Starting phenix.real_space_refine on Wed Aug 5 02:14:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ioc_35615/08_2026/8ioc_35615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ioc_35615/08_2026/8ioc_35615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2026/8ioc_35615.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2026/8ioc_35615.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2026/8ioc_35615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2026/8ioc_35615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2026/8ioc_35615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2026/8ioc_35615.map" } resolution = 2.86 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= 0.017 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 Ca 1 9.91 5 S 67 5.16 5 C 5219 2.51 5 N 1422 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8223 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "R" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2158 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain breaks: 1 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 107 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.78, per 1000 atoms: 0.22 Number of scatterers: 8223 At special positions: 0 Unit cell: (84.609, 98.532, 128.52, 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) Ca 1 19.99 S 67 16.00 O 1514 8.00 N 1422 7.00 C 5219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 35 " - pdb=" SG CYS R 276 " distance=2.03 Simple disulfide: pdb=" SG CYS R 268 " - pdb=" SG CYS R 274 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 401.8 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 40.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.867A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.802A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.674A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.587A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.558A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.613A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'R' and resid 41 through 65 removed outlier: 4.148A pdb=" N PHE R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 103 removed outlier: 3.702A pdb=" N PHE R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE R 76 " --> pdb=" O PRO R 72 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 148 removed outlier: 3.730A pdb=" N ILE R 113 " --> pdb=" O GLU R 109 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN R 114 " --> pdb=" O ASP R 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS R 115 " --> pdb=" O GLN R 111 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE R 119 " --> pdb=" O HIS R 115 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE R 120 " --> pdb=" O MET R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.505A pdb=" N TYR R 182 " --> pdb=" O VAL R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 223 removed outlier: 4.473A pdb=" N ILE R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL R 190 " --> pdb=" O LYS R 186 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET R 203 " --> pdb=" O MET R 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA R 223 " --> pdb=" O LYS R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 268 removed outlier: 3.932A pdb=" N PHE R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 271 through 279 removed outlier: 4.120A pdb=" N CYS R 276 " --> pdb=" O PRO R 272 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N TYR R 277 " --> pdb=" O TYR R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 removed outlier: 3.889A pdb=" N TYR R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.771A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 39 through 45 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.523A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.828A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.422A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.601A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.810A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.817A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.877A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.911A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.030A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.927A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.695A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1413 1.32 - 1.45: 2263 1.45 - 1.57: 4616 1.57 - 1.69: 0 1.69 - 1.82: 97 Bond restraints: 8389 Sorted by residual: bond pdb=" CA ARG L 7 " pdb=" C ARG L 7 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.24e-02 6.50e+03 1.40e+01 bond pdb=" C HIS L 5 " pdb=" O HIS L 5 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.17e-02 7.31e+03 1.08e+01 bond pdb=" N ARG L 7 " pdb=" CA ARG L 7 " ideal model delta sigma weight residual 1.455 1.419 0.036 1.32e-02 5.74e+03 7.51e+00 bond pdb=" CA HIS L 5 " pdb=" CB HIS L 5 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.44e-02 4.82e+03 5.45e+00 bond pdb=" C HIS L 5 " pdb=" N PHE L 6 " ideal model delta sigma weight residual 1.327 1.303 0.024 1.06e-02 8.90e+03 5.04e+00 ... (remaining 8384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 11138 2.17 - 4.34: 190 4.34 - 6.51: 25 6.51 - 8.67: 5 8.67 - 10.84: 2 Bond angle restraints: 11360 Sorted by residual: angle pdb=" C PHE L 6 " pdb=" CA PHE L 6 " pdb=" CB PHE L 6 " ideal model delta sigma weight residual 116.34 110.74 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" N ARG L 7 " pdb=" CA ARG L 7 " pdb=" C ARG L 7 " ideal model delta sigma weight residual 108.74 113.59 -4.85 1.38e+00 5.25e-01 1.23e+01 angle pdb=" N ASN G 24 " pdb=" CA ASN G 24 " pdb=" C ASN G 24 " ideal model delta sigma weight residual 114.56 110.57 3.99 1.27e+00 6.20e-01 9.85e+00 angle pdb=" C LYS N 33 " pdb=" N MET N 34 " pdb=" CA MET N 34 " ideal model delta sigma weight residual 122.59 118.15 4.44 1.57e+00 4.06e-01 8.00e+00 angle pdb=" CB MET R 97 " pdb=" CG MET R 97 " pdb=" SD MET R 97 " ideal model delta sigma weight residual 112.70 104.34 8.36 3.00e+00 1.11e-01 7.77e+00 ... (remaining 11355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4498 17.49 - 34.97: 413 34.97 - 52.46: 79 52.46 - 69.94: 12 69.94 - 87.42: 8 Dihedral angle restraints: 5010 sinusoidal: 1972 harmonic: 3038 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.72 34.28 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA ASP G 36 " pdb=" C ASP G 36 " pdb=" N LEU G 37 " pdb=" CA LEU G 37 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR R 182 " pdb=" C TYR R 182 " pdb=" N SER R 183 " pdb=" CA SER R 183 " ideal model delta harmonic sigma weight residual 180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 5007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 754 0.037 - 0.074: 378 0.074 - 0.111: 116 0.111 - 0.148: 38 0.148 - 0.185: 5 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA HIS L 5 " pdb=" N HIS L 5 " pdb=" C HIS L 5 " pdb=" CB HIS L 5 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA VAL L 2 " pdb=" N VAL L 2 " pdb=" C VAL L 2 " pdb=" CB VAL L 2 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 1288 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.019 2.00e-02 2.50e+03 1.37e-02 4.69e+00 pdb=" CG TRP A 281 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 256 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO R 257 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO N 14 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.026 5.00e-02 4.00e+02 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 907 2.74 - 3.28: 7965 3.28 - 3.82: 13555 3.82 - 4.36: 16080 4.36 - 4.90: 28045 Nonbonded interactions: 66552 Sorted by model distance: nonbonded pdb=" NE1 TRP R 255 " pdb=" OD1 ASN R 291 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG A 232 " pdb=" OD2 ASP N 109 " model vdw 2.227 3.120 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.228 3.120 nonbonded pdb=" OE2 GLU R 94 " pdb="CA CA R 501 " model vdw 2.243 2.510 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.244 3.040 ... (remaining 66547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.110 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.430 Find NCS groups from input model: 0.030 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:5.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.007 0.056 8393 Z= 0.334 Angle : 0.728 10.843 11368 Z= 0.406 Chirality : 0.049 0.185 1291 Planarity : 0.005 0.049 1444 Dihedral : 14.043 87.425 3030 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.11 % Allowed : 0.55 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.25), residues: 1025 helix: 0.31 (0.26), residues: 401 sheet: -0.75 (0.32), residues: 234 loop : -1.50 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 151 TYR 0.027 0.002 TYR B 59 PHE 0.030 0.002 PHE B 235 TRP 0.037 0.003 TRP A 281 HIS 0.008 0.002 HIS L 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00743 / 0.33 ( 8389) covalent geometry : angle 0.72756 / 0.41 (11360) SS BOND : bond 0.00524 / 0.25 ( 4) SS BOND : angle 1.12209 / 0.51 ( 8) hydrogen bonds : bond 0.11158 / 8.10 ( 408) hydrogen bonds : angle 5.53094 / 3.84 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 240 average time/residue: 0.4864 time to fit residues: 123.8273 Evaluate side-chains 155 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 GLN B 75 GLN B 91 HIS B 155 ASN R 291 ASN G 18 GLN G 24 ASN G 44 HIS L 5 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.127739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090479 restraints weight = 15843.037| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.94 r_work: 0.3153 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8393 Z= 0.142 Angle : 0.674 13.182 11368 Z= 0.339 Chirality : 0.042 0.140 1291 Planarity : 0.004 0.047 1444 Dihedral : 4.947 46.152 1137 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.77 % Allowed : 13.43 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.26), residues: 1025 helix: 1.16 (0.26), residues: 395 sheet: -0.33 (0.34), residues: 225 loop : -1.22 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 280 TYR 0.017 0.001 TYR R 277 PHE 0.013 0.001 PHE R 259 TRP 0.016 0.002 TRP A 234 HIS 0.003 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8389) covalent geometry : angle 0.67345 / 0.34 (11360) SS BOND : bond 0.00075 / 0.04 ( 4) SS BOND : angle 0.74963 / 0.30 ( 8) hydrogen bonds : bond 0.04314 / 3.06 ( 408) hydrogen bonds : angle 4.55439 / 3.15 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8441 (t0) cc_final: 0.7821 (t0) REVERT: A 279 ASN cc_start: 0.9114 (t0) cc_final: 0.8875 (t0) REVERT: A 349 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.8928 (p) REVERT: B 172 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8892 (tp30) REVERT: B 175 GLN cc_start: 0.8780 (mp10) cc_final: 0.8552 (mp10) REVERT: B 260 GLU cc_start: 0.8686 (pp20) cc_final: 0.8363 (tm-30) REVERT: B 280 LYS cc_start: 0.8991 (tptp) cc_final: 0.8567 (tptp) REVERT: B 292 PHE cc_start: 0.9033 (m-10) cc_final: 0.8832 (m-10) REVERT: B 300 LEU cc_start: 0.8803 (mt) cc_final: 0.8531 (mp) REVERT: B 325 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8933 (mpp) REVERT: R 41 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8307 (tmmt) REVERT: R 277 TYR cc_start: 0.8727 (t80) cc_final: 0.8319 (t80) REVERT: R 307 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.8222 (mmm-85) REVERT: G 21 MET cc_start: 0.7998 (tpt) cc_final: 0.7666 (tpt) REVERT: G 24 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8523 (m110) REVERT: G 47 GLU cc_start: 0.8133 (pm20) cc_final: 0.7502 (pm20) outliers start: 25 outliers final: 9 residues processed: 182 average time/residue: 0.4496 time to fit residues: 86.6838 Evaluate side-chains 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 ASN L 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.127041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089847 restraints weight = 15982.737| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.97 r_work: 0.3135 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8393 Z= 0.142 Angle : 0.649 13.357 11368 Z= 0.325 Chirality : 0.042 0.162 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.735 47.507 1135 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.22 % Allowed : 14.76 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.27), residues: 1025 helix: 1.58 (0.27), residues: 391 sheet: -0.25 (0.33), residues: 248 loop : -1.06 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 7 TYR 0.013 0.001 TYR L 1 PHE 0.013 0.001 PHE R 310 TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8389) covalent geometry : angle 0.64861 / 0.32 (11360) SS BOND : bond 0.00098 / 0.05 ( 4) SS BOND : angle 0.59894 / 0.22 ( 8) hydrogen bonds : bond 0.04046 / 2.87 ( 408) hydrogen bonds : angle 4.40594 / 3.05 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8454 (t0) cc_final: 0.7824 (t0) REVERT: A 279 ASN cc_start: 0.9099 (t0) cc_final: 0.8863 (t0) REVERT: A 302 LEU cc_start: 0.9734 (mm) cc_final: 0.9476 (mm) REVERT: A 349 SER cc_start: 0.9282 (OUTLIER) cc_final: 0.8863 (p) REVERT: B 160 SER cc_start: 0.9252 (t) cc_final: 0.8964 (p) REVERT: B 172 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8971 (tp30) REVERT: B 175 GLN cc_start: 0.8778 (mp10) cc_final: 0.8533 (mp10) REVERT: B 227 SER cc_start: 0.8967 (t) cc_final: 0.8740 (p) REVERT: B 259 GLN cc_start: 0.7128 (mt0) cc_final: 0.6821 (mm110) REVERT: B 280 LYS cc_start: 0.8924 (tptp) cc_final: 0.8120 (tptp) REVERT: B 291 ASP cc_start: 0.8912 (m-30) cc_final: 0.8498 (m-30) REVERT: B 292 PHE cc_start: 0.9076 (m-10) cc_final: 0.8811 (m-10) REVERT: R 41 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8107 (ttmt) REVERT: R 65 ARG cc_start: 0.8613 (ttp-170) cc_final: 0.8097 (ttm170) REVERT: R 116 MET cc_start: 0.8536 (tmm) cc_final: 0.8054 (mpt) REVERT: R 277 TYR cc_start: 0.8844 (t80) cc_final: 0.8374 (t80) REVERT: R 305 GLU cc_start: 0.8501 (pm20) cc_final: 0.8184 (pm20) REVERT: G 17 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8457 (pt0) REVERT: G 21 MET cc_start: 0.8297 (tpt) cc_final: 0.7870 (tpt) REVERT: G 24 ASN cc_start: 0.9193 (t0) cc_final: 0.8547 (m110) REVERT: G 38 MET cc_start: 0.9183 (ppp) cc_final: 0.8913 (ppp) REVERT: L 1 TYR cc_start: 0.7092 (t80) cc_final: 0.6751 (t80) outliers start: 29 outliers final: 6 residues processed: 180 average time/residue: 0.4579 time to fit residues: 87.5287 Evaluate side-chains 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.0670 chunk 32 optimal weight: 0.0060 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 371 ASN B 75 GLN B 230 ASN R 291 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.127842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.091635 restraints weight = 16143.343| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 3.86 r_work: 0.3137 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8393 Z= 0.134 Angle : 0.622 13.494 11368 Z= 0.313 Chirality : 0.041 0.185 1291 Planarity : 0.004 0.042 1444 Dihedral : 4.594 47.694 1135 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.11 % Allowed : 17.98 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.27), residues: 1025 helix: 1.65 (0.27), residues: 399 sheet: -0.15 (0.33), residues: 247 loop : -1.01 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 38 TYR 0.010 0.001 TYR L 1 PHE 0.011 0.001 PHE R 259 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8389) covalent geometry : angle 0.62234 / 0.31 (11360) SS BOND : bond 0.00139 / 0.07 ( 4) SS BOND : angle 0.55006 / 0.20 ( 8) hydrogen bonds : bond 0.03857 / 2.75 ( 408) hydrogen bonds : angle 4.25348 / 2.94 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8468 (t0) cc_final: 0.7832 (t0) REVERT: A 253 TYR cc_start: 0.8733 (m-80) cc_final: 0.8197 (m-80) REVERT: A 279 ASN cc_start: 0.9176 (t0) cc_final: 0.8938 (t0) REVERT: A 349 SER cc_start: 0.9348 (OUTLIER) cc_final: 0.8900 (p) REVERT: B 172 GLU cc_start: 0.9251 (mm-30) cc_final: 0.9039 (tp30) REVERT: B 217 MET cc_start: 0.8641 (pmt) cc_final: 0.8094 (pmm) REVERT: B 259 GLN cc_start: 0.6984 (mt0) cc_final: 0.6678 (mm110) REVERT: B 280 LYS cc_start: 0.8925 (tptp) cc_final: 0.8118 (tptp) REVERT: B 291 ASP cc_start: 0.8932 (m-30) cc_final: 0.8528 (m-30) REVERT: B 292 PHE cc_start: 0.9175 (m-10) cc_final: 0.8901 (m-10) REVERT: R 41 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8273 (ttmt) REVERT: R 65 ARG cc_start: 0.8473 (tpp-160) cc_final: 0.8079 (ttm170) REVERT: R 85 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8615 (ppp) REVERT: R 116 MET cc_start: 0.8841 (tmm) cc_final: 0.8065 (tpt) REVERT: R 191 CYS cc_start: 0.8453 (t) cc_final: 0.8118 (t) REVERT: R 277 TYR cc_start: 0.8857 (t80) cc_final: 0.8462 (t80) REVERT: R 281 PHE cc_start: 0.8198 (t80) cc_final: 0.7962 (t80) REVERT: R 305 GLU cc_start: 0.8484 (pm20) cc_final: 0.8047 (pm20) REVERT: R 307 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.7972 (mmm-85) REVERT: G 17 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8540 (pt0) REVERT: G 21 MET cc_start: 0.8326 (tpt) cc_final: 0.7805 (tpt) REVERT: G 24 ASN cc_start: 0.9232 (t0) cc_final: 0.8570 (m110) REVERT: G 38 MET cc_start: 0.9019 (ppp) cc_final: 0.8787 (ppp) REVERT: L 1 TYR cc_start: 0.7286 (t80) cc_final: 0.6975 (t80) outliers start: 28 outliers final: 9 residues processed: 173 average time/residue: 0.4425 time to fit residues: 81.4796 Evaluate side-chains 154 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN B 75 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090534 restraints weight = 16008.396| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.84 r_work: 0.3119 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8393 Z= 0.149 Angle : 0.621 12.481 11368 Z= 0.314 Chirality : 0.042 0.149 1291 Planarity : 0.004 0.044 1444 Dihedral : 4.573 48.121 1135 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.22 % Allowed : 19.76 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.26), residues: 1025 helix: 1.70 (0.26), residues: 399 sheet: -0.09 (0.34), residues: 237 loop : -0.91 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 151 TYR 0.014 0.001 TYR R 74 PHE 0.011 0.001 PHE R 310 TRP 0.011 0.001 TRP A 234 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8389) covalent geometry : angle 0.62055 / 0.31 (11360) SS BOND : bond 0.00047 / 0.02 ( 4) SS BOND : angle 0.58608 / 0.23 ( 8) hydrogen bonds : bond 0.03894 / 2.79 ( 408) hydrogen bonds : angle 4.20571 / 2.91 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8488 (t0) cc_final: 0.7827 (t0) REVERT: A 253 TYR cc_start: 0.8814 (m-80) cc_final: 0.8382 (m-80) REVERT: A 279 ASN cc_start: 0.9188 (t0) cc_final: 0.8949 (t0) REVERT: B 32 GLN cc_start: 0.8889 (mt0) cc_final: 0.8547 (mt0) REVERT: B 172 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8843 (tp30) REVERT: B 175 GLN cc_start: 0.8746 (mp10) cc_final: 0.8523 (mp10) REVERT: B 259 GLN cc_start: 0.7044 (mt0) cc_final: 0.6789 (mm110) REVERT: B 280 LYS cc_start: 0.8964 (tptp) cc_final: 0.8124 (tptp) REVERT: B 292 PHE cc_start: 0.9183 (m-10) cc_final: 0.8917 (m-10) REVERT: R 41 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8303 (ttmt) REVERT: R 65 ARG cc_start: 0.8486 (tpp-160) cc_final: 0.8050 (ttm170) REVERT: R 191 CYS cc_start: 0.8499 (t) cc_final: 0.8158 (t) REVERT: R 253 PHE cc_start: 0.8803 (m-10) cc_final: 0.8059 (t80) REVERT: R 277 TYR cc_start: 0.8855 (t80) cc_final: 0.8424 (t80) REVERT: G 17 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8585 (pt0) REVERT: G 21 MET cc_start: 0.8438 (tpt) cc_final: 0.7937 (tpt) REVERT: G 24 ASN cc_start: 0.9230 (t0) cc_final: 0.8587 (m110) REVERT: G 28 ILE cc_start: 0.8754 (mp) cc_final: 0.8362 (mp) REVERT: G 38 MET cc_start: 0.9041 (ppp) cc_final: 0.8786 (ppp) REVERT: G 47 GLU cc_start: 0.8135 (pm20) cc_final: 0.7742 (pm20) REVERT: N 47 TRP cc_start: 0.8077 (t60) cc_final: 0.7873 (t60) outliers start: 29 outliers final: 16 residues processed: 163 average time/residue: 0.4421 time to fit residues: 76.7641 Evaluate side-chains 161 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.126759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.089220 restraints weight = 15830.895| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.88 r_work: 0.3126 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8393 Z= 0.138 Angle : 0.639 13.929 11368 Z= 0.318 Chirality : 0.042 0.151 1291 Planarity : 0.004 0.044 1444 Dihedral : 4.541 47.895 1135 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.00 % Allowed : 19.98 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1025 helix: 1.71 (0.26), residues: 399 sheet: 0.03 (0.33), residues: 245 loop : -0.92 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 151 TYR 0.016 0.001 TYR L 1 PHE 0.011 0.001 PHE B 199 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8389) covalent geometry : angle 0.63940 / 0.32 (11360) SS BOND : bond 0.00132 / 0.07 ( 4) SS BOND : angle 0.59910 / 0.25 ( 8) hydrogen bonds : bond 0.03809 / 2.72 ( 408) hydrogen bonds : angle 4.20300 / 2.91 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8516 (t0) cc_final: 0.7826 (t0) REVERT: A 253 TYR cc_start: 0.8806 (m-80) cc_final: 0.8480 (m-80) REVERT: A 279 ASN cc_start: 0.9188 (t0) cc_final: 0.8944 (t0) REVERT: B 32 GLN cc_start: 0.8839 (mt0) cc_final: 0.8450 (mt0) REVERT: B 59 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.8453 (m-80) REVERT: B 172 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8846 (tp30) REVERT: B 175 GLN cc_start: 0.8748 (mp10) cc_final: 0.8531 (mp10) REVERT: B 217 MET cc_start: 0.8752 (pmt) cc_final: 0.8273 (pmm) REVERT: B 234 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: B 262 MET cc_start: 0.8442 (mpp) cc_final: 0.8119 (pmm) REVERT: B 280 LYS cc_start: 0.8920 (tptp) cc_final: 0.8136 (tptp) REVERT: B 291 ASP cc_start: 0.8922 (m-30) cc_final: 0.8540 (m-30) REVERT: B 292 PHE cc_start: 0.9213 (m-10) cc_final: 0.8941 (m-10) REVERT: R 156 MET cc_start: 0.8578 (tpp) cc_final: 0.8282 (tpp) REVERT: R 191 CYS cc_start: 0.8498 (t) cc_final: 0.8159 (t) REVERT: R 253 PHE cc_start: 0.8832 (m-10) cc_final: 0.8087 (t80) REVERT: R 277 TYR cc_start: 0.8839 (t80) cc_final: 0.8507 (t80) REVERT: R 291 ASN cc_start: 0.8090 (t0) cc_final: 0.7741 (t0) REVERT: R 307 ARG cc_start: 0.8484 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: G 17 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8624 (pt0) REVERT: G 21 MET cc_start: 0.8410 (tpt) cc_final: 0.7915 (tpt) REVERT: G 24 ASN cc_start: 0.9201 (t0) cc_final: 0.8597 (m110) REVERT: G 28 ILE cc_start: 0.8796 (mp) cc_final: 0.8407 (mp) REVERT: G 38 MET cc_start: 0.9016 (ppp) cc_final: 0.8749 (ppp) REVERT: G 47 GLU cc_start: 0.8194 (pm20) cc_final: 0.7784 (pm20) REVERT: N 83 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7472 (mmt) outliers start: 27 outliers final: 13 residues processed: 169 average time/residue: 0.4424 time to fit residues: 79.6110 Evaluate side-chains 162 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 0.0980 chunk 96 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 63 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN B 75 GLN R 70 HIS N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090058 restraints weight = 15937.697| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.90 r_work: 0.3154 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8393 Z= 0.121 Angle : 0.639 13.984 11368 Z= 0.317 Chirality : 0.042 0.166 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.448 47.530 1135 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.66 % Allowed : 21.09 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.26), residues: 1025 helix: 1.78 (0.27), residues: 399 sheet: 0.14 (0.33), residues: 243 loop : -0.95 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 151 TYR 0.017 0.001 TYR L 1 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP N 47 HIS 0.002 0.000 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 8389) covalent geometry : angle 0.63946 / 0.32 (11360) SS BOND : bond 0.00114 / 0.06 ( 4) SS BOND : angle 0.57640 / 0.26 ( 8) hydrogen bonds : bond 0.03641 / 2.58 ( 408) hydrogen bonds : angle 4.16494 / 2.89 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8535 (t0) cc_final: 0.7871 (t0) REVERT: A 253 TYR cc_start: 0.8748 (m-80) cc_final: 0.8387 (m-80) REVERT: A 279 ASN cc_start: 0.9200 (t0) cc_final: 0.8935 (t0) REVERT: B 32 GLN cc_start: 0.8814 (mt0) cc_final: 0.8461 (mt0) REVERT: B 172 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8855 (tp30) REVERT: B 175 GLN cc_start: 0.8740 (mp10) cc_final: 0.8506 (mp10) REVERT: B 217 MET cc_start: 0.8761 (pmt) cc_final: 0.8265 (pmm) REVERT: B 234 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: B 280 LYS cc_start: 0.8927 (tptp) cc_final: 0.7945 (tptp) REVERT: B 291 ASP cc_start: 0.8918 (m-30) cc_final: 0.8532 (m-30) REVERT: B 292 PHE cc_start: 0.9198 (m-10) cc_final: 0.8930 (m-10) REVERT: B 325 MET cc_start: 0.8919 (mmt) cc_final: 0.8631 (mmm) REVERT: R 41 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7859 (tmmm) REVERT: R 73 MET cc_start: 0.8883 (ptm) cc_final: 0.8273 (ppp) REVERT: R 116 MET cc_start: 0.8334 (ppp) cc_final: 0.7805 (mmt) REVERT: R 156 MET cc_start: 0.8542 (tpp) cc_final: 0.8222 (tpp) REVERT: R 191 CYS cc_start: 0.8451 (t) cc_final: 0.8120 (t) REVERT: R 253 PHE cc_start: 0.8806 (m-10) cc_final: 0.8003 (t80) REVERT: R 277 TYR cc_start: 0.8833 (t80) cc_final: 0.8448 (t80) REVERT: R 305 GLU cc_start: 0.8462 (pm20) cc_final: 0.8073 (pm20) REVERT: R 307 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.8018 (mmm-85) REVERT: G 17 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8686 (pt0) REVERT: G 21 MET cc_start: 0.8525 (tpt) cc_final: 0.8047 (tpt) REVERT: G 24 ASN cc_start: 0.9132 (t0) cc_final: 0.8577 (m-40) REVERT: G 28 ILE cc_start: 0.8818 (mp) cc_final: 0.8411 (mp) REVERT: G 38 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8714 (ppp) REVERT: G 47 GLU cc_start: 0.8246 (pm20) cc_final: 0.7838 (pm20) REVERT: N 47 TRP cc_start: 0.8356 (t60) cc_final: 0.8131 (t60) REVERT: N 83 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7481 (mmt) outliers start: 24 outliers final: 11 residues processed: 169 average time/residue: 0.4833 time to fit residues: 86.6277 Evaluate side-chains 161 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 41 LYS Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN R 37 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.124410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086267 restraints weight = 16054.778| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.92 r_work: 0.3086 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8393 Z= 0.193 Angle : 0.668 13.350 11368 Z= 0.337 Chirality : 0.043 0.158 1291 Planarity : 0.004 0.048 1444 Dihedral : 4.579 48.930 1135 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.66 % Allowed : 21.53 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.26), residues: 1025 helix: 1.76 (0.26), residues: 399 sheet: 0.09 (0.34), residues: 236 loop : -0.84 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 151 TYR 0.018 0.001 TYR L 1 PHE 0.014 0.002 PHE B 199 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 8389) covalent geometry : angle 0.66804 / 0.34 (11360) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 0.73488 / 0.33 ( 8) hydrogen bonds : bond 0.04142 / 2.95 ( 408) hydrogen bonds : angle 4.32243 / 3.00 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8589 (t0) cc_final: 0.7931 (t0) REVERT: A 253 TYR cc_start: 0.8915 (m-80) cc_final: 0.8530 (m-80) REVERT: A 268 GLU cc_start: 0.8713 (mp0) cc_final: 0.8506 (tp30) REVERT: A 279 ASN cc_start: 0.9193 (t0) cc_final: 0.8943 (t0) REVERT: B 32 GLN cc_start: 0.8896 (mt0) cc_final: 0.8588 (mt0) REVERT: B 172 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8976 (tp30) REVERT: B 175 GLN cc_start: 0.8785 (mp10) cc_final: 0.8530 (mp10) REVERT: B 217 MET cc_start: 0.8717 (pmt) cc_final: 0.8188 (pmm) REVERT: B 234 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: B 259 GLN cc_start: 0.7278 (mt0) cc_final: 0.6854 (mm-40) REVERT: B 280 LYS cc_start: 0.8991 (tptp) cc_final: 0.8262 (tptp) REVERT: B 291 ASP cc_start: 0.8939 (m-30) cc_final: 0.8539 (m-30) REVERT: B 292 PHE cc_start: 0.9223 (m-10) cc_final: 0.8983 (m-10) REVERT: B 325 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8711 (mmm) REVERT: R 41 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7929 (tmmm) REVERT: R 73 MET cc_start: 0.8906 (ptm) cc_final: 0.8226 (ppp) REVERT: R 84 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8508 (t70) REVERT: R 115 HIS cc_start: 0.7799 (OUTLIER) cc_final: 0.7177 (m90) REVERT: R 116 MET cc_start: 0.8422 (ppp) cc_final: 0.7830 (mmt) REVERT: R 156 MET cc_start: 0.8614 (tpp) cc_final: 0.8305 (tpp) REVERT: R 191 CYS cc_start: 0.8584 (t) cc_final: 0.8224 (t) REVERT: R 253 PHE cc_start: 0.8833 (m-10) cc_final: 0.8105 (t80) REVERT: R 277 TYR cc_start: 0.8893 (t80) cc_final: 0.8477 (t80) REVERT: R 291 ASN cc_start: 0.8166 (t0) cc_final: 0.7836 (t0) REVERT: G 17 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8698 (pt0) REVERT: G 21 MET cc_start: 0.8631 (tpt) cc_final: 0.8158 (tpt) REVERT: G 24 ASN cc_start: 0.9122 (t0) cc_final: 0.8601 (m110) REVERT: G 28 ILE cc_start: 0.8755 (mp) cc_final: 0.8337 (mp) REVERT: G 38 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8741 (ppp) REVERT: G 47 GLU cc_start: 0.8271 (pm20) cc_final: 0.7948 (pm20) REVERT: N 83 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7483 (mmt) outliers start: 24 outliers final: 10 residues processed: 153 average time/residue: 0.5715 time to fit residues: 92.7144 Evaluate side-chains 154 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 41 LYS Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 115 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN B 75 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.124944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087160 restraints weight = 16096.709| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 3.89 r_work: 0.3101 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8393 Z= 0.170 Angle : 0.684 12.729 11368 Z= 0.346 Chirality : 0.042 0.140 1291 Planarity : 0.004 0.047 1444 Dihedral : 4.565 48.806 1135 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.89 % Allowed : 21.53 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.27), residues: 1025 helix: 1.63 (0.26), residues: 403 sheet: 0.06 (0.34), residues: 237 loop : -0.78 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 151 TYR 0.020 0.001 TYR L 1 PHE 0.013 0.002 PHE B 199 TRP 0.011 0.001 TRP A 234 HIS 0.002 0.001 HIS R 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 8389) covalent geometry : angle 0.68423 / 0.35 (11360) SS BOND : bond 0.00094 / 0.05 ( 4) SS BOND : angle 0.78404 / 0.37 ( 8) hydrogen bonds : bond 0.04006 / 2.86 ( 408) hydrogen bonds : angle 4.35705 / 3.02 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8549 (t0) cc_final: 0.7951 (t0) REVERT: A 253 TYR cc_start: 0.8839 (m-80) cc_final: 0.8397 (m-80) REVERT: A 279 ASN cc_start: 0.9206 (t0) cc_final: 0.8941 (t0) REVERT: B 32 GLN cc_start: 0.8895 (mt0) cc_final: 0.8558 (mt0) REVERT: B 172 GLU cc_start: 0.9226 (mm-30) cc_final: 0.9013 (tp30) REVERT: B 175 GLN cc_start: 0.8787 (mp10) cc_final: 0.8527 (mp10) REVERT: B 217 MET cc_start: 0.8746 (pmt) cc_final: 0.8218 (pmm) REVERT: B 234 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: B 280 LYS cc_start: 0.8974 (tptp) cc_final: 0.8370 (tptp) REVERT: B 291 ASP cc_start: 0.8945 (m-30) cc_final: 0.8550 (m-30) REVERT: B 292 PHE cc_start: 0.9218 (m-10) cc_final: 0.8981 (m-10) REVERT: B 325 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8683 (mmm) REVERT: R 41 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7937 (tmmm) REVERT: R 73 MET cc_start: 0.8939 (ptm) cc_final: 0.8266 (ppp) REVERT: R 84 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8377 (t0) REVERT: R 97 MET cc_start: 0.8667 (tpp) cc_final: 0.8467 (tpt) REVERT: R 115 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7184 (m90) REVERT: R 116 MET cc_start: 0.8348 (ppp) cc_final: 0.7971 (mmt) REVERT: R 117 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7445 (t0) REVERT: R 156 MET cc_start: 0.8605 (tpp) cc_final: 0.8309 (tpp) REVERT: R 191 CYS cc_start: 0.8591 (t) cc_final: 0.8230 (t) REVERT: R 253 PHE cc_start: 0.8860 (m-10) cc_final: 0.8128 (t80) REVERT: R 277 TYR cc_start: 0.8889 (t80) cc_final: 0.8501 (t80) REVERT: R 291 ASN cc_start: 0.8090 (t0) cc_final: 0.7745 (t0) REVERT: G 17 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8702 (pt0) REVERT: G 21 MET cc_start: 0.8677 (tpt) cc_final: 0.8361 (tpt) REVERT: G 28 ILE cc_start: 0.8823 (mp) cc_final: 0.8427 (mp) REVERT: G 37 LEU cc_start: 0.7705 (mm) cc_final: 0.7463 (mm) REVERT: G 38 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8445 (ppp) REVERT: G 47 GLU cc_start: 0.8397 (pm20) cc_final: 0.8167 (pm20) REVERT: L 3 MET cc_start: 0.8048 (tpt) cc_final: 0.7767 (tpt) REVERT: N 83 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7637 (mmt) REVERT: N 117 TYR cc_start: 0.8140 (m-80) cc_final: 0.7905 (m-10) outliers start: 26 outliers final: 11 residues processed: 154 average time/residue: 0.5204 time to fit residues: 85.2833 Evaluate side-chains 159 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 41 LYS Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 115 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 291 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 = 0.3900 r_free = 0.3900 target = 0.128865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091572 restraints weight = 15888.177| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.90 r_work: 0.3096 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8393 Z= 0.161 Angle : 0.692 12.888 11368 Z= 0.348 Chirality : 0.042 0.158 1291 Planarity : 0.004 0.046 1444 Dihedral : 4.582 48.701 1135 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.33 % Allowed : 22.53 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.27), residues: 1025 helix: 1.59 (0.26), residues: 406 sheet: 0.07 (0.34), residues: 237 loop : -0.75 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 151 TYR 0.022 0.001 TYR R 74 PHE 0.013 0.001 PHE B 199 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 8389) covalent geometry : angle 0.69194 / 0.35 (11360) SS BOND : bond 0.00128 / 0.06 ( 4) SS BOND : angle 0.94230 / 0.48 ( 8) hydrogen bonds : bond 0.04010 / 2.86 ( 408) hydrogen bonds : angle 4.36111 / 3.03 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8586 (t0) cc_final: 0.7998 (t0) REVERT: A 253 TYR cc_start: 0.8952 (m-80) cc_final: 0.8526 (m-80) REVERT: A 279 ASN cc_start: 0.9179 (t0) cc_final: 0.8891 (t0) REVERT: B 23 LYS cc_start: 0.9107 (pmmt) cc_final: 0.8868 (pmmt) REVERT: B 32 GLN cc_start: 0.8958 (mt0) cc_final: 0.8644 (mt0) REVERT: B 172 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8982 (tp30) REVERT: B 175 GLN cc_start: 0.8790 (mp10) cc_final: 0.8539 (mp10) REVERT: B 217 MET cc_start: 0.8736 (pmt) cc_final: 0.8186 (pmm) REVERT: B 234 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: B 280 LYS cc_start: 0.8955 (tptp) cc_final: 0.8327 (tptp) REVERT: B 291 ASP cc_start: 0.8970 (m-30) cc_final: 0.8531 (m-30) REVERT: B 292 PHE cc_start: 0.9278 (m-10) cc_final: 0.9043 (m-10) REVERT: B 325 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8678 (mmm) REVERT: R 41 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7919 (tmmm) REVERT: R 73 MET cc_start: 0.9032 (ptm) cc_final: 0.8366 (ppp) REVERT: R 84 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8404 (t0) REVERT: R 115 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7154 (m-70) REVERT: R 116 MET cc_start: 0.8323 (ppp) cc_final: 0.7871 (mmt) REVERT: R 117 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7416 (t0) REVERT: R 156 MET cc_start: 0.8630 (tpp) cc_final: 0.8340 (tpp) REVERT: R 171 CYS cc_start: 0.8901 (m) cc_final: 0.8584 (m) REVERT: R 191 CYS cc_start: 0.8556 (t) cc_final: 0.8195 (t) REVERT: R 253 PHE cc_start: 0.8867 (m-10) cc_final: 0.8109 (t80) REVERT: R 277 TYR cc_start: 0.8881 (t80) cc_final: 0.8481 (t80) REVERT: G 28 ILE cc_start: 0.8818 (mp) cc_final: 0.8453 (mp) REVERT: G 47 GLU cc_start: 0.8437 (pm20) cc_final: 0.8173 (pm20) REVERT: N 83 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7639 (mmt) REVERT: N 117 TYR cc_start: 0.8104 (m-80) cc_final: 0.7832 (m-10) outliers start: 21 outliers final: 10 residues processed: 150 average time/residue: 0.5669 time to fit residues: 90.3576 Evaluate side-chains 154 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 41 LYS Chi-restraints excluded: chain R residue 84 ASP Chi-restraints excluded: chain R residue 102 HIS Chi-restraints excluded: chain R residue 115 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 245 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 91 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.092018 restraints weight = 16086.776| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.93 r_work: 0.3156 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8393 Z= 0.149 Angle : 0.703 12.449 11368 Z= 0.351 Chirality : 0.042 0.165 1291 Planarity : 0.004 0.044 1444 Dihedral : 4.573 48.319 1135 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.44 % Allowed : 22.86 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.27), residues: 1025 helix: 1.67 (0.27), residues: 400 sheet: 0.23 (0.33), residues: 244 loop : -0.73 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 151 TYR 0.020 0.001 TYR L 1 PHE 0.012 0.001 PHE B 199 TRP 0.010 0.001 TRP A 234 HIS 0.002 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 8389) covalent geometry : angle 0.70274 / 0.35 (11360) SS BOND : bond 0.00101 / 0.05 ( 4) SS BOND : angle 0.87203 / 0.45 ( 8) hydrogen bonds : bond 0.03934 / 2.81 ( 408) hydrogen bonds : angle 4.36246 / 3.04 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2897.52 seconds wall clock time: 49 minutes 57.23 seconds (2997.23 seconds total)