00447 ( 23) SS BOND : angle 1.31062 ( 46) covalent geometry : bond 0.00521 ( 6273) covalent geometry : angle 0.59583 ( 8515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8841 (mt) cc_final: 0.8506 (mp) REVERT: B 13 LYS cc_start: 0.8081 (tppt) cc_final: 0.7805 (mttp) REVERT: B 15 CYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6176 (t) REVERT: B 60 LYS cc_start: 0.8447 (mtpm) cc_final: 0.8087 (mttt) REVERT: C 77 VAL cc_start: 0.9192 (t) cc_final: 0.8831 (m) REVERT: C 132 GLU cc_start: 0.8932 (tp30) cc_final: 0.8358 (tt0) REVERT: C 195 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8002 (mm-30) REVERT: C 231 ASP cc_start: 0.8396 (m-30) cc_final: 0.7790 (m-30) REVERT: C 263 ASP cc_start: 0.8683 (m-30) cc_final: 0.8058 (t0) REVERT: C 283 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: E 21 PHE cc_start: 0.8338 (m-80) cc_final: 0.8030 (m-80) REVERT: E 28 LYS cc_start: 0.8814 (ptmm) cc_final: 0.8263 (ttpp) REVERT: E 97 PHE cc_start: 0.7598 (m-80) cc_final: 0.7086 (m-80) outliers start: 38 outliers final: 30 residues processed: 160 average time/residue: 0.1890 time to fit residues: 40.3104 Evaluate side-chains 167 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.179936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114450 restraints weight = 8006.618| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.90 r_work: 0.3239 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6296 Z= 0.133 Angle : 0.555 6.906 8561 Z= 0.278 Chirality : 0.045 0.138 934 Planarity : 0.004 0.040 1103 Dihedral : 6.119 58.022 834 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.26 % Allowed : 17.07 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.31), residues: 760 helix: 0.66 (0.59), residues: 87 sheet: -0.79 (0.31), residues: 294 loop : -0.35 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 257 HIS 0.008 0.001 HIS A 34 PHE 0.024 0.001 PHE C 113 TYR 0.024 0.001 TYR A 39 ARG 0.003 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 160) hydrogen bonds : angle 5.25897 ( 405) SS BOND : bond 0.00320 ( 23) SS BOND : angle 1.14890 ( 46) covalent geometry : bond 0.00311 ( 6273) covalent geometry : angle 0.54976 ( 8515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8126 (tt0) cc_final: 0.7362 (mt0) REVERT: A 99 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6787 (mm-30) REVERT: A 104 MET cc_start: 0.8138 (tpp) cc_final: 0.7837 (tpp) REVERT: A 105 ILE cc_start: 0.8792 (mt) cc_final: 0.8475 (mp) REVERT: B 13 LYS cc_start: 0.7973 (tppt) cc_final: 0.7739 (mttp) REVERT: B 15 CYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6357 (t) REVERT: B 60 LYS cc_start: 0.8337 (mtpm) cc_final: 0.7961 (mttt) REVERT: C 77 VAL cc_start: 0.9190 (t) cc_final: 0.8838 (m) REVERT: C 132 GLU cc_start: 0.8934 (tp30) cc_final: 0.8370 (tt0) REVERT: C 195 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7970 (mm-30) REVERT: C 231 ASP cc_start: 0.8391 (m-30) cc_final: 0.7727 (m-30) REVERT: C 256 ASN cc_start: 0.8982 (t0) cc_final: 0.8756 (t0) REVERT: C 263 ASP cc_start: 0.8650 (m-30) cc_final: 0.8013 (t0) REVERT: C 283 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: D 98 MET cc_start: 0.8459 (ppp) cc_final: 0.7590 (ttp) REVERT: E 28 LYS cc_start: 0.8812 (ptmm) cc_final: 0.8289 (ttpt) REVERT: E 45 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6588 (mt-10) REVERT: E 78 ASP cc_start: 0.6637 (t0) cc_final: 0.6348 (t0) outliers start: 37 outliers final: 31 residues processed: 166 average time/residue: 0.2144 time to fit residues: 47.7485 Evaluate side-chains 168 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 59 optimal weight: 5.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS C 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.174341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109609 restraints weight = 7989.366| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.75 r_work: 0.3163 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 6296 Z= 0.281 Angle : 0.650 6.854 8561 Z= 0.334 Chirality : 0.047 0.140 934 Planarity : 0.004 0.045 1103 Dihedral : 6.423 58.831 834 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.83 % Allowed : 17.07 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.31), residues: 760 helix: 0.48 (0.59), residues: 87 sheet: -0.93 (0.31), residues: 300 loop : -0.52 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 52 HIS 0.006 0.001 HIS A 34 PHE 0.023 0.002 PHE C 113 TYR 0.012 0.002 TYR B 58 ARG 0.004 0.001 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 160) hydrogen bonds : angle 5.55773 ( 405) SS BOND : bond 0.00551 ( 23) SS BOND : angle 1.48399 ( 46) covalent geometry : bond 0.00661 ( 6273) covalent geometry : angle 0.64231 ( 8515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 81 GLN cc_start: 0.8112 (tt0) cc_final: 0.7417 (mt0) REVERT: A 99 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7272 (mm-30) REVERT: A 105 ILE cc_start: 0.8772 (mt) cc_final: 0.8426 (mp) REVERT: B 15 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6601 (t) REVERT: B 60 LYS cc_start: 0.8523 (mtpm) cc_final: 0.8169 (mttt) REVERT: C 77 VAL cc_start: 0.9184 (t) cc_final: 0.8796 (m) REVERT: C 132 GLU cc_start: 0.8948 (tp30) cc_final: 0.8370 (tt0) REVERT: C 195 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8065 (mm-30) REVERT: C 221 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7458 (t80) REVERT: C 231 ASP cc_start: 0.8400 (m-30) cc_final: 0.7812 (m-30) REVERT: C 256 ASN cc_start: 0.9129 (t0) cc_final: 0.8827 (t0) REVERT: C 263 ASP cc_start: 0.8683 (m-30) cc_final: 0.7941 (t0) REVERT: C 283 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: E 28 LYS cc_start: 0.8858 (ptmm) cc_final: 0.8361 (ttpt) REVERT: E 78 ASP cc_start: 0.6914 (t0) cc_final: 0.6560 (t0) outliers start: 41 outliers final: 34 residues processed: 157 average time/residue: 0.1637 time to fit residues: 34.4077 Evaluate side-chains 169 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.178688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115547 restraints weight = 8172.208| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.69 r_work: 0.3276 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6296 Z= 0.138 Angle : 0.588 8.462 8561 Z= 0.296 Chirality : 0.045 0.134 934 Planarity : 0.004 0.037 1103 Dihedral : 6.202 55.625 834 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.26 % Allowed : 17.92 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.31), residues: 760 helix: 0.58 (0.59), residues: 87 sheet: -0.87 (0.31), residues: 300 loop : -0.45 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 257 HIS 0.006 0.001 HIS A 34 PHE 0.026 0.001 PHE C 113 TYR 0.011 0.001 TYR A 50 ARG 0.003 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 160) hydrogen bonds : angle 5.25008 ( 405) SS BOND : bond 0.00333 ( 23) SS BOND : angle 1.43471 ( 46) covalent geometry : bond 0.00330 ( 6273) covalent geometry : angle 0.58009 ( 8515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 141 time to evaluate : 0.684 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: A 12 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: A 81 GLN cc_start: 0.8063 (tt0) cc_final: 0.7328 (mt0) REVERT: A 99 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6857 (mm-30) REVERT: A 104 MET cc_start: 0.8237 (tpp) cc_final: 0.7984 (tpp) REVERT: A 105 ILE cc_start: 0.8813 (mt) cc_final: 0.8528 (mp) REVERT: B 13 LYS cc_start: 0.8017 (tppt) cc_final: 0.7742 (mttp) REVERT: B 15 CYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6764 (t) REVERT: B 60 LYS cc_start: 0.8458 (mtpm) cc_final: 0.8090 (mttt) REVERT: C 77 VAL cc_start: 0.9222 (t) cc_final: 0.8885 (m) REVERT: C 132 GLU cc_start: 0.8945 (tp30) cc_final: 0.8444 (tt0) REVERT: C 195 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8104 (mm-30) REVERT: C 231 ASP cc_start: 0.8285 (m-30) cc_final: 0.7722 (m-30) REVERT: C 251 CYS cc_start: 0.8669 (t) cc_final: 0.8355 (t) REVERT: C 263 ASP cc_start: 0.8469 (m-30) cc_final: 0.7871 (t0) REVERT: C 283 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: D 107 ASN cc_start: 0.8388 (p0) cc_final: 0.8097 (p0) REVERT: E 28 LYS cc_start: 0.8864 (ptmm) cc_final: 0.8433 (ttpt) REVERT: E 78 ASP cc_start: 0.6811 (t0) cc_final: 0.6554 (t0) outliers start: 37 outliers final: 30 residues processed: 163 average time/residue: 0.1704 time to fit residues: 36.9667 Evaluate side-chains 171 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 135 HIS ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.176204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114631 restraints weight = 8088.997| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.55 r_work: 0.3263 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6296 Z= 0.194 Angle : 0.613 7.849 8561 Z= 0.312 Chirality : 0.046 0.135 934 Planarity : 0.004 0.041 1103 Dihedral : 6.244 56.843 834 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 5.26 % Allowed : 17.78 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.31), residues: 760 helix: 0.53 (0.59), residues: 87 sheet: -0.91 (0.31), residues: 299 loop : -0.47 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 51 HIS 0.007 0.001 HIS A 34 PHE 0.025 0.002 PHE C 113 TYR 0.012 0.001 TYR A 50 ARG 0.005 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 160) hydrogen bonds : angle 5.32143 ( 405) SS BOND : bond 0.00401 ( 23) SS BOND : angle 1.37550 ( 46) covalent geometry : bond 0.00459 ( 6273) covalent geometry : angle 0.60617 ( 8515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8016 (tt0) cc_final: 0.7295 (mt0) REVERT: A 104 MET cc_start: 0.8358 (tpp) cc_final: 0.8081 (tpp) REVERT: A 105 ILE cc_start: 0.8844 (mt) cc_final: 0.8526 (mp) REVERT: B 13 LYS cc_start: 0.8111 (tppt) cc_final: 0.7848 (mttp) REVERT: B 15 CYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6865 (t) REVERT: B 60 LYS cc_start: 0.8457 (mtpm) cc_final: 0.8080 (mttt) REVERT: C 77 VAL cc_start: 0.9211 (t) cc_final: 0.8884 (m) REVERT: C 132 GLU cc_start: 0.8937 (tp30) cc_final: 0.8464 (tt0) REVERT: C 195 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8101 (mm-30) REVERT: C 231 ASP cc_start: 0.8303 (m-30) cc_final: 0.7762 (m-30) REVERT: C 263 ASP cc_start: 0.8427 (m-30) cc_final: 0.7839 (t0) REVERT: C 264 VAL cc_start: 0.8692 (p) cc_final: 0.8403 (m) REVERT: C 283 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: D 107 ASN cc_start: 0.8443 (p0) cc_final: 0.8152 (p0) REVERT: E 28 LYS cc_start: 0.8873 (ptmm) cc_final: 0.8479 (ttpt) REVERT: E 45 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7008 (mp0) REVERT: E 74 PHE cc_start: 0.8574 (m-80) cc_final: 0.8272 (m-80) REVERT: E 78 ASP cc_start: 0.7017 (t0) cc_final: 0.6604 (t0) outliers start: 37 outliers final: 31 residues processed: 161 average time/residue: 0.1823 time to fit residues: 38.8005 Evaluate side-chains 167 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS ** C 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.177944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114912 restraints weight = 8267.408| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.68 r_work: 0.3266 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6296 Z= 0.182 Angle : 0.633 8.164 8561 Z= 0.320 Chirality : 0.046 0.233 934 Planarity : 0.004 0.040 1103 Dihedral : 6.249 55.497 834 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.84 % Allowed : 18.49 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.30), residues: 760 helix: 0.49 (0.59), residues: 87 sheet: -0.89 (0.32), residues: 281 loop : -0.60 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 52 HIS 0.006 0.001 HIS A 34 PHE 0.025 0.002 PHE C 113 TYR 0.011 0.001 TYR A 50 ARG 0.006 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 160) hydrogen bonds : angle 5.22989 ( 405) SS BOND : bond 0.00346 ( 23) SS BOND : angle 1.26574 ( 46) covalent geometry : bond 0.00433 ( 6273) covalent geometry : angle 0.62815 ( 8515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.766 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: A 3 ASP cc_start: 0.7854 (p0) cc_final: 0.7233 (p0) REVERT: A 5 ASN cc_start: 0.9286 (OUTLIER) cc_final: 0.9008 (p0) REVERT: A 81 GLN cc_start: 0.8024 (tt0) cc_final: 0.7245 (mt0) REVERT: A 104 MET cc_start: 0.8312 (tpp) cc_final: 0.8004 (tpp) REVERT: A 105 ILE cc_start: 0.8775 (mt) cc_final: 0.8473 (mp) REVERT: B 13 LYS cc_start: 0.8100 (tppt) cc_final: 0.7862 (mttp) REVERT: B 15 CYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6834 (t) REVERT: B 60 LYS cc_start: 0.8443 (mtpm) cc_final: 0.8065 (mttt) REVERT: C 132 GLU cc_start: 0.8936 (tp30) cc_final: 0.8471 (tt0) REVERT: C 138 ARG cc_start: 0.8371 (mtm-85) cc_final: 0.8085 (mtm110) REVERT: C 195 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8116 (mm-30) REVERT: C 231 ASP cc_start: 0.8279 (m-30) cc_final: 0.7744 (m-30) REVERT: C 283 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: D 107 ASN cc_start: 0.8418 (p0) cc_final: 0.8118 (p0) REVERT: E 28 LYS cc_start: 0.8880 (ptmm) cc_final: 0.8534 (ttpt) REVERT: E 74 PHE cc_start: 0.8596 (m-80) cc_final: 0.8316 (m-80) REVERT: E 78 ASP cc_start: 0.6535 (t0) cc_final: 0.5997 (t0) REVERT: E 87 LYS cc_start: 0.7612 (mmtm) cc_final: 0.7110 (mptt) outliers start: 34 outliers final: 30 residues processed: 158 average time/residue: 0.1788 time to fit residues: 37.2638 Evaluate side-chains 166 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 16 CYS Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 15 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 0.0010 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN ** B 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.178254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114972 restraints weight = 8360.345| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.73 r_work: 0.3266 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6296 Z= 0.174 Angle : 0.626 7.832 8561 Z= 0.316 Chirality : 0.046 0.227 934 Planarity : 0.004 0.038 1103 Dihedral : 6.238 55.927 834 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.41 % Allowed : 17.92 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.30), residues: 760 helix: 0.54 (0.59), residues: 87 sheet: -1.02 (0.31), residues: 289 loop : -0.58 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 51 HIS 0.005 0.001 HIS A 34 PHE 0.025 0.002 PHE C 113 TYR 0.011 0.001 TYR B 58 ARG 0.008 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 160) hydrogen bonds : angle 5.20488 ( 405) SS BOND : bond 0.00354 ( 23) SS BOND : angle 1.24852 ( 46) covalent geometry : bond 0.00415 ( 6273) covalent geometry : angle 0.62088 ( 8515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4093.74 seconds wall clock time: 71 minutes 44.50 seconds (4304.50 seconds total)