Starting phenix.real_space_refine on Wed Feb 12 20:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6li3_0902/02_2025/6li3_0902.cif Found real_map, /net/cci-nas-00/data/ceres_data/6li3_0902/02_2025/6li3_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_0902/02_2025/6li3_0902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6li3_0902/02_2025/6li3_0902.map" model { file = "/net/cci-nas-00/data/ceres_data/6li3_0902/02_2025/6li3_0902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6li3_0902/02_2025/6li3_0902.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.97, per 1000 atoms: 0.60 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.97 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: 2.65 Time building geometry restraints manager: 2.24 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: 0.920 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.840 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- 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 8472 Z= 0.134 Angle : 0.558 5.657 11485 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 : 7.66 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.014 0.001 TRP R 197 HIS 0.002 0.000 HIS A 220 PHE 0.018 0.001 PHE B 234 TYR 0.009 0.001 TYR R 317 ARG 0.006 0.000 ARG R 330 *********************** 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 : 0.940 Fit side-chains revert: symmetry clash REVERT: R 43 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6974 (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: 0.7601 (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: 0.7662 (mp10) REVERT: N 77 ASN cc_start: 0.7711 (t0) cc_final: 0.7312 (t0) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2519 time to fit residues: 89.1961 Evaluate side-chains 194 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.0470 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN G 18 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.224418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174681 restraints weight = 9621.134| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 3.29 r_work: 0.3864 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8472 Z= 0.187 Angle : 0.572 9.369 11485 Z= 0.289 Chirality : 0.040 0.159 1291 Planarity : 0.004 0.040 1459 Dihedral : 3.329 22.206 1144 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.98 % Allowed : 14.88 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1031 helix: 0.24 (0.26), residues: 412 sheet: -0.82 (0.32), residues: 210 loop : -2.57 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 197 HIS 0.005 0.001 HIS R 247 PHE 0.018 0.001 PHE B 234 TYR 0.015 0.001 TYR R 284 ARG 0.007 0.001 ARG A 380 *********************** 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 212 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6660 (m-10) cc_final: 0.6230 (m-10) REVERT: R 186 HIS cc_start: 0.8145 (m-70) cc_final: 0.7914 (m90) REVERT: R 236 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7250 (mm-30) REVERT: A 60 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7022 (mtt) REVERT: A 277 TRP cc_start: 0.8588 (t-100) cc_final: 0.8269 (t-100) REVERT: A 370 GLU cc_start: 0.7580 (tp30) cc_final: 0.7142 (tt0) REVERT: A 386 MET cc_start: 0.7749 (ttm) cc_final: 0.7466 (ttp) REVERT: B 105 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7519 (t80) REVERT: B 170 ASP cc_start: 0.6601 (t0) cc_final: 0.6090 (t0) REVERT: B 171 ILE cc_start: 0.7484 (mt) cc_final: 0.7128 (mt) REVERT: B 172 GLU cc_start: 0.7260 (mm-30) cc_final: 0.7046 (mp0) REVERT: B 217 MET cc_start: 0.7091 (tpp) cc_final: 0.6500 (tpp) REVERT: B 266 HIS cc_start: 0.7751 (t-90) cc_final: 0.7350 (t-90) REVERT: B 301 LYS cc_start: 0.7565 (mmtp) cc_final: 0.7169 (mmtm) REVERT: G 38 MET cc_start: 0.7750 (tpt) cc_final: 0.7318 (tpt) REVERT: N 39 GLN cc_start: 0.8403 (tp40) cc_final: 0.8054 (tp40) REVERT: N 53 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7856 (mp10) REVERT: N 77 ASN cc_start: 0.7483 (t0) cc_final: 0.7256 (t0) REVERT: N 86 LEU cc_start: 0.8177 (tt) cc_final: 0.7889 (tp) outliers start: 18 outliers final: 12 residues processed: 203 average time/residue: 0.2110 time to fit residues: 58.0793 Evaluate side-chains 198 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 93 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 278 ASN A 294 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.199443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148878 restraints weight = 9584.065| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.22 r_work: 0.3542 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8472 Z= 0.258 Angle : 0.590 8.238 11485 Z= 0.306 Chirality : 0.042 0.156 1291 Planarity : 0.004 0.043 1459 Dihedral : 3.753 22.310 1144 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.64 % Allowed : 18.74 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.25), residues: 1031 helix: 0.53 (0.26), residues: 422 sheet: -0.17 (0.34), residues: 203 loop : -2.41 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 197 HIS 0.004 0.001 HIS A 387 PHE 0.018 0.002 PHE N 103 TYR 0.016 0.002 TYR A 311 ARG 0.003 0.000 ARG A 356 *********************** 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 219 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6866 (m-10) cc_final: 0.6343 (m-10) REVERT: R 197 TRP cc_start: 0.7120 (t60) cc_final: 0.6830 (t60) REVERT: R 236 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7343 (mm-30) REVERT: R 274 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4585 (p90) REVERT: R 295 ASN cc_start: 0.7445 (t0) cc_final: 0.7166 (t0) REVERT: A 333 ARG cc_start: 0.8439 (mtm180) cc_final: 0.8139 (mmm160) REVERT: A 356 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7783 (mtm180) REVERT: A 370 GLU cc_start: 0.7636 (tp30) cc_final: 0.7272 (tt0) REVERT: A 376 PHE cc_start: 0.8841 (t80) cc_final: 0.8532 (t80) REVERT: B 105 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.7726 (t80) REVERT: B 124 TYR cc_start: 0.8593 (m-80) cc_final: 0.7935 (m-80) REVERT: B 247 ASP cc_start: 0.7194 (t0) cc_final: 0.6874 (t0) REVERT: B 266 HIS cc_start: 0.8010 (t-90) cc_final: 0.7633 (t-90) REVERT: B 301 LYS cc_start: 0.7842 (mmtp) cc_final: 0.7364 (mmtm) REVERT: G 38 MET cc_start: 0.7866 (tpt) cc_final: 0.7445 (tpt) REVERT: N 39 GLN cc_start: 0.8529 (tp40) cc_final: 0.8175 (tp-100) REVERT: N 53 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7869 (mp10) REVERT: N 77 ASN cc_start: 0.7657 (t0) cc_final: 0.7307 (t0) outliers start: 33 outliers final: 27 residues processed: 205 average time/residue: 0.2100 time to fit residues: 58.3717 Evaluate side-chains 199 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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 227 PHE Chi-restraints excluded: chain R residue 229 ILE Chi-restraints excluded: chain R residue 274 PHE Chi-restraints excluded: chain R residue 308 SER 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 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 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 229 ILE 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 72 ARG 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 76 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** 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 = 0.4332 r_free = 0.4332 target = 0.198912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.148244 restraints weight = 9489.172| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.08 r_work: 0.3547 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8472 Z= 0.193 Angle : 0.549 7.759 11485 Z= 0.281 Chirality : 0.042 0.240 1291 Planarity : 0.004 0.045 1459 Dihedral : 3.629 21.526 1144 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.41 % Allowed : 21.17 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1031 helix: 0.82 (0.27), residues: 423 sheet: 0.04 (0.35), residues: 189 loop : -2.17 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.004 0.001 HIS A 220 PHE 0.019 0.001 PHE R 117 TYR 0.018 0.001 TYR R 168 ARG 0.003 0.000 ARG R 243 *********************** 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 217 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6795 (m-10) cc_final: 0.6522 (m-10) REVERT: R 110 GLU cc_start: 0.5520 (mp0) cc_final: 0.5287 (mp0) REVERT: R 236 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7338 (mm-30) REVERT: R 274 PHE cc_start: 0.5624 (OUTLIER) cc_final: 0.4515 (p90) REVERT: A 215 ASP cc_start: 0.6788 (m-30) cc_final: 0.6586 (m-30) REVERT: A 216 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7314 (mtmt) REVERT: A 333 ARG cc_start: 0.8430 (mtm180) cc_final: 0.8098 (mmm160) REVERT: A 356 ARG cc_start: 0.8177 (mtt-85) cc_final: 0.7805 (mtm180) REVERT: A 376 PHE cc_start: 0.8828 (t80) cc_final: 0.8485 (t80) REVERT: B 105 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7900 (t80) REVERT: B 124 TYR cc_start: 0.8655 (m-80) cc_final: 0.8028 (m-80) REVERT: B 225 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8074 (t-90) REVERT: B 247 ASP cc_start: 0.7213 (t0) cc_final: 0.6852 (t0) REVERT: B 266 HIS cc_start: 0.8137 (t-90) cc_final: 0.7693 (t-90) REVERT: B 298 ASP cc_start: 0.8889 (t70) cc_final: 0.7920 (t0) REVERT: B 301 LYS cc_start: 0.7877 (mmtp) cc_final: 0.7189 (mmtm) REVERT: G 38 MET cc_start: 0.7901 (tpt) cc_final: 0.7446 (tpt) REVERT: N 39 GLN cc_start: 0.8522 (tp40) cc_final: 0.8157 (tp-100) REVERT: N 77 ASN cc_start: 0.7619 (t0) cc_final: 0.7271 (t0) REVERT: N 107 CYS cc_start: 0.6721 (m) cc_final: 0.6503 (m) outliers start: 40 outliers final: 29 residues processed: 196 average time/residue: 0.2203 time to fit residues: 57.8984 Evaluate side-chains 202 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 227 PHE 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 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 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 277 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 72 ARG 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 62 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.198839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.148226 restraints weight = 9489.067| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.08 r_work: 0.3551 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8472 Z= 0.172 Angle : 0.538 8.480 11485 Z= 0.273 Chirality : 0.041 0.196 1291 Planarity : 0.003 0.046 1459 Dihedral : 3.545 21.296 1144 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.96 % Allowed : 21.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1031 helix: 1.05 (0.27), residues: 417 sheet: 0.24 (0.36), residues: 191 loop : -2.09 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS B 225 PHE 0.022 0.001 PHE R 117 TYR 0.016 0.001 TYR R 168 ARG 0.006 0.000 ARG R 243 *********************** 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 221 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: R 197 TRP cc_start: 0.7386 (t60) cc_final: 0.7069 (t60) REVERT: R 236 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7342 (mm-30) REVERT: R 243 ARG cc_start: 0.6368 (tpp80) cc_final: 0.5712 (ttt-90) REVERT: R 274 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.4245 (p90) REVERT: R 295 ASN cc_start: 0.7418 (t0) cc_final: 0.7169 (t0) REVERT: A 215 ASP cc_start: 0.6858 (m-30) cc_final: 0.6656 (m-30) REVERT: A 216 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7317 (mtmt) REVERT: A 333 ARG cc_start: 0.8518 (mtm180) cc_final: 0.8133 (mmm160) REVERT: A 356 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7788 (mtm180) REVERT: A 376 PHE cc_start: 0.8840 (t80) cc_final: 0.8478 (t80) REVERT: B 105 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7964 (t80) REVERT: B 120 ILE cc_start: 0.8388 (mt) cc_final: 0.8136 (mm) REVERT: B 225 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8212 (t-90) REVERT: B 247 ASP cc_start: 0.7406 (t0) cc_final: 0.7043 (t0) REVERT: B 266 HIS cc_start: 0.8251 (t-90) cc_final: 0.7740 (t-90) REVERT: B 298 ASP cc_start: 0.8948 (t70) cc_final: 0.7979 (t0) REVERT: B 301 LYS cc_start: 0.7760 (mmtp) cc_final: 0.7129 (mmtm) REVERT: G 38 MET cc_start: 0.8064 (tpt) cc_final: 0.7667 (tpt) REVERT: N 77 ASN cc_start: 0.7622 (t0) cc_final: 0.7278 (t0) outliers start: 45 outliers final: 35 residues processed: 202 average time/residue: 0.2166 time to fit residues: 59.1402 Evaluate side-chains 210 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 222 THR Chi-restraints excluded: chain R residue 227 PHE 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 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 105 TYR 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 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 B residue 339 TRP Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.200696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150546 restraints weight = 9488.548| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.07 r_work: 0.3574 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8472 Z= 0.137 Angle : 0.534 10.165 11485 Z= 0.268 Chirality : 0.041 0.185 1291 Planarity : 0.003 0.046 1459 Dihedral : 3.454 21.930 1144 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.08 % Allowed : 23.15 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1031 helix: 1.19 (0.27), residues: 417 sheet: 0.21 (0.36), residues: 196 loop : -2.05 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.002 0.001 HIS R 186 PHE 0.022 0.001 PHE R 117 TYR 0.015 0.001 TYR R 168 ARG 0.005 0.000 ARG R 243 *********************** 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 221 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: R 119 TYR cc_start: 0.7872 (t80) cc_final: 0.7341 (t80) REVERT: R 197 TRP cc_start: 0.7353 (t60) cc_final: 0.7027 (t60) REVERT: R 236 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7378 (mm-30) REVERT: R 243 ARG cc_start: 0.6317 (tpp80) cc_final: 0.5709 (ttt-90) REVERT: R 274 PHE cc_start: 0.5372 (OUTLIER) cc_final: 0.4452 (p90) REVERT: A 60 MET cc_start: 0.7400 (mpt) cc_final: 0.6834 (mmt) REVERT: A 215 ASP cc_start: 0.6795 (m-30) cc_final: 0.6546 (m-30) REVERT: A 216 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7271 (mtmt) REVERT: A 333 ARG cc_start: 0.8519 (mtm180) cc_final: 0.8128 (mmm160) REVERT: A 356 ARG cc_start: 0.8129 (mtt-85) cc_final: 0.7779 (mtm180) REVERT: B 105 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7934 (t80) REVERT: B 120 ILE cc_start: 0.8377 (mt) cc_final: 0.8118 (mm) REVERT: B 225 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.8001 (t-90) REVERT: B 266 HIS cc_start: 0.8292 (t-90) cc_final: 0.7737 (t-90) REVERT: G 38 MET cc_start: 0.8060 (tpt) cc_final: 0.7680 (tpt) REVERT: N 53 GLN cc_start: 0.8375 (mp-120) cc_final: 0.7942 (mp10) REVERT: N 77 ASN cc_start: 0.7587 (t0) cc_final: 0.7256 (t0) outliers start: 37 outliers final: 29 residues processed: 205 average time/residue: 0.2165 time to fit residues: 59.9273 Evaluate side-chains 206 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 193 CYS Chi-restraints excluded: chain R residue 222 THR Chi-restraints excluded: chain R residue 227 PHE 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 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 B residue 47 THR Chi-restraints excluded: chain B residue 105 TYR 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 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.193282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144288 restraints weight = 9579.502| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.21 r_work: 0.3488 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8472 Z= 0.243 Angle : 0.575 7.692 11485 Z= 0.299 Chirality : 0.043 0.206 1291 Planarity : 0.004 0.046 1459 Dihedral : 3.711 22.111 1144 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.18 % Allowed : 23.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1031 helix: 1.06 (0.26), residues: 419 sheet: 0.14 (0.36), residues: 188 loop : -2.03 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.006 0.001 HIS A 362 PHE 0.023 0.002 PHE N 108 TYR 0.016 0.001 TYR R 168 ARG 0.005 0.000 ARG R 243 *********************** 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 223 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6196 (t80) REVERT: R 236 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7401 (mm-30) REVERT: R 243 ARG cc_start: 0.6567 (tpp80) cc_final: 0.6053 (ttp80) REVERT: R 274 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.4600 (p90) REVERT: A 216 LYS cc_start: 0.7983 (mmtm) cc_final: 0.7171 (mtmt) REVERT: A 333 ARG cc_start: 0.8669 (mtm180) cc_final: 0.8180 (mmm160) REVERT: A 356 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7702 (mtm180) REVERT: A 376 PHE cc_start: 0.8824 (t80) cc_final: 0.8570 (t80) REVERT: B 266 HIS cc_start: 0.8332 (t-90) cc_final: 0.7742 (t-90) REVERT: B 298 ASP cc_start: 0.8649 (t0) cc_final: 0.8274 (t0) REVERT: B 301 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7001 (mmtp) REVERT: G 38 MET cc_start: 0.8144 (tpt) cc_final: 0.7800 (tpt) REVERT: N 53 GLN cc_start: 0.8433 (mp-120) cc_final: 0.7981 (mp10) REVERT: N 77 ASN cc_start: 0.7648 (t0) cc_final: 0.7346 (t0) REVERT: N 86 LEU cc_start: 0.8293 (tt) cc_final: 0.8061 (tp) REVERT: N 87 LYS cc_start: 0.7489 (tttm) cc_final: 0.6987 (tttm) outliers start: 47 outliers final: 37 residues processed: 199 average time/residue: 0.2241 time to fit residues: 59.6364 Evaluate side-chains 211 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 276 MET 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 184 THR Chi-restraints excluded: chain B residue 200 VAL 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 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 297 TRP 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 4 LEU Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 40 optimal weight: 0.0870 chunk 49 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 103 HIS B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.196036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.146358 restraints weight = 9585.378| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.14 r_work: 0.3517 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8472 Z= 0.174 Angle : 0.547 10.836 11485 Z= 0.280 Chirality : 0.042 0.193 1291 Planarity : 0.003 0.047 1459 Dihedral : 3.638 22.299 1144 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.41 % Allowed : 24.26 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1031 helix: 1.15 (0.26), residues: 418 sheet: 0.24 (0.36), residues: 185 loop : -1.94 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.008 0.001 HIS A 362 PHE 0.025 0.001 PHE R 117 TYR 0.015 0.001 TYR R 168 ARG 0.004 0.000 ARG R 243 *********************** 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 224 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6696 (OUTLIER) cc_final: 0.6159 (t80) REVERT: R 236 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7434 (mm-30) REVERT: R 243 ARG cc_start: 0.6433 (tpp80) cc_final: 0.5933 (ttp80) REVERT: R 274 PHE cc_start: 0.5266 (OUTLIER) cc_final: 0.4474 (p90) REVERT: R 285 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: A 216 LYS cc_start: 0.7986 (mmtm) cc_final: 0.7182 (mtmt) REVERT: A 356 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7691 (mtm180) REVERT: A 376 PHE cc_start: 0.8822 (t80) cc_final: 0.8518 (t80) REVERT: B 225 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.8129 (t-90) REVERT: B 266 HIS cc_start: 0.8340 (t-90) cc_final: 0.7765 (t-90) REVERT: G 38 MET cc_start: 0.8088 (tpt) cc_final: 0.7740 (tpt) REVERT: N 53 GLN cc_start: 0.8463 (mp-120) cc_final: 0.8006 (mp10) REVERT: N 77 ASN cc_start: 0.7548 (t0) cc_final: 0.7273 (t0) REVERT: N 87 LYS cc_start: 0.7490 (tttm) cc_final: 0.7033 (tttm) outliers start: 40 outliers final: 35 residues processed: 206 average time/residue: 0.2213 time to fit residues: 61.4767 Evaluate side-chains 212 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 285 PHE 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 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 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE 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 B residue 339 TRP Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 84 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.195329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.147119 restraints weight = 9655.522| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.17 r_work: 0.3509 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8472 Z= 0.196 Angle : 0.550 9.309 11485 Z= 0.283 Chirality : 0.042 0.193 1291 Planarity : 0.003 0.048 1459 Dihedral : 3.599 21.900 1144 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.07 % Allowed : 24.81 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1031 helix: 1.16 (0.26), residues: 418 sheet: 0.26 (0.36), residues: 196 loop : -1.98 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.006 0.001 HIS A 362 PHE 0.025 0.001 PHE R 65 TYR 0.015 0.001 TYR R 168 ARG 0.004 0.000 ARG R 243 *********************** 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 224 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 63 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6195 (t80) REVERT: R 236 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7460 (mm-30) REVERT: R 243 ARG cc_start: 0.6387 (tpp80) cc_final: 0.5951 (ttp80) REVERT: R 274 PHE cc_start: 0.5317 (OUTLIER) cc_final: 0.4522 (p90) REVERT: R 285 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 216 LYS cc_start: 0.7985 (mmtm) cc_final: 0.7168 (mtmt) REVERT: A 356 ARG cc_start: 0.7953 (mtt-85) cc_final: 0.7669 (mtm180) REVERT: A 376 PHE cc_start: 0.8804 (t80) cc_final: 0.8498 (t80) REVERT: B 225 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.8173 (t-90) REVERT: B 266 HIS cc_start: 0.8375 (t-90) cc_final: 0.7762 (t-90) REVERT: G 38 MET cc_start: 0.8039 (tpt) cc_final: 0.7729 (tpt) REVERT: N 53 GLN cc_start: 0.8507 (mp-120) cc_final: 0.7986 (mp10) REVERT: N 77 ASN cc_start: 0.7554 (t0) cc_final: 0.7182 (t0) outliers start: 46 outliers final: 39 residues processed: 203 average time/residue: 0.2164 time to fit residues: 59.0538 Evaluate side-chains 217 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 285 PHE 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 72 SER 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 270 ILE 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 B residue 339 TRP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 72 ARG 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 30 optimal weight: 0.7980 chunk 100 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 51 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.197636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148819 restraints weight = 9419.786| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 3.09 r_work: 0.3561 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 8472 Z= 0.155 Angle : 0.542 9.715 11485 Z= 0.276 Chirality : 0.042 0.196 1291 Planarity : 0.003 0.048 1459 Dihedral : 3.478 22.844 1144 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.97 % Allowed : 25.69 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1031 helix: 1.30 (0.26), residues: 417 sheet: 0.29 (0.36), residues: 185 loop : -1.88 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 197 HIS 0.005 0.001 HIS A 362 PHE 0.027 0.001 PHE R 117 TYR 0.014 0.001 TYR R 168 ARG 0.004 0.000 ARG R 243 ********************** 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 215 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 119 TYR cc_start: 0.7952 (t80) cc_final: 0.7592 (t80) REVERT: R 236 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7463 (mm-30) REVERT: R 243 ARG cc_start: 0.6373 (tpp80) cc_final: 0.5836 (ttp80) REVERT: R 285 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: R 293 LEU cc_start: 0.7846 (tt) cc_final: 0.7364 (mt) REVERT: A 60 MET cc_start: 0.6920 (mpp) cc_final: 0.6563 (mpp) REVERT: A 216 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7197 (mtmt) REVERT: A 314 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8516 (tp30) REVERT: A 356 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7682 (mtm180) REVERT: A 376 PHE cc_start: 0.8775 (t80) cc_final: 0.8354 (t80) REVERT: B 120 ILE cc_start: 0.8401 (mt) cc_final: 0.8146 (mm) REVERT: B 266 HIS cc_start: 0.8338 (t-90) cc_final: 0.7715 (t-90) REVERT: G 38 MET cc_start: 0.8144 (tpt) cc_final: 0.7850 (tpt) REVERT: N 53 GLN cc_start: 0.8601 (mp-120) cc_final: 0.8097 (mp10) REVERT: N 77 ASN cc_start: 0.7469 (t0) cc_final: 0.7133 (t0) outliers start: 36 outliers final: 32 residues processed: 203 average time/residue: 0.2265 time to fit residues: 61.5532 Evaluate side-chains 201 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 222 THR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 285 PHE 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 72 SER 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 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE 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 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 23 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.190740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138882 restraints weight = 9581.609| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.14 r_work: 0.3470 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8472 Z= 0.270 Angle : 0.611 10.438 11485 Z= 0.317 Chirality : 0.044 0.196 1291 Planarity : 0.004 0.047 1459 Dihedral : 3.791 23.429 1144 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.30 % Allowed : 26.24 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1031 helix: 1.16 (0.26), residues: 418 sheet: 0.07 (0.36), residues: 196 loop : -1.90 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 297 HIS 0.008 0.001 HIS A 362 PHE 0.029 0.002 PHE R 65 TYR 0.016 0.002 TYR R 168 ARG 0.004 0.000 ARG R 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4400.45 seconds wall clock time: 78 minutes 54.14 seconds (4734.14 seconds total)