Starting phenix.real_space_refine on Mon Jul 28 21:22:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ew0_31343/07_2025/7ew0_31343.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ew0_31343/07_2025/7ew0_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_2025/7ew0_31343.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2025/7ew0_31343.map" model { file = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2025/7ew0_31343.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ew0_31343/07_2025/7ew0_31343.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.11, per 1000 atoms: 0.79 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: 3.67 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.18 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: 3.19 Time building geometry restraints manager: 3.29 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: 59.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.720 Check model and map are aligned: 0.160 Set scattering table: 0.250 Process input model: 33.230 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:4.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.220 ------------------------------------------------------------------------------- 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 : 6.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP E 176 HIS 0.004 0.000 HIS E 35 PHE 0.010 0.001 PHE D 273 TYR 0.015 0.001 TYR A 230 ARG 0.003 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.20281 ( 385) hydrogen bonds : angle 6.64395 ( 1098) SS BOND : bond 0.00061 ( 3) SS BOND : angle 0.27613 ( 6) covalent geometry : bond 0.00324 ( 9168) covalent geometry : angle 0.63179 (12406) *********************** 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 : 1.419 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: 0.3677 time to fit residues: 87.0090 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 : 0.864 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.186329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136674 restraints weight = 10971.548| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.05 r_work: 0.3539 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9171 Z= 0.112 Angle : 0.537 10.621 12412 Z= 0.276 Chirality : 0.040 0.155 1420 Planarity : 0.003 0.049 1550 Dihedral : 3.944 47.462 1258 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1124 helix: 1.46 (0.27), residues: 373 sheet: -0.30 (0.32), residues: 268 loop : -1.63 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.019 0.001 PHE D 58 TYR 0.016 0.001 TYR E 235 ARG 0.004 0.000 ARG D 231 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 385) hydrogen bonds : angle 4.55083 ( 1098) SS BOND : bond 0.00602 ( 3) SS BOND : angle 0.80355 ( 6) covalent geometry : bond 0.00243 ( 9168) covalent geometry : angle 0.53666 (12406) *********************** 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: 15 poor density : 124 time to evaluate : 2.229 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7557 (tt0) REVERT: A 240 MET cc_start: 0.7205 (tmm) cc_final: 0.6996 (tmm) REVERT: B 255 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8331 (mm) REVERT: C 42 GLU cc_start: 0.8031 (tp30) cc_final: 0.7639 (mm-30) REVERT: D 77 HIS cc_start: 0.8050 (m90) cc_final: 0.7791 (m90) REVERT: D 183 ASN cc_start: 0.7780 (t0) cc_final: 0.7366 (t0) REVERT: E 34 MET cc_start: 0.7590 (mmm) cc_final: 0.7347 (mmm) REVERT: E 47 TRP cc_start: 0.7639 (t60) cc_final: 0.7371 (t60) REVERT: E 76 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7539 (mtmm) REVERT: E 93 MET cc_start: 0.7498 (mpp) cc_final: 0.7136 (mmt) outliers start: 15 outliers final: 9 residues processed: 133 average time/residue: 0.2417 time to fit residues: 45.7834 Evaluate side-chains 122 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 86 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 81 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 195 HIS A 294 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 GLN ** 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 = 0.4138 r_free = 0.4138 target = 0.176784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133225 restraints weight = 11289.186| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.21 r_work: 0.3397 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2117 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= 0.205 Angle : 0.621 8.553 12412 Z= 0.323 Chirality : 0.044 0.211 1420 Planarity : 0.004 0.051 1550 Dihedral : 4.392 48.300 1255 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.56 % Allowed : 15.56 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1124 helix: 1.55 (0.27), residues: 375 sheet: -0.40 (0.31), residues: 253 loop : -1.65 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.005 0.001 HIS A 195 PHE 0.021 0.002 PHE B 241 TYR 0.019 0.002 TYR E 235 ARG 0.004 0.000 ARG D 234 Details of bonding type rmsd hydrogen bonds : bond 0.05490 ( 385) hydrogen bonds : angle 4.60209 ( 1098) SS BOND : bond 0.00759 ( 3) SS BOND : angle 0.84121 ( 6) covalent geometry : bond 0.00490 ( 9168) covalent geometry : angle 0.62092 (12406) *********************** 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: 35 poor density : 120 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: A 28 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7712 (tt0) REVERT: A 306 GLN cc_start: 0.7991 (tp40) cc_final: 0.7485 (tp40) REVERT: B 197 ARG cc_start: 0.8076 (tpp80) cc_final: 0.7836 (tpp80) REVERT: D 140 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7741 (tt) REVERT: D 141 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8114 (tm-30) REVERT: D 183 ASN cc_start: 0.7875 (t0) cc_final: 0.7508 (t0) REVERT: D 299 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6848 (pp) REVERT: E 34 MET cc_start: 0.7747 (mmm) cc_final: 0.7539 (mmm) REVERT: E 76 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7814 (mtmm) REVERT: E 93 MET cc_start: 0.7677 (mpp) cc_final: 0.7322 (mmt) outliers start: 35 outliers final: 17 residues processed: 145 average time/residue: 0.2693 time to fit residues: 54.6572 Evaluate side-chains 128 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 210 LEU 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 80 MET 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 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 27 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4163 r_free = 0.4163 target = 0.179576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.134192 restraints weight = 11172.559| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.10 r_work: 0.3453 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9171 Z= 0.139 Angle : 0.555 11.173 12412 Z= 0.287 Chirality : 0.041 0.189 1420 Planarity : 0.003 0.050 1550 Dihedral : 4.202 46.857 1255 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.95 % Allowed : 18.72 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1124 helix: 1.78 (0.27), residues: 378 sheet: -0.36 (0.32), residues: 254 loop : -1.58 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE B 241 TYR 0.022 0.001 TYR E 235 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 385) hydrogen bonds : angle 4.30017 ( 1098) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.60991 ( 6) covalent geometry : bond 0.00324 ( 9168) covalent geometry : angle 0.55471 (12406) *********************** 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 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7631 (tt0) REVERT: A 306 GLN cc_start: 0.7930 (tp40) cc_final: 0.7340 (tp40) REVERT: B 197 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7830 (tpp80) REVERT: D 67 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6254 (mm) REVERT: D 140 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7654 (tt) REVERT: D 141 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7916 (tm-30) REVERT: D 183 ASN cc_start: 0.7808 (t0) cc_final: 0.7384 (t0) REVERT: D 299 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6703 (pp) REVERT: E 34 MET cc_start: 0.7737 (mmm) cc_final: 0.7439 (mmm) REVERT: E 47 TRP cc_start: 0.7851 (t60) cc_final: 0.7611 (t60) REVERT: E 76 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7763 (mtmm) REVERT: E 83 MET cc_start: 0.6184 (pmm) cc_final: 0.5299 (ppp) REVERT: E 93 MET cc_start: 0.7539 (mpp) cc_final: 0.7192 (mmt) outliers start: 29 outliers final: 20 residues processed: 142 average time/residue: 0.2119 time to fit residues: 42.2482 Evaluate side-chains 135 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 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 119 LEU 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 57 THR Chi-restraints excluded: chain E residue 91 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 58 optimal weight: 0.0270 chunk 70 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 68 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 = 0.4180 r_free = 0.4180 target = 0.182597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.130699 restraints weight = 11204.559| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.32 r_work: 0.3470 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9171 Z= 0.105 Angle : 0.518 9.891 12412 Z= 0.264 Chirality : 0.040 0.163 1420 Planarity : 0.003 0.057 1550 Dihedral : 3.941 44.756 1255 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.44 % Allowed : 19.74 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1124 helix: 2.00 (0.27), residues: 376 sheet: -0.28 (0.32), residues: 251 loop : -1.54 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.010 0.001 PHE D 58 TYR 0.018 0.001 TYR E 235 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 385) hydrogen bonds : angle 4.04687 ( 1098) SS BOND : bond 0.00732 ( 3) SS BOND : angle 1.12168 ( 6) covalent geometry : bond 0.00232 ( 9168) covalent geometry : angle 0.51731 (12406) *********************** 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 151 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.052 Fit side-chains REVERT: A 28 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7505 (tt0) REVERT: A 302 TYR cc_start: 0.7851 (t80) cc_final: 0.7467 (t80) REVERT: A 306 GLN cc_start: 0.7873 (tp40) cc_final: 0.7156 (tp40) REVERT: B 197 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7616 (tpp80) REVERT: B 256 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7553 (mtt90) REVERT: C 46 LYS cc_start: 0.8631 (mmmm) cc_final: 0.8233 (tppp) REVERT: D 183 ASN cc_start: 0.7705 (t0) cc_final: 0.7264 (t0) REVERT: D 299 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6551 (pp) REVERT: E 34 MET cc_start: 0.7486 (mmm) cc_final: 0.7192 (mmm) REVERT: E 47 TRP cc_start: 0.7598 (t60) cc_final: 0.7311 (t60) REVERT: E 76 LYS cc_start: 0.8009 (mtmm) cc_final: 0.7629 (mtmm) REVERT: E 93 MET cc_start: 0.7303 (mpp) cc_final: 0.6950 (mmt) outliers start: 24 outliers final: 17 residues processed: 145 average time/residue: 0.2252 time to fit residues: 45.5093 Evaluate side-chains 131 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 102 LEU 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 5 VAL Chi-restraints excluded: chain E residue 22 CYS 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 52 optimal weight: 0.0870 chunk 31 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 ** 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 = 0.4208 r_free = 0.4208 target = 0.184939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.131177 restraints weight = 11013.521| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.28 r_work: 0.3526 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9171 Z= 0.094 Angle : 0.510 9.263 12412 Z= 0.257 Chirality : 0.039 0.144 1420 Planarity : 0.003 0.057 1550 Dihedral : 3.558 22.862 1253 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.75 % Allowed : 20.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1124 helix: 2.17 (0.27), residues: 376 sheet: -0.10 (0.33), residues: 251 loop : -1.45 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.000 HIS E 35 PHE 0.010 0.001 PHE D 58 TYR 0.014 0.001 TYR E 235 ARG 0.004 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 385) hydrogen bonds : angle 3.89538 ( 1098) SS BOND : bond 0.00437 ( 3) SS BOND : angle 0.57405 ( 6) covalent geometry : bond 0.00202 ( 9168) covalent geometry : angle 0.50978 (12406) *********************** 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 148 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.082 Fit side-chains REVERT: A 24 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7229 (ttm170) REVERT: A 28 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7559 (tt0) REVERT: A 302 TYR cc_start: 0.7886 (t80) cc_final: 0.7523 (t80) REVERT: A 306 GLN cc_start: 0.7926 (tp40) cc_final: 0.7211 (tp40) REVERT: B 197 ARG cc_start: 0.7954 (tpp80) cc_final: 0.7683 (tpp80) REVERT: B 256 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7789 (mtt-85) REVERT: C 46 LYS cc_start: 0.8616 (mmmm) cc_final: 0.8251 (tppp) REVERT: D 140 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7268 (tt) REVERT: D 183 ASN cc_start: 0.7658 (t0) cc_final: 0.7256 (t0) REVERT: D 299 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6607 (pp) REVERT: E 47 TRP cc_start: 0.7514 (t60) cc_final: 0.7211 (t60) REVERT: E 76 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7609 (mtmm) REVERT: E 93 MET cc_start: 0.7384 (mpp) cc_final: 0.7019 (mmt) REVERT: E 177 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5694 (p90) REVERT: E 230 MET cc_start: 0.7811 (tpp) cc_final: 0.7427 (tpp) outliers start: 27 outliers final: 20 residues processed: 140 average time/residue: 0.2056 time to fit residues: 40.8459 Evaluate side-chains 138 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 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 336 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 102 LEU 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 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 4 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 93 optimal weight: 0.0470 chunk 104 optimal weight: 0.0170 chunk 53 optimal weight: 0.0050 chunk 8 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8134 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.182663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138131 restraints weight = 11095.406| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.11 r_work: 0.3469 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2573 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= 0.108 Angle : 0.516 8.835 12412 Z= 0.263 Chirality : 0.040 0.148 1420 Planarity : 0.003 0.062 1550 Dihedral : 3.570 21.947 1253 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.26 % Allowed : 20.55 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1124 helix: 2.19 (0.27), residues: 378 sheet: -0.13 (0.34), residues: 245 loop : -1.39 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.022 0.001 PHE E 239 TYR 0.013 0.001 TYR E 235 ARG 0.003 0.000 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 385) hydrogen bonds : angle 3.91900 ( 1098) SS BOND : bond 0.00710 ( 3) SS BOND : angle 1.07038 ( 6) covalent geometry : bond 0.00245 ( 9168) covalent geometry : angle 0.51573 (12406) *********************** 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 147 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7360 (ttm170) REVERT: A 28 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7739 (tt0) REVERT: A 302 TYR cc_start: 0.8036 (t80) cc_final: 0.7755 (t80) REVERT: A 306 GLN cc_start: 0.7983 (tp40) cc_final: 0.7326 (tp40) REVERT: B 197 ARG cc_start: 0.8021 (tpp80) cc_final: 0.7750 (tpp80) REVERT: B 255 LEU cc_start: 0.8441 (mm) cc_final: 0.8223 (mm) REVERT: C 46 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8262 (tppp) REVERT: D 183 ASN cc_start: 0.7684 (t0) cc_final: 0.7253 (t0) REVERT: D 299 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6864 (pp) REVERT: E 47 TRP cc_start: 0.7735 (t60) cc_final: 0.7461 (t60) REVERT: E 93 MET cc_start: 0.7540 (mpp) cc_final: 0.7189 (mmt) REVERT: E 230 MET cc_start: 0.7793 (tpp) cc_final: 0.7528 (tpp) outliers start: 32 outliers final: 23 residues processed: 139 average time/residue: 0.2144 time to fit residues: 41.7372 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 : 0.978 ------------------------------------------------------------------------------- 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 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 336 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 102 LEU 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 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 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 108 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** 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 = 0.4183 r_free = 0.4183 target = 0.181479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137406 restraints weight = 11283.084| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.19 r_work: 0.3455 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2668 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 : 0.535 8.612 12412 Z= 0.273 Chirality : 0.040 0.147 1420 Planarity : 0.003 0.061 1550 Dihedral : 3.626 21.944 1253 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.15 % Allowed : 20.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1124 helix: 2.15 (0.27), residues: 379 sheet: -0.14 (0.34), residues: 243 loop : -1.35 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE E 239 TYR 0.011 0.001 TYR E 235 ARG 0.010 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 385) hydrogen bonds : angle 3.92745 ( 1098) SS BOND : bond 0.00492 ( 3) SS BOND : angle 0.56829 ( 6) covalent geometry : bond 0.00276 ( 9168) covalent geometry : angle 0.53452 (12406) *********************** 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 145 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 24 ARG cc_start: 0.7758 (ttp80) cc_final: 0.7405 (ttm170) REVERT: A 28 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7760 (tt0) REVERT: A 306 GLN cc_start: 0.7995 (tp40) cc_final: 0.7409 (tp40) REVERT: B 219 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7762 (mtt-85) REVERT: B 256 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.8031 (mtt-85) REVERT: C 46 LYS cc_start: 0.8611 (mmmm) cc_final: 0.8271 (tppp) REVERT: D 141 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7788 (tm-30) REVERT: D 183 ASN cc_start: 0.7650 (t0) cc_final: 0.7135 (t0) REVERT: D 299 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6851 (pp) REVERT: D 324 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7652 (ttp80) REVERT: E 47 TRP cc_start: 0.7763 (t60) cc_final: 0.7502 (t60) REVERT: E 93 MET cc_start: 0.7603 (mpp) cc_final: 0.7244 (mmt) REVERT: E 230 MET cc_start: 0.7991 (tpp) cc_final: 0.7679 (tpp) outliers start: 31 outliers final: 25 residues processed: 137 average time/residue: 0.2268 time to fit residues: 42.8959 Evaluate side-chains 134 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL 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 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 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 102 LEU 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 90 ASP 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 25 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- 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 ** 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 = 0.4179 r_free = 0.4179 target = 0.181196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136913 restraints weight = 11171.083| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.16 r_work: 0.3455 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2748 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= 0.120 Angle : 0.540 8.515 12412 Z= 0.275 Chirality : 0.040 0.146 1420 Planarity : 0.003 0.062 1550 Dihedral : 3.645 22.056 1253 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.25), residues: 1124 helix: 2.17 (0.27), residues: 379 sheet: -0.23 (0.33), residues: 243 loop : -1.35 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.016 0.001 PHE E 239 TYR 0.012 0.001 TYR E 235 ARG 0.009 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 385) hydrogen bonds : angle 3.95312 ( 1098) SS BOND : bond 0.00582 ( 3) SS BOND : angle 1.06977 ( 6) covalent geometry : bond 0.00281 ( 9168) covalent geometry : angle 0.53913 (12406) *********************** 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 144 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7764 (tt0) REVERT: A 302 TYR cc_start: 0.8146 (t80) cc_final: 0.7936 (t80) REVERT: A 306 GLN cc_start: 0.8001 (tp40) cc_final: 0.7377 (tp40) REVERT: B 256 ARG cc_start: 0.8280 (mtt-85) cc_final: 0.8021 (mtt-85) REVERT: C 46 LYS cc_start: 0.8600 (mmmm) cc_final: 0.8253 (tppp) REVERT: D 67 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6328 (mm) REVERT: D 141 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7881 (tm-30) REVERT: D 183 ASN cc_start: 0.7551 (t0) cc_final: 0.7038 (t0) REVERT: D 299 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6812 (pp) REVERT: D 324 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7633 (ttp80) REVERT: E 47 TRP cc_start: 0.7755 (t60) cc_final: 0.7484 (t60) REVERT: E 93 MET cc_start: 0.7617 (mpp) cc_final: 0.7258 (mmt) REVERT: E 230 MET cc_start: 0.7945 (tpp) cc_final: 0.7525 (tpp) outliers start: 30 outliers final: 28 residues processed: 135 average time/residue: 0.2424 time to fit residues: 45.9524 Evaluate side-chains 142 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL 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 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 318 LEU Chi-restraints excluded: chain B residue 336 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 80 MET Chi-restraints excluded: chain D residue 102 LEU 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 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 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.182056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136881 restraints weight = 11173.169| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.21 r_work: 0.3452 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9171 Z= 0.113 Angle : 0.534 8.439 12412 Z= 0.272 Chirality : 0.040 0.157 1420 Planarity : 0.003 0.062 1550 Dihedral : 3.614 22.467 1253 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.95 % Allowed : 22.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1124 helix: 2.19 (0.27), residues: 379 sheet: -0.25 (0.33), residues: 243 loop : -1.33 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.002 0.000 HIS E 35 PHE 0.013 0.001 PHE D 58 TYR 0.011 0.001 TYR E 235 ARG 0.008 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 385) hydrogen bonds : angle 3.91590 ( 1098) SS BOND : bond 0.00319 ( 3) SS BOND : angle 0.62534 ( 6) covalent geometry : bond 0.00260 ( 9168) covalent geometry : angle 0.53377 (12406) ********************** 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 144 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7720 (tt0) REVERT: A 302 TYR cc_start: 0.8138 (t80) cc_final: 0.7820 (t80) REVERT: A 306 GLN cc_start: 0.8020 (tp40) cc_final: 0.7345 (tp40) REVERT: B 256 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.7964 (mtt-85) REVERT: C 38 MET cc_start: 0.8283 (mmm) cc_final: 0.7989 (tpp) REVERT: C 42 GLU cc_start: 0.8124 (tp30) cc_final: 0.7822 (mm-30) REVERT: D 67 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6361 (mm) REVERT: D 183 ASN cc_start: 0.7503 (t0) cc_final: 0.6998 (t0) REVERT: D 299 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6854 (pp) REVERT: D 324 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7632 (ttp80) REVERT: E 47 TRP cc_start: 0.7766 (t60) cc_final: 0.7483 (t60) REVERT: E 93 MET cc_start: 0.7611 (mpp) cc_final: 0.7258 (mmt) REVERT: E 230 MET cc_start: 0.8059 (tpp) cc_final: 0.7576 (tpp) outliers start: 29 outliers final: 27 residues processed: 135 average time/residue: 0.2154 time to fit residues: 40.8897 Evaluate side-chains 141 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL 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 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 318 LEU Chi-restraints excluded: chain B residue 336 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 80 MET Chi-restraints excluded: chain D residue 102 LEU 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 47 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 106 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4210 r_free = 0.4210 target = 0.183860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136770 restraints weight = 11092.620| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.89 r_work: 0.3525 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9171 Z= 0.102 Angle : 0.527 8.453 12412 Z= 0.266 Chirality : 0.039 0.149 1420 Planarity : 0.003 0.063 1550 Dihedral : 3.526 23.146 1253 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.05 % Allowed : 21.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1124 helix: 2.27 (0.27), residues: 378 sheet: -0.13 (0.34), residues: 243 loop : -1.30 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 117 HIS 0.002 0.000 HIS E 35 PHE 0.012 0.001 PHE D 58 TYR 0.010 0.001 TYR E 235 ARG 0.008 0.000 ARG D 324 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 385) hydrogen bonds : angle 3.88937 ( 1098) SS BOND : bond 0.00730 ( 3) SS BOND : angle 1.07712 ( 6) covalent geometry : bond 0.00229 ( 9168) covalent geometry : angle 0.52611 (12406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6070.84 seconds wall clock time: 110 minutes 1.33 seconds (6601.33 seconds total)