Starting phenix.real_space_refine on Tue Mar 3 19:23:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6li3_0902/03_2026/6li3_0902.cif Found real_map, /net/cci-nas-00/data/ceres_data/6li3_0902/03_2026/6li3_0902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6li3_0902/03_2026/6li3_0902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6li3_0902/03_2026/6li3_0902.map" model { file = "/net/cci-nas-00/data/ceres_data/6li3_0902/03_2026/6li3_0902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6li3_0902/03_2026/6li3_0902.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5267 2.51 5 N 1436 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 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: 8289 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2303 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1989 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 1.95, per 1000 atoms: 0.24 Number of scatterers: 8289 At special positions: 0 Unit cell: (98.1, 131.89, 82.84, 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 57 16.00 O 1529 8.00 N 1436 7.00 C 5267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 312.6 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 40.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'R' and resid 37 through 68 Processing helix chain 'R' and resid 74 through 104 removed outlier: 3.781A pdb=" N LEU R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL R 96 " --> pdb=" O VAL R 92 " (cutoff:3.500A) Proline residue: R 97 - end of helix removed outlier: 4.107A pdb=" N LEU R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 145 removed outlier: 4.269A pdb=" N LEU R 112 " --> pdb=" O VAL R 108 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL R 123 " --> pdb=" O TYR R 119 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU R 124 " --> pdb=" O ILE R 120 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER R 126 " --> pdb=" O SER R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 172 removed outlier: 3.847A pdb=" N CYS R 170 " --> pdb=" O TRP R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 178 Processing helix chain 'R' and resid 191 through 196 Processing helix chain 'R' and resid 200 through 210 removed outlier: 3.875A pdb=" N VAL R 208 " --> pdb=" O THR R 204 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU R 210 " --> pdb=" O PHE R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 244 removed outlier: 4.557A pdb=" N VAL R 219 " --> pdb=" O ALA R 215 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE R 226 " --> pdb=" O THR R 222 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU R 236 " --> pdb=" O GLN R 232 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG R 240 " --> pdb=" O GLU R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 290 removed outlier: 4.034A pdb=" N PHE R 274 " --> pdb=" O ILE R 270 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU R 279 " --> pdb=" O TYR R 275 " (cutoff:3.500A) Proline residue: R 280 - end of helix removed outlier: 3.775A pdb=" N SER R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 307 removed outlier: 3.834A pdb=" N LEU R 301 " --> pdb=" O THR R 297 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE R 307 " --> pdb=" O THR R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 321 Proline residue: R 314 - end of helix removed outlier: 4.130A pdb=" N ASN R 321 " --> pdb=" O TYR R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 337 removed outlier: 3.652A pdb=" N ARG R 329 " --> pdb=" O ARG R 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR R 334 " --> pdb=" O ARG R 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 39 removed outlier: 3.731A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.762A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.246A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.928A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.608A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 346 removed outlier: 3.640A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.669A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 348 through 353' Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.689A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.607A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.648A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.157A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 211 removed outlier: 4.152A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.058A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.088A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.524A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.917A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.528A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.522A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.985A 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 278 removed outlier: 6.625A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.745A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.546A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1083 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: 1.32 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2697 1.35 - 1.46: 2042 1.46 - 1.58: 3657 1.58 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8472 Sorted by residual: bond pdb=" C VAL N 12 " pdb=" N GLN N 13 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.47e-02 4.63e+03 2.60e+00 bond pdb=" CA ILE R 189 " pdb=" CB ILE R 189 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.87e-01 bond pdb=" CA ASN R 313 " pdb=" C ASN R 313 " ideal model delta sigma weight residual 1.521 1.532 -0.011 1.14e-02 7.69e+03 8.91e-01 bond pdb=" C ILE R 121 " pdb=" O ILE R 121 " ideal model delta sigma weight residual 1.233 1.243 -0.010 1.22e-02 6.72e+03 6.15e-01 bond pdb=" N PRO A 313 " pdb=" CA PRO A 313 " ideal model delta sigma weight residual 1.469 1.474 -0.006 7.40e-03 1.83e+04 6.02e-01 ... (remaining 8467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 10912 1.13 - 2.26: 480 2.26 - 3.39: 64 3.39 - 4.53: 13 4.53 - 5.66: 16 Bond angle restraints: 11485 Sorted by residual: angle pdb=" C ILE R 54 " pdb=" CA ILE R 54 " pdb=" CB ILE R 54 " ideal model delta sigma weight residual 111.97 108.04 3.93 1.28e+00 6.10e-01 9.41e+00 angle pdb=" N GLY N 9 " pdb=" CA GLY N 9 " pdb=" C GLY N 9 " ideal model delta sigma weight residual 111.21 113.77 -2.56 1.04e+00 9.25e-01 6.08e+00 angle pdb=" N ILE R 189 " pdb=" CA ILE R 189 " pdb=" C ILE R 189 " ideal model delta sigma weight residual 106.55 109.73 -3.18 1.45e+00 4.76e-01 4.80e+00 angle pdb=" C LEU R 71 " pdb=" N HIS R 72 " pdb=" CA HIS R 72 " ideal model delta sigma weight residual 120.79 123.77 -2.98 1.39e+00 5.18e-01 4.58e+00 angle pdb=" N VAL A 224 " pdb=" CA VAL A 224 " pdb=" C VAL A 224 " ideal model delta sigma weight residual 107.51 110.70 -3.19 1.49e+00 4.50e-01 4.58e+00 ... (remaining 11480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4513 17.71 - 35.42: 421 35.42 - 53.13: 70 53.13 - 70.83: 10 70.83 - 88.54: 7 Dihedral angle restraints: 5021 sinusoidal: 1975 harmonic: 3046 Sorted by residual: dihedral pdb=" CB CYS R 114 " pdb=" SG CYS R 114 " pdb=" SG CYS R 193 " pdb=" CB CYS R 193 " ideal model delta sinusoidal sigma weight residual -86.00 -124.55 38.55 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY A 225 " pdb=" C GLY A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 785 0.030 - 0.059: 367 0.059 - 0.089: 89 0.089 - 0.119: 46 0.119 - 0.149: 4 Chirality restraints: 1291 Sorted by residual: chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1288 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 174 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO R 175 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 313 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO R 314 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 314 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 314 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO A 332 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.016 5.00e-02 4.00e+02 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 150 2.68 - 3.23: 7621 3.23 - 3.79: 12547 3.79 - 4.34: 16315 4.34 - 4.90: 26829 Nonbonded interactions: 63462 Sorted by model distance: nonbonded pdb=" OD1 ASP R 138 " pdb=" OH TYR R 149 " model vdw 2.124 3.040 nonbonded pdb=" O VAL A 36 " pdb=" OG1 THR A 40 " model vdw 2.165 3.040 nonbonded pdb=" O GLU R 191 " pdb=" OG1 THR R 195 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.256 3.040 ... (remaining 63457 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.000 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 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 : 0.002 0.039 8475 Z= 0.121 Angle : 0.558 5.657 11491 Z= 0.344 Chirality : 0.038 0.149 1291 Planarity : 0.003 0.037 1459 Dihedral : 13.864 88.543 3044 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -2.69 (0.22), residues: 1031 helix: -1.04 (0.23), residues: 413 sheet: -0.90 (0.33), residues: 200 loop : -2.97 (0.23), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 330 TYR 0.009 0.001 TYR R 317 PHE 0.018 0.001 PHE B 234 TRP 0.014 0.001 TRP R 197 HIS 0.002 0.000 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8472) covalent geometry : angle 0.55795 (11485) SS BOND : bond 0.00227 ( 3) SS BOND : angle 1.14584 ( 6) hydrogen bonds : bond 0.15021 ( 370) hydrogen bonds : angle 4.95697 ( 1083) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: R 43 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6973 (mp0) REVERT: R 63 PHE cc_start: 0.6614 (m-10) cc_final: 0.6231 (m-10) REVERT: R 282 ILE cc_start: 0.7863 (mm) cc_final: 0.7599 (mm) REVERT: A 27 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 249 ASP cc_start: 0.7895 (t0) cc_final: 0.7614 (t0) REVERT: N 53 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7664 (mp10) REVERT: N 77 ASN cc_start: 0.7711 (t0) cc_final: 0.7311 (t0) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.1095 time to fit residues: 39.2209 Evaluate side-chains 192 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.0050 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 247 HIS R 309 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 278 ASN A 371 ASN A 387 HIS B 6 GLN B 16 ASN B 44 GLN B 62 HIS B 91 HIS B 125 ASN B 183 HIS B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.216894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.161739 restraints weight = 9353.033| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.41 r_work: 0.3769 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8475 Z= 0.147 Angle : 0.606 9.518 11491 Z= 0.309 Chirality : 0.042 0.156 1291 Planarity : 0.004 0.043 1459 Dihedral : 3.550 22.390 1144 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.32 % Allowed : 16.32 % Favored : 81.37 % 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: -1.57 (0.24), residues: 1031 helix: 0.27 (0.26), residues: 412 sheet: -0.74 (0.34), residues: 195 loop : -2.55 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 380 TYR 0.015 0.002 TYR R 284 PHE 0.020 0.002 PHE B 234 TRP 0.037 0.002 TRP R 197 HIS 0.004 0.001 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8472) covalent geometry : angle 0.60600 (11485) SS BOND : bond 0.00248 ( 3) SS BOND : angle 1.14041 ( 6) hydrogen bonds : bond 0.03870 ( 370) hydrogen bonds : angle 3.74046 ( 1083) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6745 (m-10) cc_final: 0.6322 (m-10) REVERT: R 186 HIS cc_start: 0.8256 (m-70) cc_final: 0.7997 (m90) REVERT: R 197 TRP cc_start: 0.7065 (t60) cc_final: 0.6767 (t60) REVERT: A 60 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6866 (mtt) REVERT: A 291 LEU cc_start: 0.8270 (mm) cc_final: 0.8016 (mt) REVERT: A 370 GLU cc_start: 0.7593 (tp30) cc_final: 0.7200 (tt0) REVERT: A 376 PHE cc_start: 0.8750 (t80) cc_final: 0.8339 (t80) REVERT: A 386 MET cc_start: 0.7848 (ttm) cc_final: 0.7578 (ttp) REVERT: B 105 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7392 (t80) REVERT: B 120 ILE cc_start: 0.8379 (mt) cc_final: 0.8025 (mm) REVERT: B 266 HIS cc_start: 0.7863 (t-90) cc_final: 0.7436 (t-90) REVERT: G 38 MET cc_start: 0.7776 (tpt) cc_final: 0.7315 (tpt) REVERT: N 53 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7887 (mp10) REVERT: N 77 ASN cc_start: 0.7450 (t0) cc_final: 0.7246 (t0) REVERT: N 86 LEU cc_start: 0.8277 (tt) cc_final: 0.8023 (tp) outliers start: 21 outliers final: 13 residues processed: 203 average time/residue: 0.0938 time to fit residues: 26.2326 Evaluate side-chains 180 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 183 HIS ** B 259 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 = 0.4391 r_free = 0.4391 target = 0.205920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.155872 restraints weight = 9523.899| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 3.11 r_work: 0.3642 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8475 Z= 0.120 Angle : 0.542 8.351 11491 Z= 0.276 Chirality : 0.041 0.158 1291 Planarity : 0.004 0.043 1459 Dihedral : 3.456 22.853 1144 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.20 % Allowed : 18.08 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.25), residues: 1031 helix: 0.61 (0.26), residues: 422 sheet: -0.22 (0.35), residues: 194 loop : -2.25 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 72 TYR 0.024 0.001 TYR R 168 PHE 0.017 0.001 PHE R 117 TRP 0.020 0.002 TRP R 197 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8472) covalent geometry : angle 0.54216 (11485) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.95185 ( 6) hydrogen bonds : bond 0.03562 ( 370) hydrogen bonds : angle 3.64808 ( 1083) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6817 (m-10) cc_final: 0.6296 (m-10) REVERT: R 186 HIS cc_start: 0.8309 (m-70) cc_final: 0.8096 (m90) REVERT: R 236 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7260 (mm-30) REVERT: R 274 PHE cc_start: 0.5194 (OUTLIER) cc_final: 0.4270 (p90) REVERT: A 216 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7130 (mtmt) REVERT: A 291 LEU cc_start: 0.8273 (mm) cc_final: 0.7970 (mt) REVERT: A 370 GLU cc_start: 0.7594 (tp30) cc_final: 0.7199 (tt0) REVERT: A 376 PHE cc_start: 0.8768 (t80) cc_final: 0.8440 (t80) REVERT: B 105 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7128 (t80) REVERT: B 120 ILE cc_start: 0.8415 (mt) cc_final: 0.8046 (mm) REVERT: B 217 MET cc_start: 0.7943 (tpp) cc_final: 0.7617 (tpt) REVERT: B 247 ASP cc_start: 0.7134 (t0) cc_final: 0.6695 (t0) REVERT: B 266 HIS cc_start: 0.7994 (t-90) cc_final: 0.7625 (t-90) REVERT: B 301 LYS cc_start: 0.7646 (mmtm) cc_final: 0.7255 (mmtm) REVERT: G 38 MET cc_start: 0.7857 (tpt) cc_final: 0.7499 (tpt) REVERT: N 77 ASN cc_start: 0.7526 (t0) cc_final: 0.7178 (t0) outliers start: 29 outliers final: 19 residues processed: 191 average time/residue: 0.0900 time to fit residues: 23.8939 Evaluate side-chains 190 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 138 ASP Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 220 GLN B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.195715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145088 restraints weight = 9734.103| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.21 r_work: 0.3513 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8475 Z= 0.166 Angle : 0.598 7.954 11491 Z= 0.311 Chirality : 0.043 0.161 1291 Planarity : 0.004 0.048 1459 Dihedral : 3.877 21.200 1144 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.52 % Allowed : 19.63 % Favored : 75.85 % 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: -0.81 (0.26), residues: 1031 helix: 0.82 (0.26), residues: 420 sheet: -0.05 (0.37), residues: 184 loop : -2.20 (0.26), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 243 TYR 0.016 0.002 TYR R 168 PHE 0.019 0.002 PHE R 117 TRP 0.047 0.002 TRP R 197 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8472) covalent geometry : angle 0.59754 (11485) SS BOND : bond 0.00629 ( 3) SS BOND : angle 0.97220 ( 6) hydrogen bonds : bond 0.04165 ( 370) hydrogen bonds : angle 3.78910 ( 1083) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 236 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7331 (mm-30) REVERT: R 274 PHE cc_start: 0.5521 (OUTLIER) cc_final: 0.4389 (p90) REVERT: R 295 ASN cc_start: 0.7430 (t0) cc_final: 0.7219 (t0) REVERT: A 215 ASP cc_start: 0.6914 (m-30) cc_final: 0.6710 (m-30) REVERT: A 216 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7363 (mtmt) REVERT: A 291 LEU cc_start: 0.8594 (mm) cc_final: 0.8343 (mt) REVERT: A 343 ASP cc_start: 0.8413 (m-30) cc_final: 0.8145 (m-30) REVERT: A 356 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7818 (mtm180) REVERT: A 376 PHE cc_start: 0.8819 (t80) cc_final: 0.8508 (t80) REVERT: B 124 TYR cc_start: 0.8717 (m-80) cc_final: 0.8063 (m-80) REVERT: B 247 ASP cc_start: 0.7400 (t0) cc_final: 0.7071 (t0) REVERT: B 266 HIS cc_start: 0.8179 (t-90) cc_final: 0.7730 (t-90) REVERT: B 298 ASP cc_start: 0.8894 (t70) cc_final: 0.7780 (t0) REVERT: B 301 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7337 (mmtm) REVERT: G 38 MET cc_start: 0.8101 (tpt) cc_final: 0.7703 (tpt) REVERT: N 53 GLN cc_start: 0.8349 (mp10) cc_final: 0.8045 (mp10) REVERT: N 77 ASN cc_start: 0.7714 (t0) cc_final: 0.7341 (t0) REVERT: N 107 CYS cc_start: 0.6683 (m) cc_final: 0.6443 (m) outliers start: 41 outliers final: 30 residues processed: 197 average time/residue: 0.0882 time to fit residues: 24.1374 Evaluate side-chains 195 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 138 ASP Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.195610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.147413 restraints weight = 9581.971| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.23 r_work: 0.3533 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8475 Z= 0.119 Angle : 0.553 8.405 11491 Z= 0.282 Chirality : 0.041 0.173 1291 Planarity : 0.004 0.046 1459 Dihedral : 3.724 22.663 1144 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.86 % Allowed : 22.49 % Favored : 73.65 % 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: -0.61 (0.26), residues: 1031 helix: 1.05 (0.27), residues: 417 sheet: 0.04 (0.36), residues: 184 loop : -2.14 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 243 TYR 0.016 0.001 TYR R 168 PHE 0.021 0.001 PHE R 117 TRP 0.032 0.002 TRP R 197 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8472) covalent geometry : angle 0.55239 (11485) SS BOND : bond 0.00204 ( 3) SS BOND : angle 1.35481 ( 6) hydrogen bonds : bond 0.03593 ( 370) hydrogen bonds : angle 3.66990 ( 1083) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 197 TRP cc_start: 0.7004 (t60) cc_final: 0.6320 (t60) REVERT: R 236 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7370 (mm-30) REVERT: R 274 PHE cc_start: 0.5595 (OUTLIER) cc_final: 0.4484 (p90) REVERT: R 295 ASN cc_start: 0.7390 (t0) cc_final: 0.7154 (t0) REVERT: A 27 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 60 MET cc_start: 0.7897 (mpt) cc_final: 0.7346 (mpp) REVERT: A 215 ASP cc_start: 0.6859 (m-30) cc_final: 0.6648 (m-30) REVERT: A 216 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7314 (mtmt) REVERT: A 291 LEU cc_start: 0.8378 (mm) cc_final: 0.8096 (mt) REVERT: A 356 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7817 (mtm180) REVERT: A 376 PHE cc_start: 0.8860 (t80) cc_final: 0.8546 (t80) REVERT: B 225 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.8023 (t-90) REVERT: B 266 HIS cc_start: 0.8288 (t-90) cc_final: 0.7791 (t-90) REVERT: B 298 ASP cc_start: 0.8778 (t70) cc_final: 0.8509 (t0) REVERT: G 38 MET cc_start: 0.8100 (tpt) cc_final: 0.7712 (tpt) REVERT: N 53 GLN cc_start: 0.8319 (mp10) cc_final: 0.7926 (mp10) REVERT: N 77 ASN cc_start: 0.7674 (t0) cc_final: 0.7362 (t0) outliers start: 35 outliers final: 27 residues processed: 184 average time/residue: 0.0870 time to fit residues: 22.1588 Evaluate side-chains 195 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 138 ASP Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 HIS ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146675 restraints weight = 9514.414| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.25 r_work: 0.3523 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8475 Z= 0.118 Angle : 0.548 8.869 11491 Z= 0.278 Chirality : 0.041 0.184 1291 Planarity : 0.003 0.046 1459 Dihedral : 3.634 21.947 1144 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.63 % Allowed : 22.27 % Favored : 73.10 % 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: -0.50 (0.26), residues: 1031 helix: 1.15 (0.26), residues: 417 sheet: 0.04 (0.36), residues: 188 loop : -2.08 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 243 TYR 0.015 0.001 TYR R 168 PHE 0.023 0.001 PHE R 117 TRP 0.029 0.002 TRP R 197 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8472) covalent geometry : angle 0.54756 (11485) SS BOND : bond 0.00205 ( 3) SS BOND : angle 1.35837 ( 6) hydrogen bonds : bond 0.03450 ( 370) hydrogen bonds : angle 3.60818 ( 1083) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.6192 (t80) REVERT: R 236 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7382 (mm-30) REVERT: R 274 PHE cc_start: 0.5355 (OUTLIER) cc_final: 0.4539 (p90) REVERT: R 293 LEU cc_start: 0.7853 (tt) cc_final: 0.7400 (mt) REVERT: A 27 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7885 (mm-30) REVERT: A 215 ASP cc_start: 0.6865 (m-30) cc_final: 0.6589 (m-30) REVERT: A 216 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7369 (mtmt) REVERT: A 356 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7751 (mtm180) REVERT: A 376 PHE cc_start: 0.8855 (t80) cc_final: 0.8414 (t80) REVERT: B 225 HIS cc_start: 0.8587 (OUTLIER) cc_final: 0.8023 (t-90) REVERT: B 298 ASP cc_start: 0.8808 (t70) cc_final: 0.8590 (t0) REVERT: G 38 MET cc_start: 0.8133 (tpt) cc_final: 0.7733 (tpt) REVERT: N 77 ASN cc_start: 0.7678 (t0) cc_final: 0.7264 (t0) outliers start: 42 outliers final: 32 residues processed: 199 average time/residue: 0.0934 time to fit residues: 25.4962 Evaluate side-chains 204 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 0.0870 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.194893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147024 restraints weight = 9539.806| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.21 r_work: 0.3520 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8475 Z= 0.115 Angle : 0.552 11.018 11491 Z= 0.280 Chirality : 0.041 0.187 1291 Planarity : 0.004 0.046 1459 Dihedral : 3.642 22.218 1144 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.30 % Allowed : 23.59 % Favored : 72.11 % 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: -0.41 (0.26), residues: 1031 helix: 1.20 (0.26), residues: 417 sheet: 0.09 (0.36), residues: 188 loop : -2.00 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 243 TYR 0.015 0.001 TYR R 168 PHE 0.018 0.001 PHE R 117 TRP 0.024 0.001 TRP B 297 HIS 0.002 0.001 HIS R 73 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8472) covalent geometry : angle 0.55061 (11485) SS BOND : bond 0.00378 ( 3) SS BOND : angle 1.58456 ( 6) hydrogen bonds : bond 0.03373 ( 370) hydrogen bonds : angle 3.62588 ( 1083) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6146 (t80) REVERT: R 236 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7421 (mm-30) REVERT: R 274 PHE cc_start: 0.5294 (OUTLIER) cc_final: 0.4503 (p90) REVERT: R 293 LEU cc_start: 0.7872 (tt) cc_final: 0.7462 (mt) REVERT: A 60 MET cc_start: 0.7350 (mpt) cc_final: 0.7012 (mpt) REVERT: A 216 LYS cc_start: 0.8020 (mmtm) cc_final: 0.7287 (mtmt) REVERT: A 291 LEU cc_start: 0.8377 (mm) cc_final: 0.8130 (mm) REVERT: A 356 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7767 (mtm180) REVERT: A 376 PHE cc_start: 0.8853 (t80) cc_final: 0.8515 (t80) REVERT: B 225 HIS cc_start: 0.8560 (OUTLIER) cc_final: 0.7926 (t-90) REVERT: B 301 LYS cc_start: 0.7815 (mmtm) cc_final: 0.7107 (mmtt) REVERT: G 38 MET cc_start: 0.8103 (tpt) cc_final: 0.7755 (tpt) REVERT: N 77 ASN cc_start: 0.7677 (t0) cc_final: 0.7263 (t0) REVERT: N 87 LYS cc_start: 0.7391 (tttm) cc_final: 0.7139 (tttm) outliers start: 39 outliers final: 34 residues processed: 197 average time/residue: 0.0950 time to fit residues: 25.4483 Evaluate side-chains 206 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 94 CYS Chi-restraints excluded: chain R residue 138 ASP Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.0000 chunk 72 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 79 optimal weight: 0.0980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.199119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149616 restraints weight = 9586.094| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 3.21 r_work: 0.3554 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8475 Z= 0.095 Angle : 0.533 9.401 11491 Z= 0.268 Chirality : 0.041 0.189 1291 Planarity : 0.003 0.047 1459 Dihedral : 3.499 22.396 1144 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.97 % Allowed : 23.70 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.26), residues: 1031 helix: 1.34 (0.27), residues: 417 sheet: 0.31 (0.36), residues: 185 loop : -1.89 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 243 TYR 0.015 0.001 TYR R 168 PHE 0.027 0.001 PHE R 65 TRP 0.021 0.001 TRP R 197 HIS 0.002 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 8472) covalent geometry : angle 0.53254 (11485) SS BOND : bond 0.00125 ( 3) SS BOND : angle 1.22890 ( 6) hydrogen bonds : bond 0.03019 ( 370) hydrogen bonds : angle 3.47151 ( 1083) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6170 (t80) REVERT: R 236 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7510 (mm-30) REVERT: R 243 ARG cc_start: 0.6454 (tpp80) cc_final: 0.5930 (ttp80) REVERT: R 274 PHE cc_start: 0.5387 (OUTLIER) cc_final: 0.4690 (p90) REVERT: R 293 LEU cc_start: 0.7984 (tt) cc_final: 0.7580 (mt) REVERT: A 27 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 60 MET cc_start: 0.7386 (mpt) cc_final: 0.6410 (mpt) REVERT: A 216 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7184 (mtmt) REVERT: A 356 ARG cc_start: 0.8011 (mtt-85) cc_final: 0.7773 (mtm180) REVERT: A 376 PHE cc_start: 0.8807 (t80) cc_final: 0.8404 (t80) REVERT: B 120 ILE cc_start: 0.8331 (mt) cc_final: 0.8098 (mm) REVERT: B 172 GLU cc_start: 0.7314 (mp0) cc_final: 0.7087 (mp0) REVERT: G 38 MET cc_start: 0.8024 (tpt) cc_final: 0.7703 (tpt) REVERT: N 77 ASN cc_start: 0.7643 (t0) cc_final: 0.7287 (t0) outliers start: 36 outliers final: 27 residues processed: 198 average time/residue: 0.0926 time to fit residues: 24.9783 Evaluate side-chains 200 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 7 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.194036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145878 restraints weight = 9617.349| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.21 r_work: 0.3511 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8475 Z= 0.130 Angle : 0.564 9.148 11491 Z= 0.286 Chirality : 0.042 0.195 1291 Planarity : 0.004 0.046 1459 Dihedral : 3.617 22.883 1144 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.86 % Allowed : 24.37 % Favored : 71.78 % 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: -0.20 (0.26), residues: 1031 helix: 1.34 (0.26), residues: 416 sheet: 0.32 (0.37), residues: 186 loop : -1.90 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 243 TYR 0.018 0.001 TYR R 284 PHE 0.020 0.001 PHE N 108 TRP 0.026 0.002 TRP B 297 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8472) covalent geometry : angle 0.56322 (11485) SS BOND : bond 0.00595 ( 3) SS BOND : angle 1.61790 ( 6) hydrogen bonds : bond 0.03476 ( 370) hydrogen bonds : angle 3.54367 ( 1083) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6153 (t80) REVERT: R 236 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7458 (mm-30) REVERT: R 243 ARG cc_start: 0.6592 (tpp80) cc_final: 0.6097 (ttp80) REVERT: R 274 PHE cc_start: 0.5382 (OUTLIER) cc_final: 0.4583 (p90) REVERT: A 27 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 60 MET cc_start: 0.6857 (mpt) cc_final: 0.6636 (mpp) REVERT: A 216 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7309 (mtmt) REVERT: A 356 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7763 (mtm180) REVERT: A 376 PHE cc_start: 0.8821 (t80) cc_final: 0.8343 (t80) REVERT: G 38 MET cc_start: 0.8178 (tpt) cc_final: 0.7885 (tpt) REVERT: N 77 ASN cc_start: 0.7636 (t0) cc_final: 0.7250 (t0) REVERT: N 87 LYS cc_start: 0.7445 (tttm) cc_final: 0.7024 (tttm) outliers start: 35 outliers final: 28 residues processed: 191 average time/residue: 0.0896 time to fit residues: 23.5686 Evaluate side-chains 202 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.0000 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 88 ASN ** 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 = 0.4318 r_free = 0.4318 target = 0.196494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147811 restraints weight = 9598.481| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.26 r_work: 0.3528 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8475 Z= 0.110 Angle : 0.554 9.298 11491 Z= 0.280 Chirality : 0.042 0.195 1291 Planarity : 0.003 0.047 1459 Dihedral : 3.592 22.829 1144 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.42 % Allowed : 24.81 % Favored : 71.78 % 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: -0.09 (0.26), residues: 1031 helix: 1.38 (0.26), residues: 417 sheet: 0.27 (0.36), residues: 193 loop : -1.75 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 243 TYR 0.014 0.001 TYR R 168 PHE 0.030 0.001 PHE R 65 TRP 0.019 0.001 TRP R 197 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8472) covalent geometry : angle 0.55290 (11485) SS BOND : bond 0.00464 ( 3) SS BOND : angle 1.38825 ( 6) hydrogen bonds : bond 0.03279 ( 370) hydrogen bonds : angle 3.48689 ( 1083) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.6057 (t80) REVERT: R 236 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7554 (mm-30) REVERT: R 243 ARG cc_start: 0.6566 (tpp80) cc_final: 0.6075 (ttp80) REVERT: R 274 PHE cc_start: 0.5199 (OUTLIER) cc_final: 0.4431 (p90) REVERT: R 293 LEU cc_start: 0.7917 (tt) cc_final: 0.7424 (mt) REVERT: A 27 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 59 GLN cc_start: 0.7089 (mp-120) cc_final: 0.6747 (mp10) REVERT: A 216 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7381 (mtmt) REVERT: A 314 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8538 (tp30) REVERT: A 356 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7742 (mtm180) REVERT: A 376 PHE cc_start: 0.8810 (t80) cc_final: 0.8317 (t80) REVERT: B 120 ILE cc_start: 0.8357 (mt) cc_final: 0.8124 (mm) REVERT: G 38 MET cc_start: 0.8088 (tpt) cc_final: 0.7779 (tpt) REVERT: G 62 ARG cc_start: 0.5395 (ptp90) cc_final: 0.5068 (ptt180) REVERT: N 77 ASN cc_start: 0.7625 (t0) cc_final: 0.7252 (t0) outliers start: 31 outliers final: 28 residues processed: 193 average time/residue: 0.0865 time to fit residues: 22.9271 Evaluate side-chains 203 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 PHE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.194336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143618 restraints weight = 9551.518| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.34 r_work: 0.3514 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8475 Z= 0.124 Angle : 0.585 12.284 11491 Z= 0.293 Chirality : 0.043 0.196 1291 Planarity : 0.004 0.047 1459 Dihedral : 3.657 22.951 1144 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.64 % Allowed : 25.14 % Favored : 71.22 % 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: -0.09 (0.26), residues: 1031 helix: 1.37 (0.26), residues: 417 sheet: 0.29 (0.37), residues: 195 loop : -1.75 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 243 TYR 0.014 0.001 TYR R 168 PHE 0.019 0.001 PHE N 108 TRP 0.022 0.002 TRP B 297 HIS 0.005 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8472) covalent geometry : angle 0.58511 (11485) SS BOND : bond 0.00368 ( 3) SS BOND : angle 0.95210 ( 6) hydrogen bonds : bond 0.03469 ( 370) hydrogen bonds : angle 3.56349 ( 1083) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2176.98 seconds wall clock time: 37 minutes 55.76 seconds (2275.76 seconds total)