Starting phenix.real_space_refine on Thu Jul 2 22:44:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ew0_31343/07_2026/7ew0_31343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew0_31343/07_2026/7ew0_31343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2026/7ew0_31343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2026/7ew0_31343.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2026/7ew0_31343.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2026/7ew0_31343.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2026/7ew0_31343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2026/7ew0_31343.cif" } resolution = 3.42 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= 0.002 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1983 atoms to isotropic. 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 64 5.16 5 C 5734 2.51 5 N 1519 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8987 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2280 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'JEU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8987 At special positions: 0 Unit cell: (96.05, 123.25, 129.2, 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 64 16.00 O 1670 8.00 N 1519 7.00 C 5734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " 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: 0.70 Conformation dependent library (CDL) restraints added in 399.6 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 36.9% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.542A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.568A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.876A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.997A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.757A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.725A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 removed outlier: 3.900A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.700A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 removed outlier: 4.368A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.890A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 23 through 33 removed outlier: 3.586A pdb=" N ARG D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 73 removed outlier: 3.819A pdb=" N THR D 73 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 105 removed outlier: 3.852A pdb=" N TYR D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.810A pdb=" N THR D 109 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 110 " --> pdb=" O ALA D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 110' Processing helix chain 'D' and resid 113 through 148 removed outlier: 3.514A pdb=" N LEU D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 181 removed outlier: 4.366A pdb=" N LEU D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 199 through 236 removed outlier: 3.540A pdb=" N ILE D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 269 removed outlier: 3.928A pdb=" N SER D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 removed outlier: 3.645A pdb=" N PHE D 273 " --> pdb=" O TRP D 269 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 292 Processing helix chain 'D' and resid 295 through 314 removed outlier: 4.177A pdb=" N LEU D 299 " --> pdb=" O TYR D 295 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 315 through 325 removed outlier: 3.686A pdb=" N ARG D 319 " --> pdb=" O ASN D 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.589A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.754A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.186A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.679A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.193A 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 151 removed outlier: 6.945A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.621A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.774A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.819A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.551A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.563A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.623A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.585A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL E 226 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 177 " --> pdb=" O TYR E 228 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1098 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: 1.48 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1443 1.28 - 1.41: 2324 1.41 - 1.54: 5300 1.54 - 1.68: 10 1.68 - 1.81: 91 Bond restraints: 9168 Sorted by residual: bond pdb=" C22 JEU D 401 " pdb=" O27 JEU D 401 " ideal model delta sigma weight residual 1.322 1.427 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C23 JEU D 401 " pdb=" C25 JEU D 401 " ideal model delta sigma weight residual 1.424 1.526 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C13 JEU D 401 " pdb=" C14 JEU D 401 " ideal model delta sigma weight residual 1.461 1.409 0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C VAL D 132 " pdb=" O VAL D 132 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 6.02e+00 bond pdb=" C ARG E 191 " pdb=" O ARG E 191 " ideal model delta sigma weight residual 1.242 1.217 0.024 1.00e-02 1.00e+04 5.81e+00 ... (remaining 9163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 12262 2.35 - 4.71: 113 4.71 - 7.06: 26 7.06 - 9.42: 3 9.42 - 11.77: 2 Bond angle restraints: 12406 Sorted by residual: angle pdb=" N PHE D 237 " pdb=" CA PHE D 237 " pdb=" C PHE D 237 " ideal model delta sigma weight residual 111.28 120.03 -8.75 1.09e+00 8.42e-01 6.45e+01 angle pdb=" N ILE E 189 " pdb=" CA ILE E 189 " pdb=" C ILE E 189 " ideal model delta sigma weight residual 106.61 118.33 -11.72 1.78e+00 3.16e-01 4.33e+01 angle pdb=" C ILE E 189 " pdb=" CA ILE E 189 " pdb=" CB ILE E 189 " ideal model delta sigma weight residual 111.09 103.88 7.21 1.11e+00 8.12e-01 4.22e+01 angle pdb=" N ARG D 234 " pdb=" CA ARG D 234 " pdb=" C ARG D 234 " ideal model delta sigma weight residual 111.36 117.93 -6.57 1.09e+00 8.42e-01 3.63e+01 angle pdb=" N SER E 193 " pdb=" CA SER E 193 " pdb=" C SER E 193 " ideal model delta sigma weight residual 110.80 122.57 -11.77 2.13e+00 2.20e-01 3.05e+01 ... (remaining 12401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4900 17.95 - 35.90: 431 35.90 - 53.84: 94 53.84 - 71.79: 11 71.79 - 89.74: 8 Dihedral angle restraints: 5444 sinusoidal: 2130 harmonic: 3314 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -126.70 40.70 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" SG CYS D 184 " pdb=" CB CYS D 191 " pdb=" SG CYS D 191 " pdb=" CA CYS D 191 " ideal model delta sinusoidal sigma weight residual -73.00 1.17 -74.17 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" CB CYS D 282 " pdb=" SG CYS D 282 " pdb=" SG CYS D 287 " pdb=" CB CYS D 287 " ideal model delta sinusoidal sigma weight residual 93.00 125.95 -32.95 1 1.00e+01 1.00e-02 1.54e+01 ... (remaining 5441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1299 0.072 - 0.144: 110 0.144 - 0.217: 6 0.217 - 0.289: 3 0.289 - 0.361: 2 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA PHE D 237 " pdb=" N PHE D 237 " pdb=" C PHE D 237 " pdb=" CB PHE D 237 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA TYR E 190 " pdb=" N TYR E 190 " pdb=" C TYR E 190 " pdb=" CB TYR E 190 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PHE D 133 " pdb=" N PHE D 133 " pdb=" C PHE D 133 " pdb=" CB PHE D 133 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1417 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 235 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LEU D 235 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU D 235 " -0.016 2.00e-02 2.50e+03 pdb=" N THR D 236 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 131 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C SER D 131 " -0.037 2.00e-02 2.50e+03 pdb=" O SER D 131 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL D 132 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO E 236 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.030 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 117 2.65 - 3.21: 7939 3.21 - 3.77: 13067 3.77 - 4.34: 16927 4.34 - 4.90: 28840 Nonbonded interactions: 66890 Sorted by model distance: nonbonded pdb=" O SER D 232 " pdb=" CG2 THR D 236 " model vdw 2.087 3.460 nonbonded pdb=" OG SER E 17 " pdb=" O MET E 83 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.266 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.266 3.040 nonbonded pdb=" N ASN E 194 " pdb=" OD1 ASN E 194 " model vdw 2.288 3.120 ... (remaining 66885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.080 Find NCS groups from input model: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 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 : 0.003 0.105 9171 Z= 0.189 Angle : 0.632 11.771 12412 Z= 0.379 Chirality : 0.044 0.361 1420 Planarity : 0.003 0.052 1550 Dihedral : 14.130 89.739 3297 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.71 % Allowed : 6.10 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.22), residues: 1124 helix: 0.24 (0.25), residues: 366 sheet: -0.73 (0.31), residues: 271 loop : -2.04 (0.23), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 8 TYR 0.015 0.001 TYR A 230 PHE 0.010 0.001 PHE D 273 TRP 0.014 0.001 TRP E 176 HIS 0.004 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.19 ( 9168) covalent geometry : angle 0.63179 / 0.38 (12406) SS BOND : bond 0.00061 / 0.03 ( 3) SS BOND : angle 0.27613 / 0.15 ( 6) hydrogen bonds : bond 0.20281 / 13.85 ( 385) hydrogen bonds : angle 6.64395 / 4.64 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 306 GLN cc_start: 0.7511 (mm110) cc_final: 0.6969 (tp40) REVERT: D 58 PHE cc_start: 0.7165 (t80) cc_final: 0.6132 (t80) REVERT: D 141 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 183 ASN cc_start: 0.7838 (t0) cc_final: 0.7586 (t0) REVERT: E 47 TRP cc_start: 0.7802 (t60) cc_final: 0.7602 (t60) outliers start: 7 outliers final: 3 residues processed: 170 average time/residue: 0.0895 time to fit residues: 20.9787 Evaluate side-chains 127 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 194 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0870 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 142 HIS D 63 ASN D 303 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.184386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134724 restraints weight = 11101.782| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.05 r_work: 0.3524 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9171 Z= 0.125 Angle : 0.550 10.564 12412 Z= 0.284 Chirality : 0.041 0.163 1420 Planarity : 0.004 0.049 1550 Dihedral : 4.165 48.896 1250 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.53 % Allowed : 14.14 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1124 helix: 1.41 (0.27), residues: 370 sheet: -0.29 (0.32), residues: 265 loop : -1.63 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 231 TYR 0.016 0.001 TYR E 235 PHE 0.020 0.001 PHE D 58 TRP 0.012 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 9168) covalent geometry : angle 0.54987 / 0.28 (12406) SS BOND : bond 0.00344 / 0.17 ( 3) SS BOND : angle 0.83577 / 0.43 ( 6) hydrogen bonds : bond 0.04585 / 3.16 ( 385) hydrogen bonds : angle 4.56627 / 3.16 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7566 (tt0) REVERT: A 240 MET cc_start: 0.7122 (tmm) cc_final: 0.6879 (tmm) REVERT: B 255 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8315 (mm) REVERT: D 183 ASN cc_start: 0.7821 (t0) cc_final: 0.7459 (t0) REVERT: E 34 MET cc_start: 0.7579 (mmm) cc_final: 0.7357 (mmm) REVERT: E 47 TRP cc_start: 0.7716 (t60) cc_final: 0.7500 (t60) REVERT: E 76 LYS cc_start: 0.7830 (mtmm) cc_final: 0.7594 (mtmm) REVERT: E 93 MET cc_start: 0.7545 (mpp) cc_final: 0.7199 (mmt) outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 0.0803 time to fit residues: 15.1610 Evaluate side-chains 124 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 294 ASN E 13 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.133951 restraints weight = 11234.826| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.42 r_work: 0.3412 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9171 Z= 0.159 Angle : 0.570 8.392 12412 Z= 0.296 Chirality : 0.042 0.189 1420 Planarity : 0.004 0.050 1550 Dihedral : 4.236 47.353 1247 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.56 % Allowed : 15.16 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.24), residues: 1124 helix: 1.64 (0.27), residues: 375 sheet: -0.31 (0.32), residues: 253 loop : -1.66 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 234 TYR 0.019 0.001 TYR E 235 PHE 0.018 0.002 PHE B 241 TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 9168) covalent geometry : angle 0.56988 / 0.30 (12406) SS BOND : bond 0.00321 / 0.16 ( 3) SS BOND : angle 0.81745 / 0.43 ( 6) hydrogen bonds : bond 0.04903 / 3.35 ( 385) hydrogen bonds : angle 4.42052 / 3.11 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 124 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8070 (m-30) REVERT: A 28 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7641 (tt0) REVERT: A 261 ASP cc_start: 0.8340 (t0) cc_final: 0.8123 (t0) REVERT: A 306 GLN cc_start: 0.7978 (tp40) cc_final: 0.7508 (tp40) REVERT: B 197 ARG cc_start: 0.7986 (tpp80) cc_final: 0.7713 (tpp80) REVERT: D 140 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7496 (tt) REVERT: D 141 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7891 (tm-30) REVERT: D 183 ASN cc_start: 0.7788 (t0) cc_final: 0.7412 (t0) REVERT: D 299 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6543 (pp) REVERT: E 34 MET cc_start: 0.7641 (mmm) cc_final: 0.7395 (mmm) REVERT: E 76 LYS cc_start: 0.8057 (mtmm) cc_final: 0.7696 (mtmm) REVERT: E 93 MET cc_start: 0.7497 (mpp) cc_final: 0.7151 (mmt) outliers start: 35 outliers final: 19 residues processed: 150 average time/residue: 0.0908 time to fit residues: 19.2618 Evaluate side-chains 135 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.2980 chunk 78 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN D 101 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.181475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129753 restraints weight = 11313.272| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.29 r_work: 0.3469 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9171 Z= 0.118 Angle : 0.533 11.211 12412 Z= 0.273 Chirality : 0.041 0.177 1420 Planarity : 0.003 0.052 1550 Dihedral : 4.067 45.659 1247 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.44 % Allowed : 19.02 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.25), residues: 1124 helix: 1.86 (0.27), residues: 376 sheet: -0.26 (0.32), residues: 255 loop : -1.55 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.021 0.001 TYR E 235 PHE 0.014 0.001 PHE E 203 TRP 0.019 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 9168) covalent geometry : angle 0.53314 / 0.27 (12406) SS BOND : bond 0.00097 / 0.05 ( 3) SS BOND : angle 0.62858 / 0.32 ( 6) hydrogen bonds : bond 0.04213 / 2.89 ( 385) hydrogen bonds : angle 4.17559 / 2.92 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7581 (tt0) REVERT: A 261 ASP cc_start: 0.8351 (t0) cc_final: 0.8116 (t0) REVERT: A 302 TYR cc_start: 0.7997 (t80) cc_final: 0.7524 (t80) REVERT: A 306 GLN cc_start: 0.7982 (tp40) cc_final: 0.7368 (tp40) REVERT: B 197 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7684 (tpp80) REVERT: C 46 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8194 (tppp) REVERT: D 67 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6209 (mm) REVERT: D 80 MET cc_start: 0.8201 (tpt) cc_final: 0.7994 (tpt) REVERT: D 140 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7463 (tt) REVERT: D 141 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7714 (tm-30) REVERT: D 183 ASN cc_start: 0.7735 (t0) cc_final: 0.7348 (t0) REVERT: D 299 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6488 (pp) REVERT: E 34 MET cc_start: 0.7603 (mmm) cc_final: 0.7320 (mmm) REVERT: E 47 TRP cc_start: 0.7819 (t60) cc_final: 0.7535 (t60) REVERT: E 76 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7673 (mtmm) REVERT: E 83 MET cc_start: 0.6131 (pmm) cc_final: 0.5233 (ppp) REVERT: E 93 MET cc_start: 0.7465 (mpp) cc_final: 0.7109 (mmt) REVERT: E 230 MET cc_start: 0.7263 (ttt) cc_final: 0.6977 (tpp) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.0904 time to fit residues: 17.6984 Evaluate side-chains 134 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN ** E 231 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 = 0.4161 r_free = 0.4161 target = 0.179701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134425 restraints weight = 11316.016| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.52 r_work: 0.3388 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9171 Z= 0.132 Angle : 0.538 9.600 12412 Z= 0.277 Chirality : 0.041 0.180 1420 Planarity : 0.003 0.059 1550 Dihedral : 3.854 34.950 1245 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.15 % Allowed : 19.13 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1124 helix: 1.92 (0.27), residues: 378 sheet: -0.32 (0.32), residues: 249 loop : -1.50 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.017 0.001 TYR E 235 PHE 0.014 0.001 PHE B 241 TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 9168) covalent geometry : angle 0.53771 / 0.28 (12406) SS BOND : bond 0.00430 / 0.22 ( 3) SS BOND : angle 0.82427 / 0.45 ( 6) hydrogen bonds : bond 0.04335 / 2.96 ( 385) hydrogen bonds : angle 4.14715 / 2.90 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: A 28 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7590 (tt0) REVERT: A 261 ASP cc_start: 0.8374 (t0) cc_final: 0.8146 (t0) REVERT: A 302 TYR cc_start: 0.8142 (t80) cc_final: 0.7807 (t80) REVERT: A 306 GLN cc_start: 0.8010 (tp40) cc_final: 0.7435 (tp40) REVERT: B 197 ARG cc_start: 0.7985 (tpp80) cc_final: 0.7697 (tpp80) REVERT: B 256 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.7529 (mtt90) REVERT: C 46 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8232 (tppp) REVERT: D 67 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6140 (mm) REVERT: D 80 MET cc_start: 0.8199 (tpt) cc_final: 0.7914 (tpt) REVERT: D 140 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7502 (tt) REVERT: D 141 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7499 (tm-30) REVERT: D 183 ASN cc_start: 0.7724 (t0) cc_final: 0.7310 (t0) REVERT: D 299 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6625 (pp) REVERT: E 34 MET cc_start: 0.7667 (mmm) cc_final: 0.7294 (mmm) REVERT: E 47 TRP cc_start: 0.7843 (t60) cc_final: 0.7600 (t60) REVERT: E 76 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7638 (mtmm) REVERT: E 93 MET cc_start: 0.7421 (mpp) cc_final: 0.7077 (mmt) outliers start: 31 outliers final: 20 residues processed: 143 average time/residue: 0.0899 time to fit residues: 17.8862 Evaluate side-chains 136 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 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 = 0.4181 r_free = 0.4181 target = 0.181563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136578 restraints weight = 11186.799| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.08 r_work: 0.3460 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9171 Z= 0.110 Angle : 0.509 9.240 12412 Z= 0.262 Chirality : 0.040 0.159 1420 Planarity : 0.003 0.058 1550 Dihedral : 3.726 29.026 1245 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.26 % Allowed : 19.94 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1124 helix: 2.03 (0.27), residues: 375 sheet: -0.24 (0.33), residues: 250 loop : -1.48 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.015 0.001 TYR E 235 PHE 0.011 0.001 PHE A 189 TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 9168) covalent geometry : angle 0.50894 / 0.26 (12406) SS BOND : bond 0.00494 / 0.25 ( 3) SS BOND : angle 0.59484 / 0.31 ( 6) hydrogen bonds : bond 0.03914 / 2.68 ( 385) hydrogen bonds : angle 3.98027 / 2.78 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7671 (tt0) REVERT: A 261 ASP cc_start: 0.8362 (t0) cc_final: 0.8134 (t0) REVERT: A 302 TYR cc_start: 0.8216 (t80) cc_final: 0.7904 (t80) REVERT: A 306 GLN cc_start: 0.8043 (tp40) cc_final: 0.7406 (tp40) REVERT: B 197 ARG cc_start: 0.8053 (tpp80) cc_final: 0.7790 (tpp80) REVERT: B 256 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7843 (mtt-85) REVERT: C 46 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8253 (tppp) REVERT: D 67 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6350 (mm) REVERT: D 80 MET cc_start: 0.8221 (tpt) cc_final: 0.7941 (tpt) REVERT: D 140 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7642 (tt) REVERT: D 141 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7769 (tm-30) REVERT: D 183 ASN cc_start: 0.7689 (t0) cc_final: 0.7297 (t0) REVERT: D 299 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6787 (pp) REVERT: E 34 MET cc_start: 0.7661 (mmm) cc_final: 0.7322 (mmm) REVERT: E 47 TRP cc_start: 0.7823 (t60) cc_final: 0.7592 (t60) REVERT: E 93 MET cc_start: 0.7466 (mpp) cc_final: 0.7101 (mmt) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.0941 time to fit residues: 18.8218 Evaluate side-chains 143 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.175241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.130331 restraints weight = 11212.419| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 3.10 r_work: 0.3409 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9171 Z= 0.172 Angle : 0.575 8.607 12412 Z= 0.299 Chirality : 0.042 0.174 1420 Planarity : 0.004 0.063 1550 Dihedral : 3.999 30.139 1245 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.97 % Allowed : 19.53 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1124 helix: 1.95 (0.27), residues: 377 sheet: -0.50 (0.32), residues: 249 loop : -1.49 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 324 TYR 0.014 0.001 TYR B 111 PHE 0.017 0.002 PHE B 241 TRP 0.018 0.001 TRP E 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 9168) covalent geometry : angle 0.57498 / 0.30 (12406) SS BOND : bond 0.01061 / 0.53 ( 3) SS BOND : angle 1.18087 / 0.67 ( 6) hydrogen bonds : bond 0.04742 / 3.22 ( 385) hydrogen bonds : angle 4.22065 / 2.96 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8215 (m-30) REVERT: A 28 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7787 (tt0) REVERT: A 261 ASP cc_start: 0.8428 (t0) cc_final: 0.8154 (t0) REVERT: B 197 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7828 (tpp80) REVERT: B 256 ARG cc_start: 0.8176 (mtt-85) cc_final: 0.7928 (mtt-85) REVERT: D 67 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6220 (mm) REVERT: D 140 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7725 (tt) REVERT: D 141 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7879 (tm-30) REVERT: D 183 ASN cc_start: 0.7652 (t0) cc_final: 0.7176 (t0) REVERT: D 299 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6870 (pp) REVERT: D 324 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7702 (ttp80) REVERT: E 34 MET cc_start: 0.7840 (mmm) cc_final: 0.7434 (mmm) REVERT: E 93 MET cc_start: 0.7620 (mpp) cc_final: 0.7281 (mmt) outliers start: 39 outliers final: 28 residues processed: 151 average time/residue: 0.0898 time to fit residues: 18.9709 Evaluate side-chains 146 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.177443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.131781 restraints weight = 11131.306| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.30 r_work: 0.3392 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9171 Z= 0.128 Angle : 0.545 11.518 12412 Z= 0.279 Chirality : 0.041 0.153 1420 Planarity : 0.003 0.059 1550 Dihedral : 3.862 27.727 1245 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.56 % Allowed : 20.85 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.25), residues: 1124 helix: 1.99 (0.27), residues: 377 sheet: -0.44 (0.33), residues: 243 loop : -1.46 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 324 TYR 0.019 0.001 TYR A 302 PHE 0.013 0.001 PHE B 241 TRP 0.019 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9168) covalent geometry : angle 0.54536 / 0.28 (12406) SS BOND : bond 0.00523 / 0.26 ( 3) SS BOND : angle 0.52952 / 0.27 ( 6) hydrogen bonds : bond 0.04229 / 2.89 ( 385) hydrogen bonds : angle 4.05130 / 2.83 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: A 261 ASP cc_start: 0.8445 (t0) cc_final: 0.8177 (t0) REVERT: B 197 ARG cc_start: 0.7967 (tpp80) cc_final: 0.7710 (tpp80) REVERT: B 256 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7904 (mtt-85) REVERT: D 67 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6151 (mm) REVERT: D 140 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7618 (tt) REVERT: D 141 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 183 ASN cc_start: 0.7541 (t0) cc_final: 0.7076 (t0) REVERT: D 299 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6635 (pp) REVERT: D 324 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7620 (ttp80) REVERT: E 34 MET cc_start: 0.7719 (mmm) cc_final: 0.7327 (mmm) REVERT: E 93 MET cc_start: 0.7452 (mpp) cc_final: 0.7114 (mmt) outliers start: 35 outliers final: 30 residues processed: 144 average time/residue: 0.0925 time to fit residues: 18.3527 Evaluate side-chains 150 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 41 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 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 = 0.4187 r_free = 0.4187 target = 0.181473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137223 restraints weight = 11120.758| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.12 r_work: 0.3457 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9171 Z= 0.108 Angle : 0.532 11.261 12412 Z= 0.271 Chirality : 0.040 0.163 1420 Planarity : 0.003 0.061 1550 Dihedral : 3.681 22.939 1245 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.05 % Allowed : 21.57 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1124 helix: 2.04 (0.27), residues: 378 sheet: -0.37 (0.33), residues: 244 loop : -1.47 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 324 TYR 0.017 0.001 TYR A 302 PHE 0.011 0.001 PHE D 58 TRP 0.019 0.001 TRP E 47 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9168) covalent geometry : angle 0.53195 / 0.27 (12406) SS BOND : bond 0.00316 / 0.16 ( 3) SS BOND : angle 1.00031 / 0.57 ( 6) hydrogen bonds : bond 0.03716 / 2.54 ( 385) hydrogen bonds : angle 3.89852 / 2.72 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8404 (t0) cc_final: 0.8161 (t0) REVERT: B 197 ARG cc_start: 0.7993 (tpp80) cc_final: 0.7760 (tpp80) REVERT: B 256 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7889 (mtt-85) REVERT: D 183 ASN cc_start: 0.7486 (t0) cc_final: 0.6987 (t0) REVERT: D 299 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6838 (pp) REVERT: D 324 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7649 (ttp80) REVERT: E 34 MET cc_start: 0.7664 (mmm) cc_final: 0.7259 (mmm) REVERT: E 93 MET cc_start: 0.7456 (mpp) cc_final: 0.7097 (mmt) REVERT: E 230 MET cc_start: 0.8090 (tpp) cc_final: 0.7697 (tpp) outliers start: 30 outliers final: 27 residues processed: 143 average time/residue: 0.0940 time to fit residues: 18.5699 Evaluate side-chains 140 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 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 = 0.4177 r_free = 0.4177 target = 0.180341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136388 restraints weight = 11085.081| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.22 r_work: 0.3428 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9171 Z= 0.123 Angle : 0.561 11.134 12412 Z= 0.283 Chirality : 0.040 0.147 1420 Planarity : 0.003 0.063 1550 Dihedral : 3.718 22.258 1245 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.15 % Allowed : 21.97 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1124 helix: 2.05 (0.27), residues: 378 sheet: -0.34 (0.33), residues: 244 loop : -1.46 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 324 TYR 0.021 0.001 TYR A 302 PHE 0.015 0.001 PHE E 239 TRP 0.019 0.001 TRP E 47 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 9168) covalent geometry : angle 0.56143 / 0.28 (12406) SS BOND : bond 0.00407 / 0.20 ( 3) SS BOND : angle 0.54355 / 0.27 ( 6) hydrogen bonds : bond 0.03964 / 2.70 ( 385) hydrogen bonds : angle 3.93156 / 2.75 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8429 (t0) cc_final: 0.8170 (t0) REVERT: B 197 ARG cc_start: 0.7994 (tpp80) cc_final: 0.7754 (tpp80) REVERT: B 256 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7913 (mtt-85) REVERT: D 140 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7591 (tt) REVERT: D 183 ASN cc_start: 0.7427 (t0) cc_final: 0.6897 (t0) REVERT: D 299 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6787 (pp) REVERT: D 324 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7647 (ttp80) REVERT: E 93 MET cc_start: 0.7526 (mpp) cc_final: 0.7199 (mmt) outliers start: 31 outliers final: 27 residues processed: 135 average time/residue: 0.0919 time to fit residues: 17.3345 Evaluate side-chains 139 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 5 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 294 ASN ** E 231 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 = 0.4137 r_free = 0.4137 target = 0.174101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127573 restraints weight = 11144.779| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.14 r_work: 0.3415 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9171 Z= 0.190 Angle : 0.629 10.829 12412 Z= 0.322 Chirality : 0.043 0.164 1420 Planarity : 0.004 0.064 1550 Dihedral : 4.100 26.401 1245 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.56 % Allowed : 21.46 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1124 helix: 1.86 (0.27), residues: 378 sheet: -0.52 (0.33), residues: 247 loop : -1.57 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 324 TYR 0.026 0.002 TYR A 302 PHE 0.019 0.002 PHE B 241 TRP 0.023 0.002 TRP E 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 9168) covalent geometry : angle 0.62841 / 0.32 (12406) SS BOND : bond 0.00505 / 0.25 ( 3) SS BOND : angle 1.15062 / 0.65 ( 6) hydrogen bonds : bond 0.04950 / 3.36 ( 385) hydrogen bonds : angle 4.24344 / 2.98 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.53 seconds wall clock time: 36 minutes 55.35 seconds (2215.35 seconds total)