Starting phenix.real_space_refine on Tue Mar 3 20:45:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7db6_30627/03_2026/7db6_30627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7db6_30627/03_2026/7db6_30627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7db6_30627/03_2026/7db6_30627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7db6_30627/03_2026/7db6_30627.map" model { file = "/net/cci-nas-00/data/ceres_data/7db6_30627/03_2026/7db6_30627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7db6_30627/03_2026/7db6_30627.cif" } resolution = 3.3 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5600 2.51 5 N 1479 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8767 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1764 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2210 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 1 Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'JEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.24 Number of scatterers: 8767 At special positions: 0 Unit cell: (128.246, 125.364, 89.3401, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1626 8.00 N 1479 7.00 C 5600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 177 " 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: 0.74 Conformation dependent library (CDL) restraints added in 333.6 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 33.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 4.268A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.798A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.586A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.781A pdb=" N LYS A 280 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 281' Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.627A pdb=" N ASN A 331 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 removed outlier: 4.248A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.701A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.856A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 33 through 44 removed outlier: 3.716A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.553A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.010A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'D' and resid 24 through 51 removed outlier: 4.658A pdb=" N ALA D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N CYS D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 79 removed outlier: 4.027A pdb=" N VAL D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.551A pdb=" N ASN D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 130 removed outlier: 3.786A pdb=" N GLY D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 139 Processing helix chain 'D' and resid 142 through 160 Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.757A pdb=" N VAL D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.768A pdb=" N ILE D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 4.808A pdb=" N MET D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 261 Proline residue: D 253 - end of helix Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.691A pdb=" N MET D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Proline residue: D 270 - end of helix No H-bonds generated for 'chain 'D' and resid 264 through 272' Processing helix chain 'D' and resid 273 through 298 removed outlier: 3.748A pdb=" N PHE D 277 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA D 292 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.855A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.648A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.105A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.504A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.171A 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: 4.973A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.550A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.979A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.609A 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 276 removed outlier: 6.544A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.201A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.151A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 169 through 170 381 hydrogen bonds defined for protein. 1077 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: 1.39 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2797 1.34 - 1.47: 2236 1.47 - 1.59: 3834 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 8955 Sorted by residual: bond pdb=" C ARG D 22 " pdb=" N PRO D 23 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 3.06e+01 bond pdb=" C TYR D 79 " pdb=" N PRO D 80 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.55e+00 bond pdb=" C LEU D 160 " pdb=" N PRO D 161 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.11e+00 bond pdb=" C VAL D 198 " pdb=" N PRO D 199 " ideal model delta sigma weight residual 1.333 1.362 -0.029 1.44e-02 4.82e+03 3.94e+00 bond pdb=" CA ARG D 59 " pdb=" CB ARG D 59 " ideal model delta sigma weight residual 1.541 1.560 -0.019 1.20e-02 6.94e+03 2.47e+00 ... (remaining 8950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 11812 2.56 - 5.12: 277 5.12 - 7.68: 38 7.68 - 10.24: 9 10.24 - 12.80: 1 Bond angle restraints: 12137 Sorted by residual: angle pdb=" N ARG D 59 " pdb=" CA ARG D 59 " pdb=" CB ARG D 59 " ideal model delta sigma weight residual 114.17 108.97 5.20 1.14e+00 7.69e-01 2.08e+01 angle pdb=" CA LYS D 56 " pdb=" CB LYS D 56 " pdb=" CG LYS D 56 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.69e+01 angle pdb=" C GLN E 219 " pdb=" N HIS E 220 " pdb=" CA HIS E 220 " ideal model delta sigma weight residual 121.54 113.83 7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C LEU A 232 " pdb=" N VAL A 233 " pdb=" CA VAL A 233 " ideal model delta sigma weight residual 121.70 128.58 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" N ILE D 174 " pdb=" CA ILE D 174 " pdb=" C ILE D 174 " ideal model delta sigma weight residual 109.34 101.40 7.94 2.08e+00 2.31e-01 1.46e+01 ... (remaining 12132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 4941 22.36 - 44.72: 351 44.72 - 67.08: 16 67.08 - 89.44: 4 89.44 - 111.80: 2 Dihedral angle restraints: 5314 sinusoidal: 2072 harmonic: 3242 Sorted by residual: dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual -86.00 -131.67 45.67 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1035 0.059 - 0.118: 268 0.118 - 0.177: 62 0.177 - 0.236: 7 0.236 - 0.294: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CB VAL D 198 " pdb=" CA VAL D 198 " pdb=" CG1 VAL D 198 " pdb=" CG2 VAL D 198 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA TYR E 178 " pdb=" N TYR E 178 " pdb=" C TYR E 178 " pdb=" CB TYR E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1371 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 58 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.58e+00 pdb=" C LEU D 58 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU D 58 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG D 59 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 198 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.28e+00 pdb=" N PRO D 199 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 199 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 199 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 JEV D 401 " 0.021 2.00e-02 2.50e+03 1.89e-02 8.96e+00 pdb=" C11 JEV D 401 " 0.019 2.00e-02 2.50e+03 pdb=" C12 JEV D 401 " 0.002 2.00e-02 2.50e+03 pdb=" C13 JEV D 401 " -0.002 2.00e-02 2.50e+03 pdb=" C14 JEV D 401 " 0.019 2.00e-02 2.50e+03 pdb=" C16 JEV D 401 " -0.003 2.00e-02 2.50e+03 pdb=" C6 JEV D 401 " 0.010 2.00e-02 2.50e+03 pdb=" C8 JEV D 401 " -0.030 2.00e-02 2.50e+03 pdb=" C9 JEV D 401 " 0.002 2.00e-02 2.50e+03 pdb=" O1 JEV D 401 " -0.037 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1533 2.77 - 3.30: 7830 3.30 - 3.83: 14608 3.83 - 4.37: 17024 4.37 - 4.90: 29606 Nonbonded interactions: 70601 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 163 " model vdw 2.285 3.040 nonbonded pdb=" O ASN A 256 " pdb=" OG1 THR A 260 " model vdw 2.297 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.298 3.040 ... (remaining 70596 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: 0.230 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 : 0.006 0.060 8959 Z= 0.262 Angle : 0.963 12.803 12145 Z= 0.532 Chirality : 0.057 0.294 1374 Planarity : 0.007 0.076 1530 Dihedral : 14.282 111.800 3214 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.90 % Rotamer: Outliers : 0.63 % Allowed : 8.67 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.08 (0.21), residues: 1098 helix: -2.93 (0.20), residues: 345 sheet: -2.22 (0.27), residues: 264 loop : -2.69 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 251 TYR 0.029 0.002 TYR E 178 PHE 0.024 0.003 PHE A 189 TRP 0.020 0.002 TRP B 82 HIS 0.006 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 8955) covalent geometry : angle 0.96237 (12137) SS BOND : bond 0.01219 ( 4) SS BOND : angle 1.54790 ( 8) hydrogen bonds : bond 0.13132 ( 381) hydrogen bonds : angle 7.20774 ( 1077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6552 (ttm) cc_final: 0.6179 (ttt) REVERT: A 29 LYS cc_start: 0.7616 (mppt) cc_final: 0.7035 (mmmt) REVERT: A 197 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7201 (mttm) REVERT: B 61 MET cc_start: 0.8709 (tmm) cc_final: 0.8360 (ppp) REVERT: B 217 MET cc_start: 0.6460 (ttp) cc_final: 0.5696 (tmm) REVERT: B 239 ASN cc_start: 0.7775 (m-40) cc_final: 0.7491 (t0) REVERT: B 271 CYS cc_start: 0.6295 (p) cc_final: 0.5984 (m) REVERT: B 280 LYS cc_start: 0.8129 (tttt) cc_final: 0.7836 (tptt) REVERT: E 64 VAL cc_start: 0.8215 (m) cc_final: 0.7812 (t) REVERT: E 87 ARG cc_start: 0.7091 (mpt90) cc_final: 0.6683 (mtp180) REVERT: E 93 MET cc_start: 0.7257 (tpp) cc_final: 0.6814 (tpp) REVERT: E 208 GLU cc_start: 0.7733 (tt0) cc_final: 0.7468 (mm-30) REVERT: E 222 GLU cc_start: 0.7706 (tt0) cc_final: 0.7425 (tt0) REVERT: E 232 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7643 (ttpp) REVERT: D 34 LEU cc_start: 0.7090 (tt) cc_final: 0.6633 (mt) REVERT: D 107 MET cc_start: 0.5796 (ttm) cc_final: 0.4935 (tmm) REVERT: D 116 PHE cc_start: 0.7878 (m-10) cc_final: 0.7632 (m-10) REVERT: D 126 TYR cc_start: 0.8098 (t80) cc_final: 0.7631 (t80) REVERT: D 131 HIS cc_start: 0.6741 (t70) cc_final: 0.6347 (t-170) REVERT: D 154 LEU cc_start: 0.6121 (tt) cc_final: 0.5920 (mt) REVERT: D 179 PHE cc_start: 0.6708 (t80) cc_final: 0.6352 (t80) REVERT: D 277 PHE cc_start: 0.5699 (t80) cc_final: 0.5477 (t80) REVERT: D 293 ILE cc_start: 0.7354 (mm) cc_final: 0.6975 (mm) outliers start: 6 outliers final: 0 residues processed: 193 average time/residue: 0.0932 time to fit residues: 24.5945 Evaluate side-chains 137 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 91 HIS B 142 HIS B 293 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS D 255 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.208419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157824 restraints weight = 9489.635| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.74 r_work: 0.3503 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8959 Z= 0.133 Angle : 0.671 16.063 12145 Z= 0.351 Chirality : 0.044 0.226 1374 Planarity : 0.005 0.053 1530 Dihedral : 6.324 54.364 1232 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 2.40 % Allowed : 13.58 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.10 (0.23), residues: 1098 helix: -1.60 (0.25), residues: 344 sheet: -1.70 (0.29), residues: 259 loop : -2.52 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 197 TYR 0.024 0.001 TYR E 178 PHE 0.017 0.001 PHE A 189 TRP 0.011 0.001 TRP D 93 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8955) covalent geometry : angle 0.66858 (12137) SS BOND : bond 0.01992 ( 4) SS BOND : angle 2.38614 ( 8) hydrogen bonds : bond 0.04104 ( 381) hydrogen bonds : angle 5.68842 ( 1077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7576 (ttm) cc_final: 0.7284 (ttt) REVERT: A 29 LYS cc_start: 0.7841 (mppt) cc_final: 0.7480 (mmmt) REVERT: A 33 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 185 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7663 (m) REVERT: A 197 LYS cc_start: 0.8365 (mtpt) cc_final: 0.7431 (mttm) REVERT: A 247 MET cc_start: 0.3618 (mmt) cc_final: 0.3362 (mmp) REVERT: A 349 LYS cc_start: 0.8569 (tttt) cc_final: 0.8167 (ttmm) REVERT: B 61 MET cc_start: 0.8695 (tmm) cc_final: 0.8447 (ppp) REVERT: B 118 ASP cc_start: 0.8287 (p0) cc_final: 0.7823 (p0) REVERT: B 119 ASN cc_start: 0.9288 (OUTLIER) cc_final: 0.8911 (m-40) REVERT: B 247 ASP cc_start: 0.7027 (t0) cc_final: 0.6735 (t0) REVERT: B 271 CYS cc_start: 0.6547 (p) cc_final: 0.5689 (m) REVERT: B 280 LYS cc_start: 0.8353 (tttt) cc_final: 0.8063 (tptt) REVERT: C 32 LYS cc_start: 0.6958 (mptt) cc_final: 0.6325 (ptpt) REVERT: E 18 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7234 (tpp80) REVERT: E 64 VAL cc_start: 0.8284 (m) cc_final: 0.7928 (t) REVERT: E 74 ASP cc_start: 0.7849 (m-30) cc_final: 0.7417 (m-30) REVERT: E 87 ARG cc_start: 0.7391 (mpt90) cc_final: 0.6902 (mtp180) REVERT: E 93 MET cc_start: 0.7775 (tpp) cc_final: 0.7332 (tpp) REVERT: E 190 ARG cc_start: 0.6897 (ptt-90) cc_final: 0.6616 (ptt-90) REVERT: E 208 GLU cc_start: 0.7926 (tt0) cc_final: 0.7475 (mm-30) REVERT: E 210 GLU cc_start: 0.7037 (pp20) cc_final: 0.6608 (pp20) REVERT: E 222 GLU cc_start: 0.7789 (tt0) cc_final: 0.7563 (tt0) REVERT: E 232 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8273 (ttmt) REVERT: D 34 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6801 (mp) REVERT: D 107 MET cc_start: 0.5966 (ttm) cc_final: 0.5454 (ttm) REVERT: D 131 HIS cc_start: 0.7056 (t70) cc_final: 0.6803 (t70) REVERT: D 147 TYR cc_start: 0.7148 (m-10) cc_final: 0.6035 (m-80) REVERT: D 237 PHE cc_start: 0.7269 (t80) cc_final: 0.6839 (t80) REVERT: D 251 TRP cc_start: 0.7598 (m100) cc_final: 0.6906 (m100) REVERT: D 293 ILE cc_start: 0.7294 (mm) cc_final: 0.6844 (mm) REVERT: D 303 ARG cc_start: 0.6297 (mtm180) cc_final: 0.5924 (mtm180) REVERT: D 305 GLU cc_start: 0.5031 (tm-30) cc_final: 0.4693 (tt0) outliers start: 23 outliers final: 16 residues processed: 183 average time/residue: 0.1003 time to fit residues: 24.9042 Evaluate side-chains 165 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN E 113 GLN E 130 GLN D 255 ASN D 287 ASN D 291 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.207527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.158795 restraints weight = 9422.791| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.65 r_work: 0.3541 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8959 Z= 0.137 Angle : 0.643 15.006 12145 Z= 0.335 Chirality : 0.043 0.217 1374 Planarity : 0.005 0.051 1530 Dihedral : 5.925 61.235 1232 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.92 % Favored : 93.99 % Rotamer: Outliers : 3.55 % Allowed : 16.20 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.24), residues: 1098 helix: -0.84 (0.27), residues: 342 sheet: -1.28 (0.30), residues: 261 loop : -2.24 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.021 0.001 TYR E 178 PHE 0.016 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8955) covalent geometry : angle 0.63911 (12137) SS BOND : bond 0.01136 ( 4) SS BOND : angle 2.71799 ( 8) hydrogen bonds : bond 0.03673 ( 381) hydrogen bonds : angle 5.33047 ( 1077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7525 (ttm) cc_final: 0.7186 (ttt) REVERT: A 29 LYS cc_start: 0.7836 (mppt) cc_final: 0.7431 (mmmt) REVERT: A 185 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7660 (m) REVERT: A 197 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7631 (mttm) REVERT: A 210 LYS cc_start: 0.7575 (mmmt) cc_final: 0.6977 (mmmm) REVERT: A 247 MET cc_start: 0.3790 (mmt) cc_final: 0.3433 (mmp) REVERT: A 349 LYS cc_start: 0.8562 (tttt) cc_final: 0.8190 (ttmm) REVERT: B 61 MET cc_start: 0.8748 (tmm) cc_final: 0.8345 (ppp) REVERT: B 118 ASP cc_start: 0.8137 (p0) cc_final: 0.7697 (t0) REVERT: B 247 ASP cc_start: 0.6966 (t0) cc_final: 0.6724 (t0) REVERT: B 271 CYS cc_start: 0.6441 (p) cc_final: 0.5567 (m) REVERT: B 280 LYS cc_start: 0.8390 (tttt) cc_final: 0.8088 (tptt) REVERT: E 74 ASP cc_start: 0.7540 (m-30) cc_final: 0.7188 (m-30) REVERT: E 83 MET cc_start: 0.8719 (mtm) cc_final: 0.8355 (mtp) REVERT: E 87 ARG cc_start: 0.7475 (mpt90) cc_final: 0.7021 (mtp180) REVERT: E 93 MET cc_start: 0.7767 (tpp) cc_final: 0.7330 (tpp) REVERT: E 190 ARG cc_start: 0.7165 (ptt-90) cc_final: 0.6931 (ptt-90) REVERT: E 208 GLU cc_start: 0.7919 (tt0) cc_final: 0.7450 (mm-30) REVERT: E 210 GLU cc_start: 0.7038 (pp20) cc_final: 0.6763 (pp20) REVERT: E 232 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8176 (ttmm) REVERT: D 34 LEU cc_start: 0.7186 (tt) cc_final: 0.6625 (mp) REVERT: D 107 MET cc_start: 0.6031 (ttm) cc_final: 0.5454 (ttm) REVERT: D 131 HIS cc_start: 0.7250 (t70) cc_final: 0.6989 (t70) REVERT: D 147 TYR cc_start: 0.7104 (m-10) cc_final: 0.6004 (m-80) REVERT: D 169 GLN cc_start: 0.7921 (pp30) cc_final: 0.7428 (pp30) REVERT: D 237 PHE cc_start: 0.7303 (t80) cc_final: 0.6896 (t80) REVERT: D 251 TRP cc_start: 0.7442 (m100) cc_final: 0.7231 (m100) REVERT: D 293 ILE cc_start: 0.7270 (mm) cc_final: 0.6804 (mm) REVERT: D 303 ARG cc_start: 0.6404 (mtm180) cc_final: 0.6051 (mtm180) REVERT: D 305 GLU cc_start: 0.5041 (tm-30) cc_final: 0.4772 (tt0) outliers start: 34 outliers final: 23 residues processed: 176 average time/residue: 0.0975 time to fit residues: 23.2392 Evaluate side-chains 169 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 0.0670 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.201467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152102 restraints weight = 9681.763| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.92 r_work: 0.3440 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 8959 Z= 0.214 Angle : 0.693 12.563 12145 Z= 0.364 Chirality : 0.046 0.226 1374 Planarity : 0.005 0.052 1530 Dihedral : 6.195 63.848 1232 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.29 % Favored : 92.62 % Rotamer: Outliers : 3.87 % Allowed : 18.39 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.24), residues: 1098 helix: -0.65 (0.28), residues: 341 sheet: -1.31 (0.30), residues: 262 loop : -2.20 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 197 TYR 0.024 0.002 TYR E 178 PHE 0.021 0.002 PHE B 253 TRP 0.016 0.002 TRP B 99 HIS 0.007 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 8955) covalent geometry : angle 0.69017 (12137) SS BOND : bond 0.01104 ( 4) SS BOND : angle 2.72633 ( 8) hydrogen bonds : bond 0.03944 ( 381) hydrogen bonds : angle 5.46932 ( 1077) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7815 (ttm) cc_final: 0.7446 (ttt) REVERT: A 185 VAL cc_start: 0.8060 (OUTLIER) cc_final: 0.7688 (m) REVERT: A 197 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7605 (mttm) REVERT: A 210 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7156 (mmmm) REVERT: A 247 MET cc_start: 0.3874 (mmt) cc_final: 0.3478 (mmp) REVERT: A 349 LYS cc_start: 0.8642 (tttt) cc_final: 0.8257 (ttmm) REVERT: B 118 ASP cc_start: 0.8238 (p0) cc_final: 0.7958 (p0) REVERT: B 247 ASP cc_start: 0.7231 (t0) cc_final: 0.7000 (t0) REVERT: B 264 TYR cc_start: 0.8123 (m-80) cc_final: 0.7687 (m-80) REVERT: B 280 LYS cc_start: 0.8598 (tttt) cc_final: 0.8276 (tptt) REVERT: E 83 MET cc_start: 0.8824 (mtm) cc_final: 0.8511 (mtp) REVERT: E 87 ARG cc_start: 0.7431 (mpt90) cc_final: 0.7007 (mtp180) REVERT: E 93 MET cc_start: 0.7833 (tpp) cc_final: 0.7327 (tpp) REVERT: E 190 ARG cc_start: 0.7158 (ptt-90) cc_final: 0.6911 (ptt-90) REVERT: E 208 GLU cc_start: 0.7826 (tt0) cc_final: 0.7304 (mm-30) REVERT: E 210 GLU cc_start: 0.7032 (pp20) cc_final: 0.6743 (pp20) REVERT: E 232 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8232 (ttmm) REVERT: D 107 MET cc_start: 0.6149 (ttm) cc_final: 0.5522 (ttm) REVERT: D 131 HIS cc_start: 0.7232 (t70) cc_final: 0.6950 (t70) REVERT: D 169 GLN cc_start: 0.7913 (pp30) cc_final: 0.7553 (pp30) REVERT: D 293 ILE cc_start: 0.7311 (mm) cc_final: 0.6790 (mm) REVERT: D 305 GLU cc_start: 0.5440 (tm-30) cc_final: 0.5202 (tm-30) outliers start: 37 outliers final: 29 residues processed: 178 average time/residue: 0.1030 time to fit residues: 24.6916 Evaluate side-chains 172 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 288 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 85 optimal weight: 0.0020 chunk 34 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.205961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156331 restraints weight = 9536.917| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.65 r_work: 0.3518 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 8959 Z= 0.130 Angle : 0.614 12.987 12145 Z= 0.320 Chirality : 0.043 0.191 1374 Planarity : 0.004 0.047 1530 Dihedral : 5.738 61.963 1232 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.44 % Rotamer: Outliers : 3.76 % Allowed : 20.06 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.25), residues: 1098 helix: -0.16 (0.29), residues: 336 sheet: -1.01 (0.31), residues: 257 loop : -2.09 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.024 0.001 TYR E 178 PHE 0.030 0.002 PHE A 191 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8955) covalent geometry : angle 0.61129 (12137) SS BOND : bond 0.00822 ( 4) SS BOND : angle 2.15446 ( 8) hydrogen bonds : bond 0.03355 ( 381) hydrogen bonds : angle 5.20066 ( 1077) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7623 (ttm) cc_final: 0.7243 (ttt) REVERT: A 185 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7650 (m) REVERT: A 197 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7646 (mttm) REVERT: A 247 MET cc_start: 0.3848 (mmt) cc_final: 0.3394 (mmp) REVERT: A 349 LYS cc_start: 0.8398 (tttt) cc_final: 0.8063 (ttmm) REVERT: B 157 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8553 (tt) REVERT: B 234 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: B 247 ASP cc_start: 0.7218 (t0) cc_final: 0.7011 (t70) REVERT: B 264 TYR cc_start: 0.8131 (m-80) cc_final: 0.7870 (m-80) REVERT: B 280 LYS cc_start: 0.8619 (tttt) cc_final: 0.8218 (tptt) REVERT: E 74 ASP cc_start: 0.7637 (m-30) cc_final: 0.7357 (m-30) REVERT: E 87 ARG cc_start: 0.7477 (mpt90) cc_final: 0.7052 (mtp180) REVERT: E 93 MET cc_start: 0.7786 (tpp) cc_final: 0.7329 (tpp) REVERT: E 113 GLN cc_start: 0.8331 (pt0) cc_final: 0.8131 (pt0) REVERT: E 208 GLU cc_start: 0.7788 (tt0) cc_final: 0.7425 (mm-30) REVERT: E 232 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8239 (ttmm) REVERT: D 107 MET cc_start: 0.5957 (ttm) cc_final: 0.5379 (ttm) REVERT: D 131 HIS cc_start: 0.7099 (t70) cc_final: 0.6655 (t-90) REVERT: D 147 TYR cc_start: 0.7039 (m-10) cc_final: 0.6006 (m-80) REVERT: D 169 GLN cc_start: 0.7747 (pp30) cc_final: 0.7343 (pp30) outliers start: 36 outliers final: 27 residues processed: 176 average time/residue: 0.0985 time to fit residues: 23.8017 Evaluate side-chains 173 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.208154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159130 restraints weight = 9550.969| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.69 r_work: 0.3535 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8959 Z= 0.124 Angle : 0.600 11.498 12145 Z= 0.314 Chirality : 0.043 0.206 1374 Planarity : 0.004 0.046 1530 Dihedral : 5.473 61.990 1232 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 3.34 % Allowed : 20.17 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.25), residues: 1098 helix: -0.04 (0.28), residues: 342 sheet: -0.84 (0.31), residues: 255 loop : -1.97 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 148 TYR 0.023 0.001 TYR E 178 PHE 0.024 0.001 PHE A 191 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8955) covalent geometry : angle 0.59611 (12137) SS BOND : bond 0.01216 ( 4) SS BOND : angle 2.68591 ( 8) hydrogen bonds : bond 0.03220 ( 381) hydrogen bonds : angle 5.02732 ( 1077) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7625 (ttm) cc_final: 0.7242 (ttt) REVERT: A 197 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7487 (mttm) REVERT: A 247 MET cc_start: 0.4193 (mmt) cc_final: 0.3723 (mmp) REVERT: A 349 LYS cc_start: 0.8341 (tttt) cc_final: 0.8031 (ttmm) REVERT: B 157 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8673 (tt) REVERT: B 205 ASP cc_start: 0.7298 (p0) cc_final: 0.7087 (p0) REVERT: B 234 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: B 247 ASP cc_start: 0.7127 (t0) cc_final: 0.6898 (t70) REVERT: B 264 TYR cc_start: 0.8277 (m-80) cc_final: 0.8000 (m-80) REVERT: B 280 LYS cc_start: 0.8600 (tttt) cc_final: 0.8238 (tptt) REVERT: C 48 ASP cc_start: 0.8144 (t0) cc_final: 0.7840 (t0) REVERT: E 74 ASP cc_start: 0.7773 (m-30) cc_final: 0.7497 (m-30) REVERT: E 93 MET cc_start: 0.7827 (tpp) cc_final: 0.7388 (tpp) REVERT: E 113 GLN cc_start: 0.8387 (pt0) cc_final: 0.8170 (pt0) REVERT: E 190 ARG cc_start: 0.7220 (ptt-90) cc_final: 0.6980 (ptt-90) REVERT: E 208 GLU cc_start: 0.7894 (tt0) cc_final: 0.7393 (mm-30) REVERT: E 220 HIS cc_start: 0.6940 (OUTLIER) cc_final: 0.6551 (t-90) REVERT: E 232 LYS cc_start: 0.8553 (ttpt) cc_final: 0.8219 (ttmm) REVERT: D 107 MET cc_start: 0.5977 (ttm) cc_final: 0.5445 (ttm) REVERT: D 131 HIS cc_start: 0.7040 (t70) cc_final: 0.6687 (t-90) REVERT: D 147 TYR cc_start: 0.7036 (m-10) cc_final: 0.5973 (m-80) REVERT: D 169 GLN cc_start: 0.7590 (pp30) cc_final: 0.7282 (pp30) REVERT: D 282 TYR cc_start: 0.5620 (m-80) cc_final: 0.5235 (t80) outliers start: 32 outliers final: 22 residues processed: 178 average time/residue: 0.0943 time to fit residues: 22.8934 Evaluate side-chains 163 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 230 ASN B 340 ASN D 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.201774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152600 restraints weight = 9638.561| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.99 r_work: 0.3398 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 8959 Z= 0.220 Angle : 0.714 12.305 12145 Z= 0.372 Chirality : 0.046 0.257 1374 Planarity : 0.005 0.049 1530 Dihedral : 5.998 65.158 1232 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.47 % Favored : 92.44 % Rotamer: Outliers : 3.87 % Allowed : 20.38 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.25), residues: 1098 helix: -0.16 (0.28), residues: 342 sheet: -1.04 (0.31), residues: 252 loop : -1.89 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 148 TYR 0.027 0.002 TYR E 178 PHE 0.019 0.002 PHE A 191 TRP 0.015 0.002 TRP D 93 HIS 0.007 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 8955) covalent geometry : angle 0.70981 (12137) SS BOND : bond 0.01633 ( 4) SS BOND : angle 3.25897 ( 8) hydrogen bonds : bond 0.03923 ( 381) hydrogen bonds : angle 5.33659 ( 1077) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.7848 (ttm) cc_final: 0.7532 (ttt) REVERT: A 197 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7572 (mttm) REVERT: A 247 MET cc_start: 0.3918 (mmt) cc_final: 0.3512 (mmp) REVERT: A 349 LYS cc_start: 0.8241 (tttt) cc_final: 0.7968 (ttmm) REVERT: B 234 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8524 (m-80) REVERT: B 264 TYR cc_start: 0.8235 (m-80) cc_final: 0.7774 (m-80) REVERT: B 280 LYS cc_start: 0.8565 (tttt) cc_final: 0.8332 (tptt) REVERT: C 48 ASP cc_start: 0.8261 (t0) cc_final: 0.7959 (t0) REVERT: E 74 ASP cc_start: 0.7637 (m-30) cc_final: 0.7348 (m-30) REVERT: E 93 MET cc_start: 0.7707 (tpp) cc_final: 0.7322 (tpp) REVERT: E 208 GLU cc_start: 0.7854 (tt0) cc_final: 0.7410 (mm-30) REVERT: E 232 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8380 (ttmm) REVERT: D 98 LEU cc_start: 0.7370 (tt) cc_final: 0.7148 (mm) REVERT: D 107 MET cc_start: 0.5990 (ttm) cc_final: 0.5670 (ttm) REVERT: D 131 HIS cc_start: 0.7249 (t70) cc_final: 0.6928 (t-170) REVERT: D 169 GLN cc_start: 0.7668 (pp30) cc_final: 0.7350 (pp30) REVERT: D 220 ARG cc_start: 0.5873 (ptt180) cc_final: 0.5630 (ptt90) REVERT: D 303 ARG cc_start: 0.6328 (mtm180) cc_final: 0.5857 (mtm180) outliers start: 37 outliers final: 26 residues processed: 171 average time/residue: 0.0928 time to fit residues: 22.0259 Evaluate side-chains 163 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 100 CYS Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 0.8980 chunk 51 optimal weight: 0.0770 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.205818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156405 restraints weight = 9594.370| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.48 r_work: 0.3534 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 8959 Z= 0.138 Angle : 0.647 11.934 12145 Z= 0.336 Chirality : 0.044 0.228 1374 Planarity : 0.004 0.050 1530 Dihedral : 5.619 63.507 1232 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.83 % Favored : 94.08 % Rotamer: Outliers : 2.82 % Allowed : 22.15 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.25), residues: 1098 helix: 0.00 (0.28), residues: 349 sheet: -0.77 (0.32), residues: 248 loop : -1.82 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 148 TYR 0.026 0.001 TYR E 178 PHE 0.026 0.002 PHE A 191 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8955) covalent geometry : angle 0.64318 (12137) SS BOND : bond 0.01085 ( 4) SS BOND : angle 2.88824 ( 8) hydrogen bonds : bond 0.03401 ( 381) hydrogen bonds : angle 5.11017 ( 1077) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7591 (ttm) cc_final: 0.7200 (ttt) REVERT: A 33 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 197 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7105 (mttp) REVERT: A 247 MET cc_start: 0.4211 (mmt) cc_final: 0.3727 (mmp) REVERT: A 349 LYS cc_start: 0.8117 (tttt) cc_final: 0.7875 (ttmm) REVERT: B 234 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: B 264 TYR cc_start: 0.8280 (m-80) cc_final: 0.8045 (m-80) REVERT: B 280 LYS cc_start: 0.8633 (tttt) cc_final: 0.8091 (tptt) REVERT: E 74 ASP cc_start: 0.7799 (m-30) cc_final: 0.7521 (m-30) REVERT: E 93 MET cc_start: 0.7576 (tpp) cc_final: 0.7096 (tpp) REVERT: E 208 GLU cc_start: 0.7785 (tt0) cc_final: 0.7403 (mm-30) REVERT: E 232 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8226 (ttmm) REVERT: D 107 MET cc_start: 0.5655 (ttm) cc_final: 0.5402 (ttm) REVERT: D 131 HIS cc_start: 0.7420 (t70) cc_final: 0.6885 (t-90) REVERT: D 147 TYR cc_start: 0.6974 (m-10) cc_final: 0.6069 (m-80) REVERT: D 169 GLN cc_start: 0.7566 (pp30) cc_final: 0.7249 (pp30) REVERT: D 220 ARG cc_start: 0.5791 (ptt180) cc_final: 0.5579 (ptt90) outliers start: 27 outliers final: 22 residues processed: 160 average time/residue: 0.0915 time to fit residues: 20.3727 Evaluate side-chains 158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 0.0060 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 0.0570 chunk 102 optimal weight: 0.0010 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.209884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.162063 restraints weight = 9518.811| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.54 r_work: 0.3588 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8959 Z= 0.117 Angle : 0.638 11.854 12145 Z= 0.326 Chirality : 0.043 0.205 1374 Planarity : 0.004 0.053 1530 Dihedral : 5.326 62.127 1232 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 2.51 % Allowed : 22.57 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.25), residues: 1098 helix: 0.39 (0.28), residues: 343 sheet: -0.52 (0.33), residues: 236 loop : -1.69 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 148 TYR 0.021 0.001 TYR E 178 PHE 0.023 0.001 PHE A 191 TRP 0.044 0.002 TRP D 275 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8955) covalent geometry : angle 0.63150 (12137) SS BOND : bond 0.00986 ( 4) SS BOND : angle 3.72580 ( 8) hydrogen bonds : bond 0.03205 ( 381) hydrogen bonds : angle 4.90962 ( 1077) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7435 (ttm) cc_final: 0.7056 (ttt) REVERT: A 197 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7093 (mttp) REVERT: A 349 LYS cc_start: 0.7876 (tttt) cc_final: 0.7661 (ttmm) REVERT: B 234 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: B 264 TYR cc_start: 0.8073 (m-80) cc_final: 0.7731 (m-80) REVERT: B 280 LYS cc_start: 0.8647 (tttt) cc_final: 0.8343 (ttpp) REVERT: E 74 ASP cc_start: 0.7895 (m-30) cc_final: 0.7654 (m-30) REVERT: E 93 MET cc_start: 0.7707 (tpp) cc_final: 0.7241 (tpp) REVERT: E 208 GLU cc_start: 0.8055 (tt0) cc_final: 0.7572 (mm-30) REVERT: E 220 HIS cc_start: 0.7055 (OUTLIER) cc_final: 0.6852 (t-90) REVERT: E 232 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8223 (tttp) REVERT: D 86 MET cc_start: 0.7530 (tmm) cc_final: 0.7297 (tmm) REVERT: D 107 MET cc_start: 0.5829 (ttm) cc_final: 0.5356 (ttm) REVERT: D 131 HIS cc_start: 0.7354 (t70) cc_final: 0.6823 (t-90) REVERT: D 147 TYR cc_start: 0.7017 (m-10) cc_final: 0.6071 (m-80) REVERT: D 169 GLN cc_start: 0.7540 (pp30) cc_final: 0.7325 (pp30) REVERT: D 255 ASN cc_start: 0.7616 (m-40) cc_final: 0.7123 (m110) outliers start: 24 outliers final: 20 residues processed: 157 average time/residue: 0.0852 time to fit residues: 18.9537 Evaluate side-chains 153 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 106 optimal weight: 7.9990 chunk 9 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN D 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.208204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158657 restraints weight = 9535.020| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.61 r_work: 0.3554 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 8959 Z= 0.131 Angle : 0.646 11.491 12145 Z= 0.331 Chirality : 0.044 0.215 1374 Planarity : 0.004 0.056 1530 Dihedral : 5.305 63.035 1232 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.19 % Favored : 93.72 % Rotamer: Outliers : 2.61 % Allowed : 22.88 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.25), residues: 1098 helix: 0.36 (0.28), residues: 351 sheet: -0.33 (0.33), residues: 241 loop : -1.72 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 148 TYR 0.025 0.001 TYR E 178 PHE 0.025 0.002 PHE D 179 TRP 0.028 0.002 TRP D 275 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8955) covalent geometry : angle 0.63780 (12137) SS BOND : bond 0.01065 ( 4) SS BOND : angle 3.95819 ( 8) hydrogen bonds : bond 0.03233 ( 381) hydrogen bonds : angle 4.88594 ( 1077) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.7513 (ttm) cc_final: 0.7146 (ttt) REVERT: A 197 LYS cc_start: 0.8141 (mtpt) cc_final: 0.6986 (mmtp) REVERT: B 234 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.8561 (m-80) REVERT: B 264 TYR cc_start: 0.8142 (m-80) cc_final: 0.7766 (m-80) REVERT: B 280 LYS cc_start: 0.8647 (tttt) cc_final: 0.8072 (tptt) REVERT: E 74 ASP cc_start: 0.7882 (m-30) cc_final: 0.7625 (m-30) REVERT: E 93 MET cc_start: 0.7709 (tpp) cc_final: 0.7278 (tpp) REVERT: E 208 GLU cc_start: 0.8048 (tt0) cc_final: 0.7547 (mm-30) REVERT: E 232 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8141 (tttp) REVERT: D 107 MET cc_start: 0.5887 (ttm) cc_final: 0.5396 (ttm) REVERT: D 131 HIS cc_start: 0.7383 (t70) cc_final: 0.7056 (t70) REVERT: D 147 TYR cc_start: 0.6966 (m-10) cc_final: 0.5965 (m-80) REVERT: D 169 GLN cc_start: 0.7631 (pp30) cc_final: 0.7333 (pp30) REVERT: D 220 ARG cc_start: 0.5753 (ptt180) cc_final: 0.5537 (ptt90) REVERT: D 255 ASN cc_start: 0.7631 (m-40) cc_final: 0.7131 (m110) outliers start: 25 outliers final: 22 residues processed: 158 average time/residue: 0.0929 time to fit residues: 20.4107 Evaluate side-chains 158 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 247 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 21 optimal weight: 40.0000 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.200522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151272 restraints weight = 9613.738| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.91 r_work: 0.3423 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 8959 Z= 0.249 Angle : 0.748 10.995 12145 Z= 0.389 Chirality : 0.048 0.251 1374 Planarity : 0.005 0.063 1530 Dihedral : 5.891 67.239 1232 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.19 % Favored : 92.71 % Rotamer: Outliers : 3.03 % Allowed : 22.26 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.25), residues: 1098 helix: 0.18 (0.28), residues: 343 sheet: -0.80 (0.32), residues: 258 loop : -1.65 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 148 TYR 0.027 0.002 TYR E 178 PHE 0.023 0.002 PHE A 191 TRP 0.028 0.002 TRP D 275 HIS 0.009 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00586 ( 8955) covalent geometry : angle 0.74011 (12137) SS BOND : bond 0.01367 ( 4) SS BOND : angle 4.19195 ( 8) hydrogen bonds : bond 0.03952 ( 381) hydrogen bonds : angle 5.26416 ( 1077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.65 seconds wall clock time: 39 minutes 40.87 seconds (2380.87 seconds total)