Starting phenix.real_space_refine on Thu Feb 5 18:48:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hwj_52450/02_2026/9hwj_52450.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hwj_52450/02_2026/9hwj_52450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hwj_52450/02_2026/9hwj_52450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hwj_52450/02_2026/9hwj_52450.map" model { file = "/net/cci-nas-00/data/ceres_data/9hwj_52450/02_2026/9hwj_52450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hwj_52450/02_2026/9hwj_52450.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 6100 2.51 5 N 1676 2.21 5 O 1704 1.98 5 H 9512 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19052 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 4763 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 289} Chain breaks: 2 Restraints were copied for chains: B, C, D Time building chain proxies: 3.82, per 1000 atoms: 0.20 Number of scatterers: 19052 At special positions: 0 Unit cell: (94.38, 94.38, 97.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 O 1704 8.00 N 1676 7.00 C 6100 6.00 H 9512 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 608.9 milliseconds 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 56.8% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 134 through 153 Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.591A pdb=" N HIS A 176 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 removed outlier: 3.649A pdb=" N ASN A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 232 through 261 removed outlier: 3.936A pdb=" N SER A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 304 removed outlier: 3.718A pdb=" N VAL A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 53 through 64 Processing helix chain 'B' and resid 79 through 89 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 134 through 153 Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.591A pdb=" N HIS B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 192 removed outlier: 3.649A pdb=" N ASN B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 232 through 261 removed outlier: 3.936A pdb=" N SER B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 272 through 304 removed outlier: 3.718A pdb=" N VAL B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 303 " --> pdb=" O TYR B 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 53 through 64 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 134 through 153 Processing helix chain 'C' and resid 168 through 177 removed outlier: 3.591A pdb=" N HIS C 176 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 removed outlier: 3.649A pdb=" N ASN C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 229 Processing helix chain 'C' and resid 232 through 261 removed outlier: 3.936A pdb=" N SER C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 271 No H-bonds generated for 'chain 'C' and resid 269 through 271' Processing helix chain 'C' and resid 272 through 304 removed outlier: 3.718A pdb=" N VAL C 276 " --> pdb=" O MET C 272 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 79 through 89 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 134 through 153 Processing helix chain 'D' and resid 168 through 177 removed outlier: 3.591A pdb=" N HIS D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 192 removed outlier: 3.649A pdb=" N ASN D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 229 Processing helix chain 'D' and resid 232 through 261 removed outlier: 3.936A pdb=" N SER D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'D' and resid 272 through 304 removed outlier: 3.718A pdb=" N VAL D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG D 297 " --> pdb=" O GLU D 293 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 303 " --> pdb=" O TYR D 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 200 removed outlier: 3.672A pdb=" N ARG A 164 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 10 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 44 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL A 12 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE A 46 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 14 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A 70 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 43 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A 72 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 45 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU A 74 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 71 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A 313 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU A 73 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 195 through 200 removed outlier: 3.672A pdb=" N ARG B 164 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 10 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU B 44 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL B 12 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE B 46 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 14 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL B 70 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 43 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE B 72 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 45 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 74 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER B 71 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL B 313 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 73 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 195 through 200 removed outlier: 3.672A pdb=" N ARG C 164 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 10 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 44 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 12 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE C 46 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 14 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL C 70 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 43 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE C 72 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU C 45 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU C 74 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER C 71 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 313 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU C 73 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 195 through 200 removed outlier: 3.672A pdb=" N ARG D 164 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL D 10 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU D 44 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 12 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 46 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE D 14 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL D 70 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE D 43 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE D 72 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU D 45 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU D 74 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER D 71 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 313 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU D 73 " --> pdb=" O GLN D 311 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1548 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: 4.11 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.06: 9512 1.06 - 1.25: 1304 1.25 - 1.43: 2760 1.43 - 1.62: 5548 1.62 - 1.81: 104 Bond restraints: 19228 Sorted by residual: bond pdb=" CZ ARG A 234 " pdb=" NH1 ARG A 234 " ideal model delta sigma weight residual 1.323 1.385 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" CZ ARG B 234 " pdb=" NH1 ARG B 234 " ideal model delta sigma weight residual 1.323 1.385 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" CZ ARG C 234 " pdb=" NH1 ARG C 234 " ideal model delta sigma weight residual 1.323 1.385 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" CZ ARG D 234 " pdb=" NH1 ARG D 234 " ideal model delta sigma weight residual 1.323 1.385 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" NE ARG B 76 " pdb=" CZ ARG B 76 " ideal model delta sigma weight residual 1.326 1.370 -0.044 1.10e-02 8.26e+03 1.60e+01 ... (remaining 19223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 31296 2.82 - 5.64: 3046 5.64 - 8.45: 546 8.45 - 11.27: 4 11.27 - 14.09: 8 Bond angle restraints: 34900 Sorted by residual: angle pdb=" CD ARG D 76 " pdb=" NE ARG D 76 " pdb=" CZ ARG D 76 " ideal model delta sigma weight residual 124.40 136.94 -12.54 1.40e+00 5.10e-01 8.03e+01 angle pdb=" CD ARG A 76 " pdb=" NE ARG A 76 " pdb=" CZ ARG A 76 " ideal model delta sigma weight residual 124.40 136.94 -12.54 1.40e+00 5.10e-01 8.03e+01 angle pdb=" CD ARG C 76 " pdb=" NE ARG C 76 " pdb=" CZ ARG C 76 " ideal model delta sigma weight residual 124.40 136.94 -12.54 1.40e+00 5.10e-01 8.03e+01 angle pdb=" CD ARG B 76 " pdb=" NE ARG B 76 " pdb=" CZ ARG B 76 " ideal model delta sigma weight residual 124.40 136.94 -12.54 1.40e+00 5.10e-01 8.03e+01 angle pdb=" CA HIS D 178 " pdb=" CB HIS D 178 " pdb=" CG HIS D 178 " ideal model delta sigma weight residual 113.80 121.34 -7.54 1.00e+00 1.00e+00 5.68e+01 ... (remaining 34895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.48: 7800 15.48 - 30.97: 600 30.97 - 46.45: 156 46.45 - 61.94: 192 61.94 - 77.42: 96 Dihedral angle restraints: 8844 sinusoidal: 4812 harmonic: 4032 Sorted by residual: dihedral pdb=" CA LYS A 211 " pdb=" C LYS A 211 " pdb=" N TYR A 212 " pdb=" CA TYR A 212 " ideal model delta harmonic sigma weight residual -180.00 -150.09 -29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LYS D 211 " pdb=" C LYS D 211 " pdb=" N TYR D 212 " pdb=" CA TYR D 212 " ideal model delta harmonic sigma weight residual -180.00 -150.09 -29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LYS B 211 " pdb=" C LYS B 211 " pdb=" N TYR B 212 " pdb=" CA TYR B 212 " ideal model delta harmonic sigma weight residual -180.00 -150.09 -29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 8841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 596 0.044 - 0.087: 506 0.087 - 0.131: 282 0.131 - 0.175: 108 0.175 - 0.219: 40 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CA ARG D 137 " pdb=" N ARG D 137 " pdb=" C ARG D 137 " pdb=" CB ARG D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ARG A 137 " pdb=" N ARG A 137 " pdb=" C ARG A 137 " pdb=" CB ARG A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ARG B 137 " pdb=" N ARG B 137 " pdb=" C ARG B 137 " pdb=" CB ARG B 137 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1529 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 164 " -0.549 9.50e-02 1.11e+02 1.86e-01 6.11e+01 pdb=" NE ARG C 164 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG C 164 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG C 164 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 164 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 164 " -0.033 2.00e-02 2.50e+03 pdb="HH12 ARG C 164 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG C 164 " -0.063 2.00e-02 2.50e+03 pdb="HH22 ARG C 164 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 164 " -0.549 9.50e-02 1.11e+02 1.86e-01 6.11e+01 pdb=" NE ARG B 164 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG B 164 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG B 164 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 164 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 164 " -0.033 2.00e-02 2.50e+03 pdb="HH12 ARG B 164 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 164 " -0.063 2.00e-02 2.50e+03 pdb="HH22 ARG B 164 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 164 " 0.549 9.50e-02 1.11e+02 1.86e-01 6.11e+01 pdb=" NE ARG D 164 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG D 164 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG D 164 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 164 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 164 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG D 164 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG D 164 " 0.063 2.00e-02 2.50e+03 pdb="HH22 ARG D 164 " -0.021 2.00e-02 2.50e+03 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 56 1.85 - 2.54: 14568 2.54 - 3.22: 59495 3.22 - 3.91: 74333 3.91 - 4.60: 115158 Nonbonded interactions: 263610 Sorted by model distance: nonbonded pdb=" HG2 GLU A 179 " pdb=" HA ARG D 303 " model vdw 1.162 2.440 nonbonded pdb=" HA ARG C 303 " pdb=" HG2 GLU D 179 " model vdw 1.162 2.440 nonbonded pdb=" HA ARG A 303 " pdb=" HG2 GLU B 179 " model vdw 1.163 2.440 nonbonded pdb=" HA ARG B 303 " pdb=" HG2 GLU C 179 " model vdw 1.163 2.440 nonbonded pdb=" HA ASN B 219 " pdb="HH12 ARG C 234 " model vdw 1.234 2.270 ... (remaining 263605 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.070 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.600 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.010 0.062 9716 Z= 0.629 Angle : 1.569 14.091 13140 Z= 1.026 Chirality : 0.079 0.219 1532 Planarity : 0.019 0.253 1664 Dihedral : 13.380 77.422 3608 Min Nonbonded Distance : 1.464 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.38 % Allowed : 4.60 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1180 helix: -0.37 (0.17), residues: 620 sheet: 0.74 (0.37), residues: 184 loop : -1.73 (0.23), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.005 ARG C 180 TYR 0.039 0.010 TYR C 159 PHE 0.030 0.007 PHE D 278 TRP 0.020 0.007 TRP B 135 HIS 0.013 0.005 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00955 ( 9716) covalent geometry : angle 1.56875 (13140) hydrogen bonds : bond 0.15973 ( 520) hydrogen bonds : angle 6.85066 ( 1548) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 296 time to evaluate : 0.396 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 223 ASP cc_start: 0.8808 (m-30) cc_final: 0.8106 (m-30) outliers start: 4 outliers final: 4 residues processed: 300 average time/residue: 0.2398 time to fit residues: 96.8670 Evaluate side-chains 192 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain D residue 166 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.102817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.090429 restraints weight = 103756.318| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 4.91 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9716 Z= 0.153 Angle : 0.655 4.566 13140 Z= 0.359 Chirality : 0.046 0.182 1532 Planarity : 0.006 0.062 1664 Dihedral : 6.394 29.809 1336 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.30 % Allowed : 10.44 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1180 helix: 1.24 (0.20), residues: 628 sheet: 0.84 (0.36), residues: 188 loop : -1.31 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 234 TYR 0.009 0.001 TYR D 294 PHE 0.013 0.001 PHE D 280 TRP 0.001 0.000 TRP B 135 HIS 0.013 0.002 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9716) covalent geometry : angle 0.65534 (13140) hydrogen bonds : bond 0.05460 ( 520) hydrogen bonds : angle 5.26300 ( 1548) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.346 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 219 ASN cc_start: 0.8752 (t0) cc_final: 0.8488 (t0) REVERT: D 223 ASP cc_start: 0.8791 (m-30) cc_final: 0.8494 (m-30) outliers start: 24 outliers final: 8 residues processed: 219 average time/residue: 0.2275 time to fit residues: 67.1359 Evaluate side-chains 194 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 186 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 166 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 0.0020 chunk 7 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086986 restraints weight = 110017.039| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 5.10 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9716 Z= 0.225 Angle : 0.615 5.848 13140 Z= 0.341 Chirality : 0.042 0.128 1532 Planarity : 0.004 0.031 1664 Dihedral : 5.812 29.320 1336 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.01 % Allowed : 14.56 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1180 helix: 1.31 (0.20), residues: 640 sheet: 0.88 (0.36), residues: 180 loop : -1.79 (0.26), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 180 TYR 0.011 0.002 TYR D 159 PHE 0.012 0.001 PHE B 183 TRP 0.003 0.001 TRP A 135 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9716) covalent geometry : angle 0.61478 (13140) hydrogen bonds : bond 0.04642 ( 520) hydrogen bonds : angle 5.21644 ( 1548) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.453 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 219 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8699 (t0) REVERT: D 223 ASP cc_start: 0.8865 (m-30) cc_final: 0.8581 (m-30) outliers start: 21 outliers final: 16 residues processed: 211 average time/residue: 0.2601 time to fit residues: 72.6503 Evaluate side-chains 198 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 166 TYR Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 243 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 105 ASN B 77 ASN B 105 ASN C 77 ASN C 105 ASN D 77 ASN D 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.100524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.087401 restraints weight = 109162.885| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 5.08 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 9716 Z= 0.166 Angle : 0.546 4.985 13140 Z= 0.302 Chirality : 0.042 0.123 1532 Planarity : 0.004 0.027 1664 Dihedral : 5.422 28.597 1336 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.63 % Allowed : 14.66 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1180 helix: 1.61 (0.20), residues: 648 sheet: 0.72 (0.38), residues: 184 loop : -1.72 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 216 TYR 0.010 0.002 TYR D 294 PHE 0.006 0.001 PHE D 309 TRP 0.002 0.001 TRP D 135 HIS 0.004 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9716) covalent geometry : angle 0.54569 (13140) hydrogen bonds : bond 0.04107 ( 520) hydrogen bonds : angle 4.84952 ( 1548) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.534 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8422 (mmt) cc_final: 0.8122 (mmt) REVERT: B 235 MET cc_start: 0.8431 (mmt) cc_final: 0.8122 (mmt) REVERT: C 235 MET cc_start: 0.8440 (mmt) cc_final: 0.8144 (mmt) REVERT: D 219 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8691 (t0) REVERT: D 223 ASP cc_start: 0.8826 (m-30) cc_final: 0.8565 (m-30) REVERT: D 235 MET cc_start: 0.8435 (mmt) cc_final: 0.8139 (mmt) outliers start: 17 outliers final: 12 residues processed: 201 average time/residue: 0.2531 time to fit residues: 68.5519 Evaluate side-chains 194 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 166 TYR Chi-restraints excluded: chain D residue 219 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085893 restraints weight = 110036.165| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 4.97 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 9716 Z= 0.214 Angle : 0.555 4.659 13140 Z= 0.312 Chirality : 0.042 0.124 1532 Planarity : 0.004 0.028 1664 Dihedral : 5.224 27.577 1336 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.68 % Allowed : 15.13 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1180 helix: 1.55 (0.20), residues: 644 sheet: 0.93 (0.40), residues: 156 loop : -1.67 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 131 TYR 0.012 0.002 TYR A 159 PHE 0.005 0.001 PHE C 309 TRP 0.001 0.001 TRP D 135 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9716) covalent geometry : angle 0.55543 (13140) hydrogen bonds : bond 0.03982 ( 520) hydrogen bonds : angle 4.91963 ( 1548) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.659 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 HIS cc_start: 0.8589 (t70) cc_final: 0.8359 (t-90) REVERT: A 221 MET cc_start: 0.9440 (tmm) cc_final: 0.9184 (tmm) REVERT: A 235 MET cc_start: 0.8443 (mmt) cc_final: 0.8140 (mmt) REVERT: B 221 MET cc_start: 0.9437 (tmm) cc_final: 0.9181 (tmm) REVERT: B 235 MET cc_start: 0.8447 (mmt) cc_final: 0.8147 (mmt) REVERT: C 221 MET cc_start: 0.9439 (tmm) cc_final: 0.9183 (tmm) REVERT: C 235 MET cc_start: 0.8443 (mmt) cc_final: 0.8147 (mmt) REVERT: D 221 MET cc_start: 0.9438 (tmm) cc_final: 0.9184 (tmm) REVERT: D 223 ASP cc_start: 0.8828 (m-30) cc_final: 0.8625 (m-30) REVERT: D 235 MET cc_start: 0.8441 (mmt) cc_final: 0.8141 (mmt) outliers start: 28 outliers final: 24 residues processed: 203 average time/residue: 0.2530 time to fit residues: 69.7727 Evaluate side-chains 194 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 166 TYR Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 302 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 0.0870 chunk 118 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.100436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087775 restraints weight = 107456.134| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 5.05 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9716 Z= 0.103 Angle : 0.523 4.817 13140 Z= 0.279 Chirality : 0.042 0.148 1532 Planarity : 0.004 0.030 1664 Dihedral : 5.013 27.515 1336 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.01 % Allowed : 16.86 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.24), residues: 1180 helix: 2.10 (0.20), residues: 636 sheet: 1.31 (0.39), residues: 156 loop : -1.35 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 131 TYR 0.011 0.001 TYR D 222 PHE 0.005 0.001 PHE C 309 TRP 0.001 0.000 TRP B 135 HIS 0.008 0.001 HIS D 178 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9716) covalent geometry : angle 0.52323 (13140) hydrogen bonds : bond 0.03668 ( 520) hydrogen bonds : angle 4.45648 ( 1548) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.558 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8478 (mmmm) REVERT: A 178 HIS cc_start: 0.8539 (t70) cc_final: 0.8222 (t70) REVERT: A 235 MET cc_start: 0.8359 (mmt) cc_final: 0.8084 (mmt) REVERT: B 154 LYS cc_start: 0.8870 (mmmm) cc_final: 0.8453 (mmmm) REVERT: B 235 MET cc_start: 0.8364 (mmt) cc_final: 0.8135 (mmt) REVERT: C 154 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8449 (mmmm) REVERT: C 235 MET cc_start: 0.8373 (mmt) cc_final: 0.8082 (mmt) REVERT: D 154 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8472 (mmmm) REVERT: D 223 ASP cc_start: 0.8781 (m-30) cc_final: 0.8578 (m-30) REVERT: D 235 MET cc_start: 0.8370 (mmt) cc_final: 0.8076 (mmt) outliers start: 21 outliers final: 17 residues processed: 193 average time/residue: 0.2451 time to fit residues: 63.9169 Evaluate side-chains 185 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 20 GLN Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 166 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 70 optimal weight: 0.0270 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.099902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086888 restraints weight = 105983.832| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.92 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 9716 Z= 0.140 Angle : 0.519 5.217 13140 Z= 0.283 Chirality : 0.041 0.125 1532 Planarity : 0.004 0.029 1664 Dihedral : 4.866 27.240 1336 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.78 % Allowed : 17.24 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1180 helix: 2.21 (0.20), residues: 636 sheet: 1.31 (0.38), residues: 164 loop : -1.39 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 131 TYR 0.013 0.001 TYR A 222 PHE 0.005 0.001 PHE A 248 TRP 0.001 0.000 TRP A 135 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9716) covalent geometry : angle 0.51886 (13140) hydrogen bonds : bond 0.03611 ( 520) hydrogen bonds : angle 4.45752 ( 1548) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.374 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.9625 (tt0) cc_final: 0.9389 (tm-30) REVERT: A 235 MET cc_start: 0.8402 (mmt) cc_final: 0.8165 (mmt) REVERT: B 149 GLN cc_start: 0.9624 (tt0) cc_final: 0.9388 (tm-30) REVERT: B 178 HIS cc_start: 0.8502 (t-90) cc_final: 0.8154 (t-90) REVERT: B 235 MET cc_start: 0.8411 (mmt) cc_final: 0.8126 (mmt) REVERT: C 149 GLN cc_start: 0.9622 (tt0) cc_final: 0.9385 (tm-30) REVERT: C 178 HIS cc_start: 0.8494 (t-90) cc_final: 0.8148 (t-90) REVERT: C 235 MET cc_start: 0.8415 (mmt) cc_final: 0.8132 (mmt) REVERT: D 149 GLN cc_start: 0.9622 (tt0) cc_final: 0.9382 (tm-30) REVERT: D 178 HIS cc_start: 0.8501 (t-90) cc_final: 0.8154 (t-90) REVERT: D 235 MET cc_start: 0.8411 (mmt) cc_final: 0.8129 (mmt) outliers start: 29 outliers final: 21 residues processed: 187 average time/residue: 0.2215 time to fit residues: 56.4666 Evaluate side-chains 189 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 166 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN D 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.099416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086739 restraints weight = 107461.574| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 4.95 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9716 Z= 0.147 Angle : 0.528 5.925 13140 Z= 0.290 Chirality : 0.041 0.125 1532 Planarity : 0.004 0.029 1664 Dihedral : 4.778 26.924 1336 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.01 % Allowed : 18.30 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1180 helix: 2.27 (0.20), residues: 640 sheet: 1.22 (0.37), residues: 164 loop : -1.29 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 131 TYR 0.012 0.001 TYR A 222 PHE 0.005 0.001 PHE B 248 TRP 0.001 0.000 TRP A 135 HIS 0.011 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9716) covalent geometry : angle 0.52797 (13140) hydrogen bonds : bond 0.03536 ( 520) hydrogen bonds : angle 4.43014 ( 1548) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.376 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.9630 (tt0) cc_final: 0.9386 (tm-30) REVERT: A 235 MET cc_start: 0.8411 (mmt) cc_final: 0.8179 (mmt) REVERT: B 149 GLN cc_start: 0.9631 (tt0) cc_final: 0.9385 (tm-30) REVERT: B 235 MET cc_start: 0.8412 (mmt) cc_final: 0.8131 (mmt) REVERT: C 149 GLN cc_start: 0.9631 (tt0) cc_final: 0.9386 (tm-30) REVERT: C 235 MET cc_start: 0.8419 (mmt) cc_final: 0.8142 (mmt) REVERT: D 149 GLN cc_start: 0.9632 (tt0) cc_final: 0.9385 (tm-30) REVERT: D 235 MET cc_start: 0.8418 (mmt) cc_final: 0.8138 (mmt) outliers start: 21 outliers final: 18 residues processed: 182 average time/residue: 0.2356 time to fit residues: 57.4737 Evaluate side-chains 189 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 166 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 20 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.085976 restraints weight = 109001.407| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 5.00 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9716 Z= 0.144 Angle : 0.534 5.332 13140 Z= 0.293 Chirality : 0.041 0.125 1532 Planarity : 0.004 0.035 1664 Dihedral : 4.744 26.711 1336 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.63 % Allowed : 18.58 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1180 helix: 2.32 (0.20), residues: 640 sheet: 1.22 (0.37), residues: 164 loop : -1.26 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 131 TYR 0.010 0.001 TYR A 222 PHE 0.005 0.001 PHE B 248 TRP 0.001 0.000 TRP A 135 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9716) covalent geometry : angle 0.53430 (13140) hydrogen bonds : bond 0.03502 ( 520) hydrogen bonds : angle 4.40378 ( 1548) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.526 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 HIS cc_start: 0.8597 (t-90) cc_final: 0.8379 (t-90) REVERT: A 235 MET cc_start: 0.8430 (mmt) cc_final: 0.8192 (mmt) REVERT: B 178 HIS cc_start: 0.8421 (t-90) cc_final: 0.8094 (t-90) REVERT: B 235 MET cc_start: 0.8430 (mmt) cc_final: 0.8145 (mmt) REVERT: C 178 HIS cc_start: 0.8410 (t-90) cc_final: 0.8084 (t-90) REVERT: C 235 MET cc_start: 0.8432 (mmt) cc_final: 0.8149 (mmt) REVERT: D 178 HIS cc_start: 0.8445 (t-90) cc_final: 0.8118 (t-90) REVERT: D 221 MET cc_start: 0.9259 (tmm) cc_final: 0.8669 (ttm) REVERT: D 235 MET cc_start: 0.8432 (mmt) cc_final: 0.8146 (mmt) outliers start: 17 outliers final: 17 residues processed: 182 average time/residue: 0.2426 time to fit residues: 60.0390 Evaluate side-chains 184 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 35 GLU Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 166 TYR Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 145 ASN Chi-restraints excluded: chain D residue 166 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 64 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.099986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086818 restraints weight = 107523.806| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 5.10 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9716 Z= 0.102 Angle : 0.518 4.958 13140 Z= 0.277 Chirality : 0.041 0.130 1532 Planarity : 0.004 0.032 1664 Dihedral : 4.580 26.821 1336 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.86 % Allowed : 19.73 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.25), residues: 1180 helix: 2.49 (0.21), residues: 636 sheet: 1.36 (0.37), residues: 164 loop : -1.01 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 131 TYR 0.017 0.002 TYR C 212 PHE 0.007 0.001 PHE A 214 TRP 0.001 0.000 TRP A 135 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9716) covalent geometry : angle 0.51827 (13140) hydrogen bonds : bond 0.03307 ( 520) hydrogen bonds : angle 4.17102 ( 1548) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2360 Ramachandran restraints generated. 1180 Oldfield, 0 Emsley, 1180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue TYR 17 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue THR 31 is missing expected H atoms. Skipping. Residue THR 32 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue TYR 41 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue SER 62 is missing expected H atoms. Skipping. Residue SER 67 is missing expected H atoms. Skipping. Residue SER 71 is missing expected H atoms. Skipping. Residue TYR 78 is missing expected H atoms. Skipping. Residue SER 82 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue TYR 121 is missing expected H atoms. Skipping. Residue THR 126 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue THR 139 is missing expected H atoms. Skipping. Residue SER 141 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue THR 152 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue TYR 166 is missing expected H atoms. Skipping. Residue SER 181 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue TYR 212 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue TYR 222 is missing expected H atoms. Skipping. Residue THR 226 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 241 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue THR 260 is missing expected H atoms. Skipping. Residue THR 279 is missing expected H atoms. Skipping. Residue TYR 294 is missing expected H atoms. Skipping. Residue TYR 299 is missing expected H atoms. Skipping. Residue THR 300 is missing expected H atoms. Skipping. Residue TYR 308 is missing expected H atoms. Skipping. Evaluate side-chains 186 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.516 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.9277 (tmm) cc_final: 0.8638 (ttm) REVERT: A 235 MET cc_start: 0.8386 (mmt) cc_final: 0.8134 (mmt) REVERT: B 221 MET cc_start: 0.9288 (tmm) cc_final: 0.8656 (ttm) REVERT: B 235 MET cc_start: 0.8383 (mmt) cc_final: 0.8143 (mmt) REVERT: C 221 MET cc_start: 0.9284 (tmm) cc_final: 0.8653 (ttm) REVERT: C 235 MET cc_start: 0.8400 (mmt) cc_final: 0.8165 (mmt) REVERT: D 221 MET cc_start: 0.9233 (tmm) cc_final: 0.8635 (ttm) REVERT: D 235 MET cc_start: 0.8400 (mmt) cc_final: 0.8148 (mmt) outliers start: 9 outliers final: 9 residues processed: 178 average time/residue: 0.2232 time to fit residues: 54.1337 Evaluate side-chains 181 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain D residue 66 ASN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 145 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 119 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086930 restraints weight = 107844.153| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 5.04 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9716 Z= 0.098 Angle : 0.512 4.668 13140 Z= 0.273 Chirality : 0.042 0.137 1532 Planarity : 0.003 0.033 1664 Dihedral : 4.210 18.746 1328 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.72 % Allowed : 18.87 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.25), residues: 1180 helix: 2.55 (0.20), residues: 636 sheet: 1.42 (0.39), residues: 164 loop : -0.88 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 131 TYR 0.011 0.001 TYR C 212 PHE 0.009 0.001 PHE C 214 TRP 0.001 0.000 TRP C 135 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 9716) covalent geometry : angle 0.51164 (13140) hydrogen bonds : bond 0.03193 ( 520) hydrogen bonds : angle 4.10940 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3353.29 seconds wall clock time: 57 minutes 49.83 seconds (3469.83 seconds total)