Starting phenix.real_space_refine on Sat May 10 11:18:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fdy_50333/05_2025/9fdy_50333.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fdy_50333/05_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_50333/05_2025/9fdy_50333.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fdy_50333/05_2025/9fdy_50333.map" model { file = "/net/cci-nas-00/data/ceres_data/9fdy_50333/05_2025/9fdy_50333.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fdy_50333/05_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-5687/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: 4.50, per 1000 atoms: 0.74 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: 1.54 Conformation dependent library (CDL) restraints added in 900.9 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: 0.98 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: 1.74 Time building geometry restraints manager: 1.82 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: 1.490 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.800 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.770 ------------------------------------------------------------------------------- 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 : 0.771 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: 0.2011 time to fit residues: 55.7963 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 : 0.673 ------------------------------------------------------------------------------- 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 = 0.182150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116674 restraints weight = 7900.610| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.80 r_work: 0.3246 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 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= 0.155 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 5.76847 ( 405) SS BOND : bond 0.00447 ( 23) SS BOND : angle 1.25689 ( 46) covalent geometry : bond 0.00362 ( 6273) covalent geometry : angle 0.58288 ( 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 : 0.691 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: 0.7848 (tp30) cc_final: 0.7447 (mm-30) REVERT: A 104 MET cc_start: 0.8874 (mmm) cc_final: 0.7850 (mmm) REVERT: A 105 ILE cc_start: 0.8793 (mt) cc_final: 0.8445 (mp) REVERT: B 60 LYS cc_start: 0.8391 (mtpm) cc_final: 0.8083 (mttt) REVERT: B 102 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8777 (m) REVERT: C 132 GLU cc_start: 0.8938 (tp30) cc_final: 0.8316 (tt0) REVERT: C 195 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7792 (mm-30) REVERT: C 231 ASP cc_start: 0.8332 (m-30) cc_final: 0.7624 (m-30) REVERT: C 251 CYS cc_start: 0.8728 (t) cc_final: 0.8383 (t) REVERT: C 263 ASP cc_start: 0.8724 (m-30) cc_final: 0.8096 (t0) REVERT: C 283 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: E 18 ASP cc_start: 0.7748 (m-30) cc_final: 0.7531 (m-30) REVERT: E 21 PHE cc_start: 0.8442 (m-80) cc_final: 0.8123 (m-80) REVERT: E 28 LYS cc_start: 0.8721 (ptmm) cc_final: 0.8058 (ttpt) REVERT: E 87 LYS cc_start: 0.7652 (mtmm) cc_final: 0.7443 (mtmm) REVERT: E 91 LYS cc_start: 0.7371 (tppt) cc_final: 0.6821 (tptt) REVERT: E 96 PHE cc_start: 0.7224 (t80) cc_final: 0.6577 (t80) REVERT: E 97 PHE cc_start: 0.7715 (m-80) cc_final: 0.6593 (m-80) outliers start: 36 outliers final: 20 residues processed: 175 average time/residue: 0.1767 time to fit residues: 40.3009 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 : 0.663 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 43 optimal weight: 0.0570 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.182090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116357 restraints weight = 8042.142| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.91 r_work: 0.3249 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2614 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= 0.128 Angle : 0.556 10.589 8561 Z= 0.276 Chirality : 0.045 0.136 934 Planarity : 0.004 0.042 1103 Dihedral : 6.106 58.817 834 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.12 % Allowed : 15.08 % 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: -0.50 (0.31), residues: 760 helix: 1.18 (0.63), residues: 81 sheet: -0.77 (0.31), residues: 279 loop : -0.18 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 257 HIS 0.008 0.001 HIS A 34 PHE 0.020 0.001 PHE C 113 TYR 0.010 0.001 TYR A 50 ARG 0.002 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 160) hydrogen bonds : angle 5.50743 ( 405) SS BOND : bond 0.00364 ( 23) SS BOND : angle 1.08535 ( 46) covalent geometry : bond 0.00302 ( 6273) covalent geometry : angle 0.55168 ( 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 186 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.711 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: 0.7734 (p0) cc_final: 0.7217 (p0) REVERT: A 5 ASN cc_start: 0.9439 (m-40) cc_final: 0.9030 (p0) REVERT: A 99 GLU cc_start: 0.7793 (tp30) cc_final: 0.7381 (mm-30) REVERT: A 105 ILE cc_start: 0.8864 (mt) cc_final: 0.8548 (mp) REVERT: B 13 LYS cc_start: 0.8063 (tppt) cc_final: 0.7761 (mttp) REVERT: B 60 LYS cc_start: 0.8419 (mtpm) cc_final: 0.8075 (mttt) REVERT: C 23 THR cc_start: 0.8826 (m) cc_final: 0.8491 (p) REVERT: C 77 VAL cc_start: 0.9168 (t) cc_final: 0.8835 (m) REVERT: C 132 GLU cc_start: 0.8961 (tp30) cc_final: 0.8392 (tt0) REVERT: C 195 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7843 (mm-30) REVERT: C 231 ASP cc_start: 0.8276 (m-30) cc_final: 0.7598 (m-30) REVERT: C 251 CYS cc_start: 0.8706 (t) cc_final: 0.8375 (t) REVERT: C 263 ASP cc_start: 0.8666 (m-30) cc_final: 0.8085 (t0) REVERT: C 283 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: D 31 MET cc_start: 0.8070 (tpp) cc_final: 0.7613 (tpt) REVERT: E 21 PHE cc_start: 0.8394 (m-80) cc_final: 0.8156 (m-80) REVERT: E 28 LYS cc_start: 0.8744 (ptmm) cc_final: 0.8132 (ttpt) REVERT: E 78 ASP cc_start: 0.7295 (t0) cc_final: 0.6975 (t0) REVERT: E 97 PHE cc_start: 0.7841 (m-80) cc_final: 0.6451 (m-80) outliers start: 36 outliers final: 21 residues processed: 173 average time/residue: 0.1745 time to fit residues: 39.4416 Evaluate side-chains 162 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 124 THR 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: 0.4980 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 ** D 27 GLN ** 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 = 0.4188 r_free = 0.4188 target = 0.181462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117909 restraints weight = 7949.895| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.73 r_work: 0.3278 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6296 Z= 0.110 Angle : 0.529 6.818 8561 Z= 0.265 Chirality : 0.044 0.136 934 Planarity : 0.003 0.035 1103 Dihedral : 6.097 59.832 834 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.84 % Allowed : 16.93 % 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: -0.56 (0.31), residues: 760 helix: 1.05 (0.62), residues: 81 sheet: -0.82 (0.31), residues: 292 loop : -0.16 (0.31), residues: 387 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 0.022 0.001 PHE C 113 TYR 0.008 0.001 TYR A 90 ARG 0.003 0.000 ARG C 330 Details of bonding type rmsd hydrogen bonds : bond 0.02844 ( 160) hydrogen bonds : angle 5.31433 ( 405) SS BOND : bond 0.00292 ( 23) SS BOND : angle 1.01237 ( 46) covalent geometry : bond 0.00258 ( 6273) covalent geometry : angle 0.52483 ( 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 181 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.728 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: 0.8718 (p90) cc_final: 0.8432 (p90) REVERT: A 99 GLU cc_start: 0.7746 (tp30) cc_final: 0.7219 (mm-30) REVERT: A 104 MET cc_start: 0.8201 (tpp) cc_final: 0.7877 (tpp) REVERT: A 105 ILE cc_start: 0.8825 (mt) cc_final: 0.8519 (mp) REVERT: B 13 LYS cc_start: 0.7985 (tppt) cc_final: 0.7741 (mttp) REVERT: B 15 CYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6077 (t) REVERT: B 60 LYS cc_start: 0.8302 (mtpm) cc_final: 0.7907 (mttt) REVERT: C 77 VAL cc_start: 0.9168 (t) cc_final: 0.8826 (m) REVERT: C 132 GLU cc_start: 0.8948 (tp30) cc_final: 0.8315 (tt0) REVERT: C 195 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7787 (mm-30) REVERT: C 231 ASP cc_start: 0.8324 (m-30) cc_final: 0.7610 (m-30) REVERT: C 263 ASP cc_start: 0.8699 (m-30) cc_final: 0.8074 (t0) REVERT: C 283 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: E 28 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8176 (ttpp) REVERT: E 78 ASP cc_start: 0.7452 (t0) cc_final: 0.7249 (t0) REVERT: E 97 PHE cc_start: 0.7674 (m-80) cc_final: 0.7430 (m-80) REVERT: E 98 MET cc_start: 0.8468 (ttp) cc_final: 0.8223 (ttt) outliers start: 34 outliers final: 26 residues processed: 172 average time/residue: 0.1814 time to fit residues: 40.7507 Evaluate side-chains 166 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 54 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 E 72 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.179733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.115516 restraints weight = 7852.119| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 3.70 r_work: 0.3250 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6296 Z= 0.147 Angle : 0.554 6.924 8561 Z= 0.278 Chirality : 0.045 0.140 934 Planarity : 0.004 0.050 1103 Dihedral : 6.090 58.706 834 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.83 % Allowed : 16.36 % Favored : 77.81 % 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: -0.62 (0.31), residues: 760 helix: 0.69 (0.59), residues: 87 sheet: -0.72 (0.30), residues: 308 loop : -0.23 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 257 HIS 0.010 0.001 HIS A 34 PHE 0.025 0.001 PHE C 113 TYR 0.010 0.001 TYR B 58 ARG 0.003 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.02856 ( 160) hydrogen bonds : angle 5.28181 ( 405) SS BOND : bond 0.00316 ( 23) SS BOND : angle 1.07024 ( 46) covalent geometry : bond 0.00346 ( 6273) covalent geometry : angle 0.54971 ( 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 178 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 137 time to evaluate : 0.705 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 99 GLU cc_start: 0.7667 (tp30) cc_final: 0.7119 (mm-30) REVERT: A 105 ILE cc_start: 0.8811 (mt) cc_final: 0.8484 (mp) REVERT: B 13 LYS cc_start: 0.8081 (tppt) cc_final: 0.7827 (mttp) REVERT: B 15 CYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6149 (t) REVERT: B 60 LYS cc_start: 0.8302 (mtpm) cc_final: 0.7935 (mttt) REVERT: C 77 VAL cc_start: 0.9154 (t) cc_final: 0.8815 (m) REVERT: C 132 GLU cc_start: 0.8949 (tp30) cc_final: 0.8325 (tt0) REVERT: C 195 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7937 (mm-30) REVERT: C 231 ASP cc_start: 0.8404 (m-30) cc_final: 0.7723 (m-30) REVERT: C 263 ASP cc_start: 0.8727 (m-30) cc_final: 0.8070 (t0) REVERT: C 283 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7410 (mp0) REVERT: D 31 MET cc_start: 0.8041 (mmm) cc_final: 0.7634 (tpt) REVERT: E 21 PHE cc_start: 0.8268 (m-80) cc_final: 0.7973 (m-80) REVERT: E 28 LYS cc_start: 0.8806 (ptmm) cc_final: 0.8255 (ttpp) REVERT: E 78 ASP cc_start: 0.7391 (t0) cc_final: 0.7169 (t0) REVERT: E 96 PHE cc_start: 0.7189 (t80) cc_final: 0.6987 (t80) outliers start: 41 outliers final: 31 residues processed: 162 average time/residue: 0.1756 time to fit residues: 37.7268 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 : 0.690 ------------------------------------------------------------------------------- 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 54 LEU 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 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: 7.9990 chunk 61 optimal weight: 0.0050 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 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 = 0.181486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116592 restraints weight = 7962.011| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.82 r_work: 0.3263 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6296 Z= 0.117 Angle : 0.533 6.818 8561 Z= 0.267 Chirality : 0.044 0.137 934 Planarity : 0.004 0.041 1103 Dihedral : 6.006 58.338 834 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.55 % Allowed : 18.21 % Favored : 77.24 % 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: -0.64 (0.31), residues: 760 helix: 0.69 (0.58), residues: 87 sheet: -0.73 (0.30), residues: 308 loop : -0.26 (0.32), residues: 365 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 0.024 0.001 PHE C 113 TYR 0.023 0.001 TYR A 39 ARG 0.003 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.02767 ( 160) hydrogen bonds : angle 5.12021 ( 405) SS BOND : bond 0.00265 ( 23) SS BOND : angle 1.14484 ( 46) covalent geometry : bond 0.00276 ( 6273) covalent geometry : angle 0.52815 ( 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 170 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.715 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: 0.7628 (tp30) cc_final: 0.7082 (mm-30) REVERT: A 105 ILE cc_start: 0.8728 (mt) cc_final: 0.8426 (mp) REVERT: B 13 LYS cc_start: 0.7996 (tppt) cc_final: 0.7788 (mttp) REVERT: B 15 CYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6364 (t) REVERT: B 60 LYS cc_start: 0.8302 (mtpm) cc_final: 0.7935 (mttt) REVERT: C 77 VAL cc_start: 0.9175 (t) cc_final: 0.8850 (m) REVERT: C 132 GLU cc_start: 0.8945 (tp30) cc_final: 0.8301 (tt0) REVERT: C 195 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7879 (mm-30) REVERT: C 231 ASP cc_start: 0.8317 (m-30) cc_final: 0.7654 (m-30) REVERT: C 256 ASN cc_start: 0.8940 (t0) cc_final: 0.8714 (t0) REVERT: C 263 ASP cc_start: 0.8648 (m-30) cc_final: 0.8016 (t0) REVERT: C 283 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: D 27 GLN cc_start: 0.6566 (pm20) cc_final: 0.6338 (pm20) REVERT: D 98 MET cc_start: 0.8534 (ppp) cc_final: 0.7627 (ttp) REVERT: E 28 LYS cc_start: 0.8800 (ptmm) cc_final: 0.8293 (ttpt) REVERT: E 78 ASP cc_start: 0.7374 (t0) cc_final: 0.7144 (t0) outliers start: 32 outliers final: 25 residues processed: 161 average time/residue: 0.1722 time to fit residues: 36.9676 Evaluate side-chains 161 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 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 75 ILE 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: 1.9990 chunk 62 optimal weight: 0.0370 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- 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 C 333 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.178424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112666 restraints weight = 8019.762| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.90 r_work: 0.3212 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6296 Z= 0.194 Angle : 0.592 10.333 8561 Z= 0.298 Chirality : 0.046 0.212 934 Planarity : 0.004 0.044 1103 Dihedral : 6.146 57.633 834 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.69 % Allowed : 17.21 % 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: -0.75 (0.31), residues: 760 helix: 0.56 (0.58), residues: 87 sheet: -0.77 (0.31), residues: 306 loop : -0.34 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 51 HIS 0.007 0.001 HIS A 34 PHE 0.023 0.002 PHE C 113 TYR 0.013 0.001 TYR B 58 ARG 0.004 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.03016 ( 160) hydrogen bonds : angle 5.23767 ( 405) SS BOND : bond 0.00413 ( 23) SS BOND : angle 1.39833 ( 46) covalent geometry : bond 0.00457 ( 6273) covalent geometry : angle 0.58504 ( 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 177 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8753 (mt) cc_final: 0.8441 (mp) REVERT: B 15 CYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6715 (t) REVERT: C 77 VAL cc_start: 0.9191 (t) cc_final: 0.8834 (m) REVERT: C 132 GLU cc_start: 0.8928 (tp30) cc_final: 0.8342 (tt0) REVERT: C 195 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7901 (mm-30) REVERT: C 231 ASP cc_start: 0.8421 (m-30) cc_final: 0.7789 (m-30) REVERT: C 256 ASN cc_start: 0.9040 (t0) cc_final: 0.8766 (t0) REVERT: C 263 ASP cc_start: 0.8640 (m-30) cc_final: 0.8024 (t0) REVERT: C 283 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: D 31 MET cc_start: 0.8168 (mmm) cc_final: 0.7743 (tpt) REVERT: D 98 MET cc_start: 0.8499 (ppp) cc_final: 0.7634 (ttp) REVERT: E 28 LYS cc_start: 0.8835 (ptmm) cc_final: 0.8366 (ttpt) REVERT: E 45 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6586 (mt-10) REVERT: E 97 PHE cc_start: 0.7662 (m-80) cc_final: 0.7449 (m-80) outliers start: 40 outliers final: 33 residues processed: 164 average time/residue: 0.1724 time to fit residues: 37.3053 Evaluate side-chains 171 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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 A residue 102 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 299 THR Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 46 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.181468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116902 restraints weight = 7958.336| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.83 r_work: 0.3252 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6296 Z= 0.127 Angle : 0.575 8.786 8561 Z= 0.289 Chirality : 0.045 0.197 934 Planarity : 0.004 0.037 1103 Dihedral : 6.079 55.915 834 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.98 % Allowed : 17.78 % Favored : 77.24 % 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: -0.78 (0.31), residues: 760 helix: 0.58 (0.57), residues: 87 sheet: -0.73 (0.30), residues: 312 loop : -0.44 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.002 0.000 ARG C 330 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 160) hydrogen bonds : angle 5.04861 ( 405) SS BOND : bond 0.00286 ( 23) SS BOND : angle 1.20806 ( 46) covalent geometry : bond 0.00298 ( 6273) covalent geometry : angle 0.56993 ( 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 175 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6763 (mm-30) REVERT: A 105 ILE cc_start: 0.8759 (mt) cc_final: 0.8464 (mp) REVERT: B 13 LYS cc_start: 0.8242 (tptp) cc_final: 0.7926 (mttp) REVERT: B 15 CYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6886 (t) REVERT: C 77 VAL cc_start: 0.9189 (t) cc_final: 0.8845 (m) REVERT: C 132 GLU cc_start: 0.8927 (tp30) cc_final: 0.8353 (tt0) REVERT: C 195 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7982 (mm-30) REVERT: C 231 ASP cc_start: 0.8283 (m-30) cc_final: 0.7655 (m-30) REVERT: C 263 ASP cc_start: 0.8621 (m-30) cc_final: 0.8001 (t0) REVERT: C 283 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: D 27 GLN cc_start: 0.6477 (pm20) cc_final: 0.6192 (pm20) REVERT: D 98 MET cc_start: 0.8501 (ppp) cc_final: 0.7798 (ttt) REVERT: E 28 LYS cc_start: 0.8833 (ptmm) cc_final: 0.8443 (tmmt) REVERT: E 45 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6541 (mt-10) outliers start: 35 outliers final: 28 residues processed: 166 average time/residue: 0.1744 time to fit residues: 38.2468 Evaluate side-chains 165 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 A residue 102 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 16 optimal weight: 0.0010 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.114414 restraints weight = 8091.156| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.93 r_work: 0.3233 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3604 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= 0.151 Angle : 0.590 8.185 8561 Z= 0.298 Chirality : 0.045 0.183 934 Planarity : 0.004 0.041 1103 Dihedral : 6.076 56.047 834 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.84 % Allowed : 17.92 % Favored : 77.24 % 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: -0.81 (0.31), residues: 760 helix: 0.61 (0.58), residues: 87 sheet: -0.87 (0.30), residues: 308 loop : -0.34 (0.32), residues: 365 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 0.001 PHE C 113 TYR 0.010 0.001 TYR B 58 ARG 0.003 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 160) hydrogen bonds : angle 5.08780 ( 405) SS BOND : bond 0.00349 ( 23) SS BOND : angle 1.25374 ( 46) covalent geometry : bond 0.00357 ( 6273) covalent geometry : angle 0.58465 ( 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 170 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6868 (mm-30) REVERT: A 105 ILE cc_start: 0.8795 (mt) cc_final: 0.8502 (mp) REVERT: B 13 LYS cc_start: 0.8313 (tptp) cc_final: 0.7947 (mttp) REVERT: B 15 CYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6944 (t) REVERT: C 77 VAL cc_start: 0.9185 (t) cc_final: 0.8818 (m) REVERT: C 132 GLU cc_start: 0.8916 (tp30) cc_final: 0.8338 (tt0) REVERT: C 138 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.8064 (mtm110) REVERT: C 195 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7983 (mm-30) REVERT: C 231 ASP cc_start: 0.8355 (m-30) cc_final: 0.7731 (m-30) REVERT: C 263 ASP cc_start: 0.8621 (m-30) cc_final: 0.7894 (t0) REVERT: C 283 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: D 98 MET cc_start: 0.8539 (ppp) cc_final: 0.7875 (ttt) REVERT: E 28 LYS cc_start: 0.8844 (ptmm) cc_final: 0.8491 (tmmt) REVERT: E 45 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6565 (mt-10) outliers start: 34 outliers final: 29 residues processed: 159 average time/residue: 0.1725 time to fit residues: 36.3401 Evaluate side-chains 166 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 A residue 102 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 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 9 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 43 optimal weight: 0.0020 chunk 42 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.180437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.115710 restraints weight = 8063.137| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.90 r_work: 0.3251 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6296 Z= 0.133 Angle : 0.589 8.288 8561 Z= 0.297 Chirality : 0.045 0.179 934 Planarity : 0.004 0.039 1103 Dihedral : 6.074 56.150 834 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.55 % Allowed : 18.92 % Favored : 76.53 % 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: -0.82 (0.31), residues: 760 helix: 0.86 (0.59), residues: 81 sheet: -0.89 (0.30), residues: 316 loop : -0.38 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 52 HIS 0.006 0.001 HIS A 34 PHE 0.026 0.001 PHE C 113 TYR 0.010 0.001 TYR B 58 ARG 0.003 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.02822 ( 160) hydrogen bonds : angle 5.07961 ( 405) SS BOND : bond 0.00355 ( 23) SS BOND : angle 1.30844 ( 46) covalent geometry : bond 0.00314 ( 6273) covalent geometry : angle 0.58307 ( 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 172 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7851 (mm-40) REVERT: A 99 GLU cc_start: 0.7509 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 105 ILE cc_start: 0.8828 (mt) cc_final: 0.8542 (mp) REVERT: B 13 LYS cc_start: 0.8269 (tptp) cc_final: 0.7906 (mttp) REVERT: B 15 CYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6904 (t) REVERT: C 77 VAL cc_start: 0.9187 (t) cc_final: 0.8827 (m) REVERT: C 132 GLU cc_start: 0.8917 (tp30) cc_final: 0.8336 (tt0) REVERT: C 138 ARG cc_start: 0.8370 (mtm-85) cc_final: 0.8071 (mtm110) REVERT: C 195 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8012 (mm-30) REVERT: C 231 ASP cc_start: 0.8332 (m-30) cc_final: 0.7705 (m-30) REVERT: C 263 ASP cc_start: 0.8551 (m-30) cc_final: 0.7840 (t0) REVERT: C 283 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: D 86 MET cc_start: 0.7770 (mmp) cc_final: 0.7566 (mmp) REVERT: D 98 MET cc_start: 0.8515 (ppp) cc_final: 0.7841 (ttt) REVERT: E 28 LYS cc_start: 0.8808 (ptmm) cc_final: 0.8484 (tmmt) REVERT: E 45 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6558 (mt-10) REVERT: E 87 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7685 (mmtm) REVERT: E 98 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7491 (tmm) outliers start: 32 outliers final: 27 residues processed: 162 average time/residue: 0.1771 time to fit residues: 37.7273 Evaluate side-chains 168 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 59 SER Chi-restraints excluded: chain A residue 102 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 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 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 98 MET 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: 0.6980 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.179231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118877 restraints weight = 8129.516| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.60 r_work: 0.3319 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6296 Z= 0.140 Angle : 0.588 7.918 8561 Z= 0.298 Chirality : 0.045 0.170 934 Planarity : 0.004 0.038 1103 Dihedral : 6.071 56.270 834 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 4.55 % Allowed : 19.06 % Favored : 76.39 % 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: 0.90 (0.59), residues: 81 sheet: -0.92 (0.30), residues: 316 loop : -0.42 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 51 HIS 0.006 0.001 HIS A 34 PHE 0.025 0.001 PHE C 113 TYR 0.010 0.001 TYR B 58 ARG 0.004 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.02876 ( 160) hydrogen bonds : angle 5.07168 ( 405) SS BOND : bond 0.00294 ( 23) SS BOND : angle 1.25017 ( 46) covalent geometry : bond 0.00332 ( 6273) covalent geometry : angle 0.58239 ( 8515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3825.96 seconds wall clock time: 66 minutes 56.74 seconds (4016.74 seconds total)