Starting phenix.real_space_refine on Fri Aug 22 21:58:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ioc_35615/08_2025/8ioc_35615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ioc_35615/08_2025/8ioc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2025/8ioc_35615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2025/8ioc_35615.map" model { file = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2025/8ioc_35615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ioc_35615/08_2025/8ioc_35615.cif" } 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-2.0-5787/lib/python3.9/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: 2.11, per 1000 atoms: 0.26 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: 0.68 Conformation dependent library (CDL) restraints added in 476.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.41 Time building geometry restraints manager: 0.92 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.570 Find NCS groups from input model: 0.020 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:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 aren 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 covalent geometry : bond 0.00743 ( 8389) covalent geometry : angle 0.72756 (11360) SS BOND : bond 0.00524 ( 4) SS BOND : angle 1.12209 ( 8) hydrogen bonds : bond 0.11158 ( 408) hydrogen bonds : angle 5.53094 ( 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 : 0.336 Fit side-chains revert: symmetry clash 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: 0.6493 time to fit residues: 164.6940 Evaluate side-chains 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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: 0.3980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 75 GLN B 91 HIS B 155 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3913 r_free = 0.3913 target = 0.128088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.090854 restraints weight = 15806.602| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.95 r_work: 0.3158 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2639 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 : 0.673 13.315 11368 Z= 0.338 Chirality : 0.042 0.142 1291 Planarity : 0.004 0.046 1444 Dihedral : 4.920 46.068 1137 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.00 % Allowed : 13.32 % Favored : 83.68 % 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 aren not related in a simple way. whole: -0.12 (0.26), residues: 1025 helix: 1.19 (0.26), residues: 395 sheet: -0.28 (0.34), residues: 223 loop : -1.19 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 280 TYR 0.015 0.001 TYR R 277 PHE 0.013 0.001 PHE R 259 TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8389) covalent geometry : angle 0.67281 (11360) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.74557 ( 8) hydrogen bonds : bond 0.04251 ( 408) hydrogen bonds : angle 4.53869 ( 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 203 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8442 (t0) cc_final: 0.7804 (t0) REVERT: A 279 ASN cc_start: 0.9108 (t0) cc_final: 0.8865 (t0) REVERT: B 172 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8911 (tp30) REVERT: B 175 GLN cc_start: 0.8773 (mp10) cc_final: 0.8546 (mp10) REVERT: B 227 SER cc_start: 0.8937 (t) cc_final: 0.8620 (p) REVERT: B 260 GLU cc_start: 0.8737 (pp20) cc_final: 0.8411 (tm-30) REVERT: B 280 LYS cc_start: 0.9002 (tptp) cc_final: 0.8489 (tptp) REVERT: B 292 PHE cc_start: 0.9027 (m-10) cc_final: 0.8823 (m-10) REVERT: B 300 LEU cc_start: 0.8806 (mt) cc_final: 0.8534 (mp) REVERT: B 325 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8875 (mpp) REVERT: R 41 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8286 (tmmt) REVERT: R 85 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8563 (ppp) REVERT: R 277 TYR cc_start: 0.8715 (t80) cc_final: 0.8262 (t80) REVERT: R 307 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8226 (mmm-85) REVERT: G 17 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8471 (pt0) REVERT: G 21 MET cc_start: 0.7981 (tpt) cc_final: 0.7625 (tpt) REVERT: G 24 ASN cc_start: 0.9164 (t160) cc_final: 0.8501 (m110) REVERT: G 47 GLU cc_start: 0.8103 (pm20) cc_final: 0.7694 (pm20) outliers start: 27 outliers final: 11 residues processed: 188 average time/residue: 0.6721 time to fit residues: 133.3824 Evaluate side-chains 158 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 A residue 366 SER Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 96 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 20 optimal weight: 0.0270 chunk 65 optimal weight: 1.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 291 ASN G 24 ASN L 5 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.127334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.090833 restraints weight = 16010.244| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.92 r_work: 0.3134 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8393 Z= 0.154 Angle : 0.651 13.342 11368 Z= 0.324 Chirality : 0.042 0.157 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.714 47.687 1135 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.44 % Allowed : 14.87 % Favored : 81.69 % 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 aren not related in a simple way. whole: 0.17 (0.26), residues: 1025 helix: 1.54 (0.27), residues: 391 sheet: -0.28 (0.33), residues: 239 loop : -1.04 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 7 TYR 0.012 0.001 TYR L 1 PHE 0.012 0.001 PHE R 310 TRP 0.014 0.001 TRP A 234 HIS 0.008 0.001 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8389) covalent geometry : angle 0.65121 (11360) SS BOND : bond 0.00067 ( 4) SS BOND : angle 0.58648 ( 8) hydrogen bonds : bond 0.04094 ( 408) hydrogen bonds : angle 4.42466 ( 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 190 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8472 (t0) cc_final: 0.7854 (t0) REVERT: A 279 ASN cc_start: 0.9110 (t0) cc_final: 0.8864 (t0) REVERT: A 302 LEU cc_start: 0.9731 (mm) cc_final: 0.9473 (mm) REVERT: A 349 SER cc_start: 0.9288 (OUTLIER) cc_final: 0.8873 (p) REVERT: B 160 SER cc_start: 0.9255 (t) cc_final: 0.8974 (p) REVERT: B 172 GLU cc_start: 0.9263 (mm-30) cc_final: 0.8967 (tp30) REVERT: B 175 GLN cc_start: 0.8776 (mp10) cc_final: 0.8550 (mp10) REVERT: B 227 SER cc_start: 0.8941 (t) cc_final: 0.8683 (p) REVERT: B 280 LYS cc_start: 0.8964 (tptp) cc_final: 0.8336 (tptp) REVERT: B 292 PHE cc_start: 0.9072 (m-10) cc_final: 0.8813 (m-10) REVERT: R 41 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8159 (tmmt) REVERT: R 65 ARG cc_start: 0.8594 (ttp-170) cc_final: 0.8093 (ttm170) REVERT: R 85 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8501 (ppp) REVERT: R 116 MET cc_start: 0.8602 (tmm) cc_final: 0.8027 (mpt) REVERT: R 277 TYR cc_start: 0.8807 (t80) cc_final: 0.8360 (t80) REVERT: R 305 GLU cc_start: 0.8460 (pm20) cc_final: 0.8099 (pm20) REVERT: R 307 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8412 (mmm-85) REVERT: G 17 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8463 (pt0) REVERT: G 21 MET cc_start: 0.8284 (tpt) cc_final: 0.7823 (tpt) REVERT: G 24 ASN cc_start: 0.9256 (t0) cc_final: 0.8750 (m110) REVERT: G 38 MET cc_start: 0.9221 (ppp) cc_final: 0.8948 (ppp) REVERT: G 47 GLU cc_start: 0.8035 (pm20) cc_final: 0.7807 (pm20) REVERT: L 1 TYR cc_start: 0.7088 (t80) cc_final: 0.6763 (t80) outliers start: 31 outliers final: 7 residues processed: 171 average time/residue: 0.6506 time to fit residues: 117.6547 Evaluate side-chains 153 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 R residue 73 MET Chi-restraints excluded: chain R residue 85 MET Chi-restraints excluded: chain R residue 96 ILE 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: 0.7980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 371 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3911 r_free = 0.3911 target = 0.127198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090225 restraints weight = 16147.920| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.91 r_work: 0.3148 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3570 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= 0.125 Angle : 0.618 13.604 11368 Z= 0.310 Chirality : 0.041 0.145 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.536 47.229 1135 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.89 % Allowed : 17.31 % Favored : 79.80 % 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 aren not related in a simple way. whole: 0.38 (0.27), residues: 1025 helix: 1.65 (0.27), residues: 399 sheet: -0.11 (0.33), residues: 245 loop : -0.96 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 151 TYR 0.009 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 covalent geometry : bond 0.00280 ( 8389) covalent geometry : angle 0.61803 (11360) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.54253 ( 8) hydrogen bonds : bond 0.03743 ( 408) hydrogen bonds : angle 4.24691 ( 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 188 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8453 (t0) cc_final: 0.7815 (t0) REVERT: A 253 TYR cc_start: 0.8681 (m-80) cc_final: 0.8035 (m-80) REVERT: A 279 ASN cc_start: 0.9161 (t0) cc_final: 0.8918 (t0) REVERT: A 349 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.8888 (p) REVERT: B 175 GLN cc_start: 0.8760 (mp10) cc_final: 0.8491 (mp10) REVERT: B 259 GLN cc_start: 0.7121 (mt0) cc_final: 0.6808 (mm110) REVERT: B 280 LYS cc_start: 0.8925 (tptp) cc_final: 0.8227 (tptp) REVERT: B 291 ASP cc_start: 0.8921 (m-30) cc_final: 0.8529 (m-30) REVERT: B 292 PHE cc_start: 0.9181 (m-10) cc_final: 0.8916 (m-10) REVERT: R 41 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8411 (ttmt) REVERT: R 65 ARG cc_start: 0.8473 (tpp-160) cc_final: 0.8083 (ttm170) REVERT: R 191 CYS cc_start: 0.8437 (t) cc_final: 0.8105 (t) REVERT: R 277 TYR cc_start: 0.8852 (t80) cc_final: 0.8433 (t80) REVERT: R 281 PHE cc_start: 0.8190 (t80) cc_final: 0.7981 (t80) REVERT: R 304 LEU cc_start: 0.9289 (mt) cc_final: 0.9088 (mm) REVERT: R 305 GLU cc_start: 0.8440 (pm20) cc_final: 0.7958 (pm20) REVERT: R 307 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8156 (mmm-85) REVERT: G 17 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8542 (pt0) REVERT: G 21 MET cc_start: 0.8387 (tpt) cc_final: 0.7872 (tpt) REVERT: G 24 ASN cc_start: 0.9148 (t0) cc_final: 0.8707 (m110) REVERT: G 38 MET cc_start: 0.8969 (ppp) cc_final: 0.8744 (ppp) REVERT: L 1 TYR cc_start: 0.7282 (t80) cc_final: 0.6963 (t80) outliers start: 26 outliers final: 5 residues processed: 176 average time/residue: 0.6308 time to fit residues: 117.6402 Evaluate side-chains 146 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 140 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain R residue 102 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 88 optimal weight: 0.0170 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3900 r_free = 0.3900 target = 0.126776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.089598 restraints weight = 15936.444| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.87 r_work: 0.3142 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8393 Z= 0.130 Angle : 0.614 12.461 11368 Z= 0.309 Chirality : 0.042 0.151 1291 Planarity : 0.004 0.043 1444 Dihedral : 4.479 47.641 1135 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.77 % Allowed : 19.87 % Favored : 77.36 % 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 aren not related in a simple way. whole: 0.50 (0.27), residues: 1025 helix: 1.74 (0.27), residues: 399 sheet: -0.09 (0.33), residues: 245 loop : -0.86 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 151 TYR 0.014 0.001 TYR R 74 PHE 0.012 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 covalent geometry : bond 0.00296 ( 8389) covalent geometry : angle 0.61452 (11360) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.53787 ( 8) hydrogen bonds : bond 0.03727 ( 408) hydrogen bonds : angle 4.20567 ( 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 172 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9333 (pptt) cc_final: 0.9032 (pptt) REVERT: A 229 ASP cc_start: 0.8485 (t0) cc_final: 0.7821 (t0) REVERT: A 253 TYR cc_start: 0.8798 (m-80) cc_final: 0.8513 (m-80) REVERT: A 279 ASN cc_start: 0.9180 (t0) cc_final: 0.8942 (t0) REVERT: B 175 GLN cc_start: 0.8745 (mp10) cc_final: 0.8454 (mp10) REVERT: B 259 GLN cc_start: 0.6951 (mt0) cc_final: 0.6650 (mm110) REVERT: B 280 LYS cc_start: 0.8964 (tptp) cc_final: 0.8358 (tptp) REVERT: B 292 PHE cc_start: 0.9185 (m-10) cc_final: 0.8928 (m-10) REVERT: R 41 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8165 (ttmt) REVERT: R 65 ARG cc_start: 0.8462 (tpp-160) cc_final: 0.8034 (ttm170) REVERT: R 191 CYS cc_start: 0.8438 (t) cc_final: 0.8097 (t) REVERT: R 253 PHE cc_start: 0.8805 (m-10) cc_final: 0.8057 (t80) REVERT: R 277 TYR cc_start: 0.8851 (t80) cc_final: 0.8466 (t80) REVERT: R 281 PHE cc_start: 0.8224 (t80) cc_final: 0.8017 (t80) REVERT: G 17 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8557 (pt0) REVERT: G 21 MET cc_start: 0.8567 (tpt) cc_final: 0.8305 (tpt) REVERT: G 28 ILE cc_start: 0.8713 (mp) cc_final: 0.8304 (mp) REVERT: G 38 MET cc_start: 0.9007 (ppp) cc_final: 0.8779 (ppp) REVERT: L 1 TYR cc_start: 0.7345 (t80) cc_final: 0.7000 (t80) REVERT: N 47 TRP cc_start: 0.8282 (t60) cc_final: 0.7979 (t60) outliers start: 25 outliers final: 16 residues processed: 160 average time/residue: 0.6411 time to fit residues: 108.5989 Evaluate side-chains 158 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 260 GLU 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 G residue 19 LEU Chi-restraints excluded: chain G residue 51 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: 5.9990 chunk 33 optimal weight: 0.6980 chunk 92 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 64 optimal weight: 0.1980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 75 GLN ** R 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.125120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088530 restraints weight = 16055.745| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.80 r_work: 0.3088 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 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 : 0.005 0.043 8393 Z= 0.210 Angle : 0.673 14.083 11368 Z= 0.338 Chirality : 0.043 0.132 1291 Planarity : 0.004 0.047 1444 Dihedral : 4.666 49.084 1135 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.11 % Allowed : 20.53 % Favored : 76.36 % 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 aren not related in a simple way. whole: 0.47 (0.27), residues: 1025 helix: 1.63 (0.26), residues: 405 sheet: -0.08 (0.34), residues: 234 loop : -0.81 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 151 TYR 0.011 0.001 TYR R 207 PHE 0.015 0.002 PHE B 199 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 217 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 8389) covalent geometry : angle 0.67300 (11360) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.68515 ( 8) hydrogen bonds : bond 0.04188 ( 408) hydrogen bonds : angle 4.40719 ( 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 176 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8762 (tt0) cc_final: 0.8534 (tt0) REVERT: A 229 ASP cc_start: 0.8563 (t0) cc_final: 0.7937 (t0) REVERT: A 253 TYR cc_start: 0.8911 (m-80) cc_final: 0.8517 (m-80) REVERT: A 279 ASN cc_start: 0.9195 (t0) cc_final: 0.8945 (t0) REVERT: B 32 GLN cc_start: 0.8860 (mt0) cc_final: 0.8659 (mt0) REVERT: B 175 GLN cc_start: 0.8769 (mp10) cc_final: 0.8436 (mp10) REVERT: B 226 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 234 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: B 280 LYS cc_start: 0.9005 (tptp) cc_final: 0.8249 (tptp) REVERT: B 292 PHE cc_start: 0.9189 (m-10) cc_final: 0.8948 (m-10) REVERT: R 41 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8315 (ttmt) REVERT: R 156 MET cc_start: 0.8601 (tpp) cc_final: 0.8324 (tpp) REVERT: R 191 CYS cc_start: 0.8583 (t) cc_final: 0.8235 (t) REVERT: R 253 PHE cc_start: 0.8841 (m-10) cc_final: 0.8109 (t80) REVERT: R 277 TYR cc_start: 0.8876 (t80) cc_final: 0.8443 (t80) REVERT: R 307 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8425 (mmm-85) REVERT: G 17 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8592 (pt0) REVERT: G 21 MET cc_start: 0.8665 (tpt) cc_final: 0.8455 (tpt) REVERT: G 28 ILE cc_start: 0.8801 (mp) cc_final: 0.8333 (mp) REVERT: G 38 MET cc_start: 0.9004 (ppp) cc_final: 0.8795 (ppp) outliers start: 28 outliers final: 14 residues processed: 163 average time/residue: 0.6449 time to fit residues: 111.2250 Evaluate side-chains 157 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 R residue 59 VAL 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 R residue 168 ILE Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.129831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092845 restraints weight = 16049.786| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.90 r_work: 0.3125 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8393 Z= 0.135 Angle : 0.657 12.994 11368 Z= 0.328 Chirality : 0.042 0.138 1291 Planarity : 0.004 0.046 1444 Dihedral : 4.545 47.853 1135 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.55 % Allowed : 21.98 % Favored : 75.47 % 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 aren not related in a simple way. whole: 0.59 (0.27), residues: 1025 helix: 1.76 (0.26), residues: 404 sheet: 0.03 (0.33), residues: 243 loop : -0.82 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 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 0.003 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8389) covalent geometry : angle 0.65659 (11360) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.62369 ( 8) hydrogen bonds : bond 0.03802 ( 408) hydrogen bonds : angle 4.28238 ( 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 169 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9274 (pptt) cc_final: 0.9024 (pptt) REVERT: A 59 GLN cc_start: 0.8726 (tt0) cc_final: 0.8453 (tt0) REVERT: A 229 ASP cc_start: 0.8557 (t0) cc_final: 0.7893 (t0) REVERT: A 253 TYR cc_start: 0.8782 (m-80) cc_final: 0.8368 (m-80) REVERT: A 279 ASN cc_start: 0.9173 (t0) cc_final: 0.8932 (t0) REVERT: B 32 GLN cc_start: 0.8842 (mt0) cc_final: 0.8520 (mt0) REVERT: B 59 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: B 175 GLN cc_start: 0.8808 (mp10) cc_final: 0.8461 (mp10) REVERT: B 217 MET cc_start: 0.8782 (pmt) cc_final: 0.8265 (pmm) REVERT: B 226 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 234 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8010 (m-80) REVERT: B 280 LYS cc_start: 0.8973 (tptp) cc_final: 0.8114 (tptp) REVERT: B 292 PHE cc_start: 0.9193 (m-10) cc_final: 0.8922 (m-10) REVERT: B 325 MET cc_start: 0.8978 (mmt) cc_final: 0.8682 (mmm) REVERT: R 73 MET cc_start: 0.8922 (ptm) cc_final: 0.8576 (ppp) REVERT: R 84 ASP cc_start: 0.8938 (m-30) cc_final: 0.8732 (t0) REVERT: R 156 MET cc_start: 0.8560 (tpp) cc_final: 0.8247 (tpp) REVERT: R 191 CYS cc_start: 0.8519 (t) cc_final: 0.8183 (t) REVERT: R 253 PHE cc_start: 0.8844 (m-10) cc_final: 0.8104 (t80) REVERT: R 277 TYR cc_start: 0.8849 (t80) cc_final: 0.8512 (t80) REVERT: R 281 PHE cc_start: 0.8254 (t80) cc_final: 0.8044 (t80) REVERT: R 291 ASN cc_start: 0.7948 (t0) cc_final: 0.7565 (t0) REVERT: R 305 GLU cc_start: 0.8430 (pm20) cc_final: 0.7787 (pm20) REVERT: R 307 ARG cc_start: 0.8744 (mmm-85) cc_final: 0.8090 (mmm-85) REVERT: G 17 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8615 (pt0) REVERT: G 21 MET cc_start: 0.8600 (tpt) cc_final: 0.8318 (tpt) REVERT: G 28 ILE cc_start: 0.8820 (mp) cc_final: 0.8400 (mp) REVERT: N 47 TRP cc_start: 0.8238 (t60) cc_final: 0.8006 (t60) outliers start: 23 outliers final: 11 residues processed: 160 average time/residue: 0.6520 time to fit residues: 110.2986 Evaluate side-chains 153 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 102 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 0.0370 chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN R 70 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.130338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093451 restraints weight = 15963.011| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.89 r_work: 0.3134 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4308 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= 0.129 Angle : 0.664 12.741 11368 Z= 0.330 Chirality : 0.042 0.144 1291 Planarity : 0.004 0.045 1444 Dihedral : 4.490 47.750 1135 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.44 % Allowed : 22.20 % Favored : 75.36 % 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 aren not related in a simple way. whole: 0.70 (0.27), residues: 1025 helix: 1.85 (0.26), residues: 404 sheet: 0.13 (0.34), residues: 231 loop : -0.78 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 151 TYR 0.021 0.001 TYR L 1 PHE 0.011 0.001 PHE B 199 TRP 0.011 0.001 TRP A 234 HIS 0.002 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8389) covalent geometry : angle 0.66444 (11360) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.65980 ( 8) hydrogen bonds : bond 0.03744 ( 408) hydrogen bonds : angle 4.26923 ( 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 173 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 58 LYS cc_start: 0.9252 (pptt) cc_final: 0.8952 (pptt) REVERT: A 59 GLN cc_start: 0.8736 (tt0) cc_final: 0.8427 (tt0) REVERT: A 229 ASP cc_start: 0.8483 (t0) cc_final: 0.7807 (t0) REVERT: A 253 TYR cc_start: 0.8822 (m-80) cc_final: 0.8396 (m-80) REVERT: A 279 ASN cc_start: 0.9214 (t0) cc_final: 0.8951 (t0) REVERT: B 32 GLN cc_start: 0.8977 (mt0) cc_final: 0.8604 (mt0) REVERT: B 59 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8467 (m-80) REVERT: B 175 GLN cc_start: 0.8802 (mp10) cc_final: 0.8551 (mp10) REVERT: B 217 MET cc_start: 0.8763 (pmt) cc_final: 0.8243 (pmm) REVERT: B 226 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 234 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: B 280 LYS cc_start: 0.9017 (tptp) cc_final: 0.8120 (tptp) REVERT: B 291 ASP cc_start: 0.8938 (m-30) cc_final: 0.8550 (m-30) REVERT: B 292 PHE cc_start: 0.9282 (m-10) cc_final: 0.9025 (m-10) REVERT: B 325 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8632 (mmm) REVERT: R 37 GLN cc_start: 0.8806 (tp40) cc_final: 0.8602 (tm-30) REVERT: R 41 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7991 (tmmm) REVERT: R 73 MET cc_start: 0.8853 (ptm) cc_final: 0.8175 (ppp) REVERT: R 74 TYR cc_start: 0.9013 (m-80) cc_final: 0.8765 (m-80) REVERT: R 85 MET cc_start: 0.8736 (ppp) cc_final: 0.8476 (ppp) REVERT: R 156 MET cc_start: 0.8525 (tpp) cc_final: 0.8217 (tpp) REVERT: R 191 CYS cc_start: 0.8526 (t) cc_final: 0.8192 (t) REVERT: R 253 PHE cc_start: 0.8833 (m-10) cc_final: 0.8041 (t80) REVERT: R 277 TYR cc_start: 0.8866 (t80) cc_final: 0.8491 (t80) REVERT: R 281 PHE cc_start: 0.8316 (t80) cc_final: 0.8084 (t80) REVERT: R 291 ASN cc_start: 0.7972 (t0) cc_final: 0.7646 (t0) REVERT: R 305 GLU cc_start: 0.8132 (pm20) cc_final: 0.7529 (pm20) REVERT: G 17 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8623 (pt0) REVERT: G 21 MET cc_start: 0.8659 (tpt) cc_final: 0.8428 (tpt) REVERT: G 28 ILE cc_start: 0.8839 (mp) cc_final: 0.8428 (mp) outliers start: 22 outliers final: 11 residues processed: 163 average time/residue: 0.6557 time to fit residues: 113.1250 Evaluate side-chains 156 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 B residue 325 MET 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 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.125959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088515 restraints weight = 16133.934| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.88 r_work: 0.3125 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8393 Z= 0.148 Angle : 0.712 12.607 11368 Z= 0.353 Chirality : 0.042 0.149 1291 Planarity : 0.004 0.045 1444 Dihedral : 4.481 47.956 1135 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.22 % Allowed : 23.20 % Favored : 74.58 % 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 aren not related in a simple way. whole: 0.68 (0.27), residues: 1025 helix: 1.83 (0.27), residues: 405 sheet: -0.00 (0.33), residues: 243 loop : -0.71 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 151 TYR 0.018 0.001 TYR L 1 PHE 0.014 0.001 PHE R 310 TRP 0.010 0.001 TRP A 234 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8389) covalent geometry : angle 0.71223 (11360) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.76499 ( 8) hydrogen bonds : bond 0.03815 ( 408) hydrogen bonds : angle 4.30630 ( 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 167 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.533 Fit side-chains REVERT: A 229 ASP cc_start: 0.8507 (t0) cc_final: 0.7827 (t0) REVERT: A 253 TYR cc_start: 0.8825 (m-80) cc_final: 0.8402 (m-80) REVERT: A 279 ASN cc_start: 0.9192 (t0) cc_final: 0.8932 (t0) REVERT: B 32 GLN cc_start: 0.8930 (mt0) cc_final: 0.8579 (mt0) REVERT: B 59 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: B 75 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8038 (mm-40) REVERT: B 175 GLN cc_start: 0.8747 (mp10) cc_final: 0.8425 (mp10) REVERT: B 217 MET cc_start: 0.8732 (pmt) cc_final: 0.8215 (pmm) REVERT: B 226 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 234 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7993 (m-80) REVERT: B 280 LYS cc_start: 0.9037 (tptp) cc_final: 0.8221 (tptp) REVERT: B 291 ASP cc_start: 0.8938 (m-30) cc_final: 0.8542 (m-30) REVERT: B 292 PHE cc_start: 0.9272 (m-10) cc_final: 0.9013 (m-10) REVERT: B 325 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8662 (mmm) REVERT: R 37 GLN cc_start: 0.8850 (tp40) cc_final: 0.8612 (tm-30) REVERT: R 41 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7857 (tmmm) REVERT: R 73 MET cc_start: 0.8881 (ptm) cc_final: 0.8177 (ppp) REVERT: R 84 ASP cc_start: 0.8917 (m-30) cc_final: 0.8579 (t0) REVERT: R 85 MET cc_start: 0.8776 (ppp) cc_final: 0.8529 (ppp) REVERT: R 115 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7135 (m-70) REVERT: R 156 MET cc_start: 0.8508 (tpp) cc_final: 0.8204 (tpp) REVERT: R 191 CYS cc_start: 0.8526 (t) cc_final: 0.8199 (t) REVERT: R 253 PHE cc_start: 0.8809 (m-10) cc_final: 0.8040 (t80) REVERT: R 277 TYR cc_start: 0.8878 (t80) cc_final: 0.8501 (t80) REVERT: R 291 ASN cc_start: 0.8005 (t0) cc_final: 0.7659 (t0) REVERT: G 17 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8645 (pt0) REVERT: G 21 MET cc_start: 0.8725 (tpt) cc_final: 0.8465 (tpt) REVERT: G 28 ILE cc_start: 0.8801 (mp) cc_final: 0.8374 (mp) REVERT: G 47 GLU cc_start: 0.8336 (pm20) cc_final: 0.7991 (pm20) REVERT: N 117 TYR cc_start: 0.8037 (m-80) cc_final: 0.7751 (m-10) outliers start: 20 outliers final: 10 residues processed: 156 average time/residue: 0.6624 time to fit residues: 109.2424 Evaluate side-chains 154 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 B residue 325 MET Chi-restraints excluded: chain R residue 41 LYS 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 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** 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 = 0.3886 r_free = 0.3886 target = 0.125258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.087796 restraints weight = 15959.255| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.86 r_work: 0.3114 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4423 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= 0.166 Angle : 0.733 12.561 11368 Z= 0.363 Chirality : 0.043 0.168 1291 Planarity : 0.004 0.047 1444 Dihedral : 4.512 48.199 1135 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.33 % Allowed : 23.64 % Favored : 74.03 % 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 aren not related in a simple way. whole: 0.63 (0.27), residues: 1025 helix: 1.77 (0.27), residues: 401 sheet: -0.05 (0.32), residues: 248 loop : -0.68 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 151 TYR 0.027 0.001 TYR R 74 PHE 0.012 0.001 PHE B 199 TRP 0.010 0.001 TRP A 234 HIS 0.002 0.001 HIS R 70 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8389) covalent geometry : angle 0.73282 (11360) SS BOND : bond 0.00105 ( 4) SS BOND : angle 0.88414 ( 8) hydrogen bonds : bond 0.03954 ( 408) hydrogen bonds : angle 4.35706 ( 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 162 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.8551 (t0) cc_final: 0.7868 (t0) REVERT: A 253 TYR cc_start: 0.8806 (m-80) cc_final: 0.8316 (m-80) REVERT: A 279 ASN cc_start: 0.9200 (t0) cc_final: 0.8936 (t0) REVERT: B 32 GLN cc_start: 0.8942 (mt0) cc_final: 0.8625 (mt0) REVERT: B 59 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8521 (m-80) REVERT: B 175 GLN cc_start: 0.8752 (mp10) cc_final: 0.8363 (mp10) REVERT: B 217 MET cc_start: 0.8753 (pmt) cc_final: 0.8226 (pmm) REVERT: B 226 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7784 (mm-30) REVERT: B 234 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: B 280 LYS cc_start: 0.9048 (tptp) cc_final: 0.8285 (tptp) REVERT: B 292 PHE cc_start: 0.9276 (m-10) cc_final: 0.9024 (m-10) REVERT: B 325 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8645 (mmm) REVERT: R 37 GLN cc_start: 0.8890 (tp40) cc_final: 0.8609 (tm-30) REVERT: R 41 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7905 (tmmm) REVERT: R 73 MET cc_start: 0.8922 (ptm) cc_final: 0.8227 (ppp) REVERT: R 84 ASP cc_start: 0.8935 (m-30) cc_final: 0.8582 (t0) REVERT: R 85 MET cc_start: 0.8802 (ppp) cc_final: 0.8550 (ppp) REVERT: R 115 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.6964 (m-70) REVERT: R 156 MET cc_start: 0.8521 (tpp) cc_final: 0.8233 (tpp) REVERT: R 191 CYS cc_start: 0.8550 (t) cc_final: 0.8069 (t) REVERT: R 253 PHE cc_start: 0.8835 (m-10) cc_final: 0.8102 (t80) REVERT: R 277 TYR cc_start: 0.8902 (t80) cc_final: 0.8512 (t80) REVERT: R 291 ASN cc_start: 0.8141 (t0) cc_final: 0.7823 (t0) REVERT: R 305 GLU cc_start: 0.8486 (pm20) cc_final: 0.8131 (pm20) REVERT: G 28 ILE cc_start: 0.8832 (mp) cc_final: 0.8369 (mp) REVERT: G 47 GLU cc_start: 0.8304 (pm20) cc_final: 0.8047 (pm20) REVERT: N 117 TYR cc_start: 0.8135 (m-80) cc_final: 0.7749 (m-10) outliers start: 21 outliers final: 12 residues processed: 151 average time/residue: 0.6453 time to fit residues: 103.2953 Evaluate side-chains 155 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET 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 B residue 325 MET Chi-restraints excluded: chain R residue 41 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.0370 chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 59 GLN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.126797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.089153 restraints weight = 16162.710| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.93 r_work: 0.3141 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4582 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= 0.136 Angle : 0.733 13.208 11368 Z= 0.361 Chirality : 0.043 0.173 1291 Planarity : 0.004 0.045 1444 Dihedral : 4.429 47.615 1135 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.00 % Allowed : 23.97 % Favored : 74.03 % 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 aren not related in a simple way. whole: 0.68 (0.27), residues: 1025 helix: 1.86 (0.26), residues: 403 sheet: 0.07 (0.33), residues: 234 loop : -0.77 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 151 TYR 0.021 0.001 TYR L 1 PHE 0.016 0.001 PHE R 310 TRP 0.009 0.001 TRP A 234 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8389) covalent geometry : angle 0.73250 (11360) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.79354 ( 8) hydrogen bonds : bond 0.03748 ( 408) hydrogen bonds : angle 4.36922 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3985.18 seconds wall clock time: 68 minutes 45.38 seconds (4125.38 seconds total)