Starting phenix.real_space_refine on Wed Mar 4 04:04:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ew0_31343/03_2026/7ew0_31343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew0_31343/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ew0_31343/03_2026/7ew0_31343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew0_31343/03_2026/7ew0_31343.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ew0_31343/03_2026/7ew0_31343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew0_31343/03_2026/7ew0_31343.map" } 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-5986/lib/python3.9/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: 2.06, per 1000 atoms: 0.23 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: 0.64 Conformation dependent library (CDL) restraints added in 266.8 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: 0.42 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: 1.26 Time building geometry restraints manager: 0.86 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: 4905 17.95 - 35.90: 434 35.90 - 53.84: 94 53.84 - 71.79: 11 71.79 - 89.74: 8 Dihedral angle restraints: 5452 sinusoidal: 2138 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 5449 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.140 Find NCS groups from input model: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 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 : 14.139 89.739 3305 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 covalent geometry : bond 0.00324 ( 9168) covalent geometry : angle 0.63179 (12406) SS BOND : bond 0.00061 ( 3) SS BOND : angle 0.27613 ( 6) hydrogen bonds : bond 0.20281 ( 385) hydrogen bonds : angle 6.64395 ( 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 : 0.285 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: 0.0966 time to fit residues: 22.7030 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 : 0.296 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 142 HIS D 63 ASN D 303 ASN E 13 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.184615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134645 restraints weight = 11110.867| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.09 r_work: 0.3528 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1355 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 10.490 12412 Z= 0.284 Chirality : 0.041 0.164 1420 Planarity : 0.004 0.050 1550 Dihedral : 4.009 47.875 1258 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.42 % Allowed : 14.04 % Favored : 84.54 % 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: -0.42 (0.24), residues: 1124 helix: 1.42 (0.27), residues: 369 sheet: -0.28 (0.32), residues: 265 loop : -1.64 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 covalent geometry : bond 0.00280 ( 9168) covalent geometry : angle 0.55007 (12406) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.86124 ( 6) hydrogen bonds : bond 0.04689 ( 385) hydrogen bonds : angle 4.63020 ( 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 139 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7604 (tt0) REVERT: A 240 MET cc_start: 0.7129 (tmm) cc_final: 0.6874 (tmm) REVERT: B 255 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8272 (mm) REVERT: D 183 ASN cc_start: 0.7822 (t0) cc_final: 0.7399 (t0) REVERT: E 34 MET cc_start: 0.7619 (mmm) cc_final: 0.7346 (mmm) REVERT: E 47 TRP cc_start: 0.7737 (t60) cc_final: 0.7527 (t60) REVERT: E 76 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7537 (mtmm) REVERT: E 93 MET cc_start: 0.7576 (mpp) cc_final: 0.7217 (mmt) outliers start: 14 outliers final: 9 residues processed: 133 average time/residue: 0.0893 time to fit residues: 16.6694 Evaluate side-chains 119 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4174 r_free = 0.4174 target = 0.180221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136615 restraints weight = 11127.385| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 3.17 r_work: 0.3446 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1899 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= 0.150 Angle : 0.560 8.355 12412 Z= 0.291 Chirality : 0.042 0.184 1420 Planarity : 0.004 0.049 1550 Dihedral : 4.098 47.226 1255 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.05 % Allowed : 15.77 % Favored : 81.18 % 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: -0.29 (0.25), residues: 1124 helix: 1.65 (0.27), residues: 375 sheet: -0.40 (0.31), residues: 270 loop : -1.59 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 234 TYR 0.020 0.001 TYR E 235 PHE 0.017 0.002 PHE B 241 TRP 0.015 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9168) covalent geometry : angle 0.55959 (12406) SS BOND : bond 0.00558 ( 3) SS BOND : angle 0.93064 ( 6) hydrogen bonds : bond 0.04789 ( 385) hydrogen bonds : angle 4.40006 ( 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 155 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7704 (tt0) REVERT: A 261 ASP cc_start: 0.8321 (t0) cc_final: 0.8089 (t0) REVERT: A 306 GLN cc_start: 0.8022 (tp40) cc_final: 0.7513 (tp40) REVERT: B 197 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7825 (tpp80) REVERT: D 140 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7676 (tt) REVERT: D 141 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 183 ASN cc_start: 0.7821 (t0) cc_final: 0.7435 (t0) REVERT: D 299 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6738 (pp) REVERT: E 34 MET cc_start: 0.7722 (mmm) cc_final: 0.7422 (mmm) REVERT: E 76 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7731 (mtmm) REVERT: E 93 MET cc_start: 0.7632 (mpp) cc_final: 0.7286 (mmt) outliers start: 30 outliers final: 16 residues processed: 147 average time/residue: 0.0933 time to fit residues: 19.2208 Evaluate side-chains 134 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 177 PHE 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: 1.9990 chunk 78 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4182 r_free = 0.4182 target = 0.181019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136799 restraints weight = 11233.137| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.22 r_work: 0.3455 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9171 Z= 0.127 Angle : 0.542 11.428 12412 Z= 0.278 Chirality : 0.041 0.186 1420 Planarity : 0.003 0.059 1550 Dihedral : 4.020 45.849 1255 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.54 % Allowed : 18.92 % 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: -0.15 (0.25), residues: 1124 helix: 1.81 (0.27), residues: 378 sheet: -0.41 (0.31), residues: 272 loop : -1.51 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 24 TYR 0.030 0.001 TYR E 235 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 covalent geometry : bond 0.00291 ( 9168) covalent geometry : angle 0.54163 (12406) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.64054 ( 6) hydrogen bonds : bond 0.04303 ( 385) hydrogen bonds : angle 4.20086 ( 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 151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8228 (m-30) REVERT: A 28 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7692 (tt0) REVERT: A 261 ASP cc_start: 0.8340 (t0) cc_final: 0.8111 (t0) REVERT: A 302 TYR cc_start: 0.7987 (t80) cc_final: 0.7625 (t80) REVERT: A 306 GLN cc_start: 0.8123 (tp40) cc_final: 0.7592 (tp40) REVERT: B 197 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7880 (tpp80) REVERT: B 239 ASN cc_start: 0.7839 (t0) cc_final: 0.7400 (t0) REVERT: C 46 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8194 (tppp) REVERT: D 67 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6396 (mm) REVERT: D 80 MET cc_start: 0.8294 (tpt) cc_final: 0.8089 (tpt) REVERT: D 140 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7716 (tt) REVERT: D 141 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7820 (tm-30) REVERT: D 183 ASN cc_start: 0.7782 (t0) cc_final: 0.7390 (t0) REVERT: D 299 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6735 (pp) REVERT: E 34 MET cc_start: 0.7771 (mmm) cc_final: 0.7469 (mmm) REVERT: E 47 TRP cc_start: 0.7888 (t60) cc_final: 0.7650 (t60) REVERT: E 76 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7726 (mtmm) REVERT: E 83 MET cc_start: 0.6153 (pmm) cc_final: 0.5274 (ppp) REVERT: E 93 MET cc_start: 0.7618 (mpp) cc_final: 0.7252 (mmt) outliers start: 25 outliers final: 15 residues processed: 146 average time/residue: 0.0957 time to fit residues: 19.4386 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 : 0.327 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 43 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4173 r_free = 0.4173 target = 0.180774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136461 restraints weight = 11279.143| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.22 r_work: 0.3461 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2343 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= 0.121 Angle : 0.524 9.605 12412 Z= 0.271 Chirality : 0.040 0.170 1420 Planarity : 0.003 0.059 1550 Dihedral : 3.747 27.455 1253 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.26 % Allowed : 18.72 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.25), residues: 1124 helix: 1.94 (0.27), residues: 376 sheet: -0.44 (0.32), residues: 267 loop : -1.43 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.022 0.001 TYR E 235 PHE 0.013 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 covalent geometry : bond 0.00278 ( 9168) covalent geometry : angle 0.52369 (12406) SS BOND : bond 0.00437 ( 3) SS BOND : angle 1.09703 ( 6) hydrogen bonds : bond 0.04120 ( 385) hydrogen bonds : angle 4.08016 ( 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 150 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8223 (m-30) REVERT: A 28 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7686 (tt0) REVERT: A 261 ASP cc_start: 0.8341 (t0) cc_final: 0.8121 (t0) REVERT: A 302 TYR cc_start: 0.8243 (t80) cc_final: 0.7942 (t80) REVERT: A 306 GLN cc_start: 0.8098 (tp40) cc_final: 0.7542 (tp40) REVERT: B 197 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7811 (tpp80) REVERT: C 46 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8220 (tppp) REVERT: D 67 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6389 (mm) REVERT: D 80 MET cc_start: 0.8256 (tpt) cc_final: 0.7963 (tpt) REVERT: D 140 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7691 (tt) REVERT: D 141 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7852 (tm-30) REVERT: D 183 ASN cc_start: 0.7741 (t0) cc_final: 0.7340 (t0) REVERT: D 299 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6854 (pp) REVERT: E 34 MET cc_start: 0.7738 (mmm) cc_final: 0.7446 (mmm) REVERT: E 47 TRP cc_start: 0.7855 (t60) cc_final: 0.7626 (t60) REVERT: E 76 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7694 (mtmm) REVERT: E 93 MET cc_start: 0.7546 (mpp) cc_final: 0.7194 (mmt) outliers start: 32 outliers final: 22 residues processed: 142 average time/residue: 0.0869 time to fit residues: 17.2431 Evaluate side-chains 138 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 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 32 THR 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 238 THR 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: 0.0870 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 43 optimal weight: 0.0170 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4191 r_free = 0.4191 target = 0.182601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137347 restraints weight = 11163.550| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.13 r_work: 0.3465 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2441 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= 0.105 Angle : 0.515 9.284 12412 Z= 0.263 Chirality : 0.040 0.156 1420 Planarity : 0.003 0.061 1550 Dihedral : 3.632 22.845 1253 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.05 % Allowed : 19.74 % Favored : 77.21 % 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: 2.07 (0.27), residues: 376 sheet: -0.33 (0.32), residues: 267 loop : -1.38 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 24 TYR 0.016 0.001 TYR E 235 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9168) covalent geometry : angle 0.51518 (12406) SS BOND : bond 0.00477 ( 3) SS BOND : angle 0.64684 ( 6) hydrogen bonds : bond 0.03763 ( 385) hydrogen bonds : angle 3.91699 ( 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 153 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8222 (m-30) REVERT: A 28 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7645 (tt0) REVERT: A 261 ASP cc_start: 0.8360 (t0) cc_final: 0.8137 (t0) REVERT: A 302 TYR cc_start: 0.8137 (t80) cc_final: 0.7851 (t80) REVERT: A 306 GLN cc_start: 0.8056 (tp40) cc_final: 0.7411 (tp40) REVERT: B 197 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7803 (tpp80) REVERT: B 256 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7704 (mtt90) REVERT: C 46 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8220 (tppp) REVERT: D 80 MET cc_start: 0.8208 (tpt) cc_final: 0.7878 (tpt) REVERT: D 140 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7631 (tt) REVERT: D 141 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7724 (tm-30) REVERT: D 183 ASN cc_start: 0.7683 (t0) cc_final: 0.7301 (t0) REVERT: D 299 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6840 (pp) REVERT: E 34 MET cc_start: 0.7680 (mmm) cc_final: 0.7337 (mmm) REVERT: E 47 TRP cc_start: 0.7808 (t60) cc_final: 0.7543 (t60) REVERT: E 93 MET cc_start: 0.7455 (mpp) cc_final: 0.7087 (mmt) outliers start: 30 outliers final: 25 residues processed: 146 average time/residue: 0.0936 time to fit residues: 18.9973 Evaluate side-chains 142 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 190 LEU 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 271 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 50 LEU 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 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: 4.9990 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4142 r_free = 0.4142 target = 0.176820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131971 restraints weight = 11312.092| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.23 r_work: 0.3391 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9171 Z= 0.182 Angle : 0.588 8.555 12412 Z= 0.305 Chirality : 0.042 0.170 1420 Planarity : 0.004 0.063 1550 Dihedral : 4.001 25.922 1253 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.17 % Allowed : 19.84 % Favored : 75.99 % 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: 1.95 (0.27), residues: 377 sheet: -0.43 (0.32), residues: 248 loop : -1.50 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 324 TYR 0.016 0.001 TYR E 235 PHE 0.019 0.002 PHE B 241 TRP 0.018 0.002 TRP E 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9168) covalent geometry : angle 0.58748 (12406) SS BOND : bond 0.00626 ( 3) SS BOND : angle 1.19776 ( 6) hydrogen bonds : bond 0.04839 ( 385) hydrogen bonds : angle 4.22189 ( 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 161 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: A 28 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7795 (tt0) REVERT: A 261 ASP cc_start: 0.8437 (t0) cc_final: 0.8167 (t0) REVERT: B 197 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7841 (tpp80) REVERT: B 256 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7931 (mtt-85) REVERT: D 67 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6399 (mm) REVERT: D 140 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7768 (tt) REVERT: D 141 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 183 ASN cc_start: 0.7620 (t0) cc_final: 0.7149 (t0) REVERT: D 299 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6886 (pp) REVERT: D 324 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7730 (ttp80) REVERT: E 34 MET cc_start: 0.7862 (mmm) cc_final: 0.7477 (mmm) REVERT: E 93 MET cc_start: 0.7627 (mpp) cc_final: 0.7298 (mmt) outliers start: 41 outliers final: 29 residues processed: 155 average time/residue: 0.0913 time to fit residues: 19.4362 Evaluate side-chains 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 B residue 271 CYS Chi-restraints excluded: chain C residue 50 LEU 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: 5.9990 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.0370 chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4193 r_free = 0.4193 target = 0.182008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137336 restraints weight = 11130.615| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 3.20 r_work: 0.3449 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9171 Z= 0.104 Angle : 0.531 11.725 12412 Z= 0.268 Chirality : 0.040 0.156 1420 Planarity : 0.003 0.061 1550 Dihedral : 3.690 23.390 1253 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.85 % Allowed : 21.97 % Favored : 75.18 % 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: 0.03 (0.25), residues: 1124 helix: 2.09 (0.27), residues: 378 sheet: -0.29 (0.33), residues: 244 loop : -1.49 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 324 TYR 0.019 0.001 TYR A 302 PHE 0.011 0.001 PHE D 58 TRP 0.017 0.001 TRP E 47 HIS 0.003 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9168) covalent geometry : angle 0.53063 (12406) SS BOND : bond 0.00374 ( 3) SS BOND : angle 0.50957 ( 6) hydrogen bonds : bond 0.03742 ( 385) hydrogen bonds : angle 3.90686 ( 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 143 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7746 (tt0) REVERT: A 261 ASP cc_start: 0.8399 (t0) cc_final: 0.8170 (t0) REVERT: B 197 ARG cc_start: 0.8027 (tpp80) cc_final: 0.7797 (tpp80) REVERT: B 256 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.7962 (mtt-85) REVERT: D 141 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8051 (tm-30) REVERT: D 183 ASN cc_start: 0.7566 (t0) cc_final: 0.7072 (t0) REVERT: D 299 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6840 (pp) REVERT: D 324 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7629 (ttp80) REVERT: E 34 MET cc_start: 0.7681 (mmm) cc_final: 0.7365 (mmm) REVERT: E 93 MET cc_start: 0.7453 (mpp) cc_final: 0.7099 (mmt) outliers start: 28 outliers final: 25 residues processed: 137 average time/residue: 0.1053 time to fit residues: 19.4895 Evaluate side-chains 136 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 MET Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 134 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4162 r_free = 0.4162 target = 0.178763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134417 restraints weight = 11173.746| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.21 r_work: 0.3430 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2820 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= 0.141 Angle : 0.569 11.079 12412 Z= 0.289 Chirality : 0.041 0.155 1420 Planarity : 0.004 0.065 1550 Dihedral : 3.799 22.312 1253 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.26 % Allowed : 21.57 % Favored : 75.18 % 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: -0.00 (0.25), residues: 1124 helix: 2.06 (0.27), residues: 376 sheet: -0.32 (0.33), residues: 243 loop : -1.48 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 324 TYR 0.019 0.001 TYR A 302 PHE 0.015 0.001 PHE B 241 TRP 0.021 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9168) covalent geometry : angle 0.56834 (12406) SS BOND : bond 0.00277 ( 3) SS BOND : angle 1.20585 ( 6) hydrogen bonds : bond 0.04287 ( 385) hydrogen bonds : angle 4.01272 ( 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 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7798 (tt0) REVERT: A 261 ASP cc_start: 0.8420 (t0) cc_final: 0.8163 (t0) REVERT: B 197 ARG cc_start: 0.8029 (tpp80) cc_final: 0.7801 (tpp80) REVERT: B 256 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7949 (mtt-85) REVERT: D 67 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6280 (mm) REVERT: D 183 ASN cc_start: 0.7484 (t0) cc_final: 0.6975 (t0) REVERT: D 299 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6849 (pp) REVERT: D 324 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7691 (ttp80) REVERT: E 34 MET cc_start: 0.7773 (mmm) cc_final: 0.7351 (mmm) REVERT: E 93 MET cc_start: 0.7541 (mpp) cc_final: 0.7199 (mmt) outliers start: 32 outliers final: 28 residues processed: 140 average time/residue: 0.1002 time to fit residues: 19.1550 Evaluate side-chains 145 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 167 CYS 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 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: 3.9990 chunk 107 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.0270 chunk 44 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4169 r_free = 0.4169 target = 0.179703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134010 restraints weight = 11121.354| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.10 r_work: 0.3456 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9171 Z= 0.130 Angle : 0.566 11.158 12412 Z= 0.288 Chirality : 0.041 0.147 1420 Planarity : 0.003 0.065 1550 Dihedral : 3.792 23.016 1253 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.95 % Allowed : 22.38 % Favored : 74.67 % 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: -0.03 (0.25), residues: 1124 helix: 2.06 (0.27), residues: 376 sheet: -0.36 (0.33), residues: 244 loop : -1.50 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 324 TYR 0.022 0.001 TYR A 302 PHE 0.013 0.001 PHE B 241 TRP 0.020 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9168) covalent geometry : angle 0.56609 (12406) SS BOND : bond 0.00423 ( 3) SS BOND : angle 0.54169 ( 6) hydrogen bonds : bond 0.04132 ( 385) hydrogen bonds : angle 3.96992 ( 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 146 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.8410 (t0) cc_final: 0.8161 (t0) REVERT: B 197 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7719 (tpp80) REVERT: B 256 ARG cc_start: 0.8246 (mtt-85) cc_final: 0.7621 (mtt-85) REVERT: C 42 GLU cc_start: 0.8084 (tp30) cc_final: 0.7761 (mm-30) REVERT: D 141 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8079 (tm-30) REVERT: D 183 ASN cc_start: 0.7400 (t0) cc_final: 0.6866 (t0) REVERT: D 299 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6726 (pp) REVERT: D 324 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7673 (ttp80) REVERT: E 34 MET cc_start: 0.7681 (mmm) cc_final: 0.7259 (mmm) REVERT: E 93 MET cc_start: 0.7457 (mpp) cc_final: 0.7119 (mmt) REVERT: E 230 MET cc_start: 0.8077 (tpp) cc_final: 0.7867 (ttm) outliers start: 29 outliers final: 27 residues processed: 140 average time/residue: 0.0994 time to fit residues: 19.1242 Evaluate side-chains 144 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 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 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 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: 20.0000 chunk 55 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4144 r_free = 0.4144 target = 0.177778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131041 restraints weight = 11244.802| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.19 r_work: 0.3400 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9171 Z= 0.158 Angle : 0.596 10.934 12412 Z= 0.304 Chirality : 0.042 0.154 1420 Planarity : 0.004 0.066 1550 Dihedral : 3.922 23.822 1253 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.76 % Allowed : 21.36 % 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: -0.12 (0.25), residues: 1124 helix: 1.94 (0.27), residues: 378 sheet: -0.41 (0.33), residues: 247 loop : -1.54 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 324 TYR 0.024 0.001 TYR A 302 PHE 0.016 0.002 PHE B 241 TRP 0.022 0.001 TRP E 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9168) covalent geometry : angle 0.59587 (12406) SS BOND : bond 0.00595 ( 3) SS BOND : angle 1.12243 ( 6) hydrogen bonds : bond 0.04558 ( 385) hydrogen bonds : angle 4.09867 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.02 seconds wall clock time: 35 minutes 58.95 seconds (2158.95 seconds total)