Starting phenix.real_space_refine on Tue Apr 29 21:36:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g05_29645/04_2025/8g05_29645_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g05_29645/04_2025/8g05_29645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g05_29645/04_2025/8g05_29645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g05_29645/04_2025/8g05_29645.map" model { file = "/net/cci-nas-00/data/ceres_data/8g05_29645/04_2025/8g05_29645_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g05_29645/04_2025/8g05_29645_neut.cif" } resolution = 3.0 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= 0.011 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 61 5.16 5 C 5701 2.51 5 N 1525 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8944 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2256 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 274} Chain breaks: 1 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 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: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CLR': 1, 'YI9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.86, per 1000 atoms: 0.66 Number of scatterers: 8944 At special positions: 0 Unit cell: (109.14, 128.4, 113.42, 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 61 16.00 O 1657 8.00 N 1525 7.00 C 5701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 166 " distance=2.02 Simple disulfide: pdb=" SG CYS R 93 " - pdb=" SG CYS R 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 13 sheets defined 35.9% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'R' and resid 15 through 34 removed outlier: 4.648A pdb=" N TYR R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TYR R 21 " --> pdb=" O LEU R 17 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TRP R 26 " --> pdb=" O VAL R 22 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL R 29 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL R 32 " --> pdb=" O VAL R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 48 removed outlier: 3.514A pdb=" N LEU R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR R 41 " --> pdb=" O GLY R 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU R 42 " --> pdb=" O ASN R 38 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 52 removed outlier: 3.801A pdb=" N ARG R 52 " --> pdb=" O PRO R 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 49 through 52' Processing helix chain 'R' and resid 55 through 66 removed outlier: 3.627A pdb=" N ILE R 59 " --> pdb=" O PHE R 55 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 72 Processing helix chain 'R' and resid 79 through 84 Processing helix chain 'R' and resid 89 through 120 removed outlier: 3.821A pdb=" N VAL R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU R 98 " --> pdb=" O ARG R 94 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE R 101 " --> pdb=" O GLY R 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU R 116 " --> pdb=" O CYS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 135 through 149 removed outlier: 3.798A pdb=" N THR R 144 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 147 " --> pdb=" O SER R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 189 Processing helix chain 'R' and resid 196 through 210 removed outlier: 3.771A pdb=" N HIS R 202 " --> pdb=" O TYR R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 330 removed outlier: 3.787A pdb=" N ARG R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE R 325 " --> pdb=" O CYS R 321 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N CYS R 327 " --> pdb=" O ALA R 323 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE R 328 " --> pdb=" O VAL R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 342 removed outlier: 4.267A pdb=" N PHE R 335 " --> pdb=" O SER R 331 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE R 340 " --> pdb=" O LEU R 336 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU R 341 " --> pdb=" O LEU R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 358 removed outlier: 3.562A pdb=" N HIS R 352 " --> pdb=" O PRO R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 364 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 374 through 387 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.614A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.085A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.958A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 331 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.638A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.578A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.965A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.883A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.729A pdb=" N ASP E 223 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 220 through 224' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'G' and resid 44 through 48 Processing sheet with id=AA1, first strand: chain 'R' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 5.990A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.607A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.669A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.000A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.537A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.458A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.837A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.398A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.752A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.970A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 155 through 160 395 hydrogen bonds defined for protein. 1104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1442 1.31 - 1.43: 2517 1.43 - 1.56: 5085 1.56 - 1.69: 1 1.69 - 1.81: 86 Bond restraints: 9131 Sorted by residual: bond pdb=" C11 YI9 R 401 " pdb=" C12 YI9 R 401 " ideal model delta sigma weight residual 1.506 1.365 0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C10 YI9 R 401 " pdb=" C11 YI9 R 401 " ideal model delta sigma weight residual 1.501 1.371 0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C10 YI9 R 401 " pdb=" N09 YI9 R 401 " ideal model delta sigma weight residual 1.325 1.445 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C15 YI9 R 401 " pdb=" N14 YI9 R 401 " ideal model delta sigma weight residual 1.408 1.323 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C ASN R 366 " pdb=" N PRO R 367 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.11e-02 8.12e+03 6.93e+00 ... (remaining 9126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 12261 3.43 - 6.87: 99 6.87 - 10.30: 11 10.30 - 13.73: 3 13.73 - 17.16: 1 Bond angle restraints: 12375 Sorted by residual: angle pdb=" C ASN A 269 " pdb=" N LYS A 270 " pdb=" CA LYS A 270 " ideal model delta sigma weight residual 122.82 128.48 -5.66 1.42e+00 4.96e-01 1.59e+01 angle pdb=" CA ARG E 218 " pdb=" CB ARG E 218 " pdb=" CG ARG E 218 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" N VAL R 146 " pdb=" CA VAL R 146 " pdb=" C VAL R 146 " ideal model delta sigma weight residual 112.29 109.25 3.04 9.40e-01 1.13e+00 1.05e+01 angle pdb=" CA LEU B 70 " pdb=" CB LEU B 70 " pdb=" CG LEU B 70 " ideal model delta sigma weight residual 116.30 127.58 -11.28 3.50e+00 8.16e-02 1.04e+01 ... (remaining 12370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4918 17.83 - 35.67: 450 35.67 - 53.50: 70 53.50 - 71.33: 13 71.33 - 89.17: 13 Dihedral angle restraints: 5464 sinusoidal: 2163 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS R 11 " pdb=" SG CYS R 11 " pdb=" SG CYS R 166 " pdb=" CB CYS R 166 " ideal model delta sinusoidal sigma weight residual -86.00 -150.17 64.17 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CA LYS R 135 " pdb=" C LYS R 135 " pdb=" N GLY R 136 " pdb=" CA GLY R 136 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA THR E 172 " pdb=" C THR E 172 " pdb=" N TYR E 173 " pdb=" CA TYR E 173 " ideal model delta harmonic sigma weight residual 180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.991: 1409 0.991 - 1.981: 0 1.981 - 2.972: 0 2.972 - 3.962: 0 3.962 - 4.953: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 -2.40 4.95 2.00e-01 2.50e+01 6.13e+02 chirality pdb=" CB VAL A 339 " pdb=" CA VAL A 339 " pdb=" CG1 VAL A 339 " pdb=" CG2 VAL A 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE B 232 " pdb=" CA ILE B 232 " pdb=" CG1 ILE B 232 " pdb=" CG2 ILE B 232 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1407 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C08 YI9 R 401 " -0.082 2.00e-02 2.50e+03 3.84e-02 3.32e+01 pdb=" C10 YI9 R 401 " 0.034 2.00e-02 2.50e+03 pdb=" C11 YI9 R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C12 YI9 R 401 " 0.004 2.00e-02 2.50e+03 pdb=" C15 YI9 R 401 " -0.012 2.00e-02 2.50e+03 pdb=" N09 YI9 R 401 " 0.057 2.00e-02 2.50e+03 pdb=" N14 YI9 R 401 " -0.011 2.00e-02 2.50e+03 pdb=" N17 YI9 R 401 " 0.012 2.00e-02 2.50e+03 pdb=" O16 YI9 R 401 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 153 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO R 154 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 154 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 154 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 366 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO R 367 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 367 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 367 " -0.035 5.00e-02 4.00e+02 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2156 2.79 - 3.31: 7662 3.31 - 3.84: 15070 3.84 - 4.37: 18207 4.37 - 4.90: 31481 Nonbonded interactions: 74576 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.257 3.040 nonbonded pdb=" O VAL R 106 " pdb=" OG1 THR R 110 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" OD1 ASP B 290 " model vdw 2.305 3.040 nonbonded pdb=" OG SER R 105 " pdb=" OH TYR R 186 " model vdw 2.312 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.316 3.040 ... (remaining 74571 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: 0.550 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.007 0.141 9135 Z= 0.296 Angle : 0.908 17.165 12383 Z= 0.491 Chirality : 0.143 4.953 1410 Planarity : 0.007 0.065 1559 Dihedral : 14.307 89.168 3326 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.62 % Allowed : 7.33 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -3.23 (0.21), residues: 1124 helix: -3.16 (0.19), residues: 359 sheet: -0.93 (0.29), residues: 284 loop : -1.91 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.023 0.002 PHE B 199 TYR 0.019 0.002 TYR B 59 ARG 0.014 0.001 ARG E 98 Details of bonding type rmsd hydrogen bonds : bond 0.14780 ( 395) hydrogen bonds : angle 7.05514 ( 1104) SS BOND : bond 0.00501 ( 4) SS BOND : angle 1.55746 ( 8) covalent geometry : bond 0.00656 ( 9131) covalent geometry : angle 0.90776 (12375) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 1.056 Fit side-chains REVERT: R 186 TYR cc_start: 0.6991 (m-80) cc_final: 0.6775 (m-80) REVERT: R 316 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7323 (tttm) REVERT: A 204 GLN cc_start: 0.7891 (mt0) cc_final: 0.7583 (mm-40) REVERT: B 16 ASN cc_start: 0.7828 (m110) cc_final: 0.7602 (m110) REVERT: B 46 ARG cc_start: 0.6933 (mtp-110) cc_final: 0.6647 (mmt180) REVERT: B 188 MET cc_start: 0.8124 (mmm) cc_final: 0.7846 (mmp) REVERT: B 214 ARG cc_start: 0.6800 (mmp-170) cc_final: 0.5932 (mmm-85) REVERT: G 38 MET cc_start: 0.7873 (ttp) cc_final: 0.7515 (ttp) outliers start: 6 outliers final: 2 residues processed: 201 average time/residue: 1.2517 time to fit residues: 268.6840 Evaluate side-chains 151 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 0.0570 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 74 GLN R 83 HIS R 85 HIS R 357 ASN R 379 GLN A 22 ASN A 241 ASN A 256 ASN A 306 GLN B 91 HIS B 156 GLN B 259 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121770 restraints weight = 10538.977| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.14 r_work: 0.3245 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9135 Z= 0.154 Angle : 0.606 8.587 12383 Z= 0.316 Chirality : 0.043 0.175 1410 Planarity : 0.004 0.046 1559 Dihedral : 7.005 59.366 1314 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.20 % Allowed : 14.46 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.89 (0.24), residues: 1124 helix: -1.53 (0.25), residues: 368 sheet: -0.63 (0.30), residues: 279 loop : -1.22 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.006 0.001 HIS R 85 PHE 0.016 0.001 PHE A 334 TYR 0.011 0.001 TYR G 40 ARG 0.006 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 395) hydrogen bonds : angle 5.17340 ( 1104) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.89283 ( 8) covalent geometry : bond 0.00354 ( 9131) covalent geometry : angle 0.60601 (12375) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.059 Fit side-chains REVERT: R 186 TYR cc_start: 0.7088 (m-80) cc_final: 0.6858 (m-80) REVERT: R 316 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7059 (tttm) REVERT: R 344 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7432 (mtm110) REVERT: R 376 GLN cc_start: 0.7943 (mp10) cc_final: 0.7562 (mm-40) REVERT: A 204 GLN cc_start: 0.7881 (mt0) cc_final: 0.7333 (mm-40) REVERT: A 298 GLU cc_start: 0.7820 (tp30) cc_final: 0.7145 (tm-30) REVERT: B 10 GLU cc_start: 0.8953 (tp30) cc_final: 0.8415 (tp30) REVERT: B 16 ASN cc_start: 0.7856 (m110) cc_final: 0.7518 (m110) REVERT: B 42 ARG cc_start: 0.7526 (tpt170) cc_final: 0.7140 (tpp-160) REVERT: B 46 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.7000 (mmt180) REVERT: B 214 ARG cc_start: 0.6645 (mmp-170) cc_final: 0.5766 (mmm160) REVERT: E 17 SER cc_start: 0.8322 (m) cc_final: 0.7880 (p) REVERT: G 42 GLU cc_start: 0.7217 (mp0) cc_final: 0.6874 (tm-30) outliers start: 31 outliers final: 13 residues processed: 183 average time/residue: 1.1616 time to fit residues: 227.2727 Evaluate side-chains 160 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 85 HIS R 357 ASN R 379 GLN A 241 ASN A 256 ASN A 311 ASN B 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.161283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122115 restraints weight = 10633.378| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.22 r_work: 0.3234 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9135 Z= 0.164 Angle : 0.607 8.869 12383 Z= 0.311 Chirality : 0.043 0.138 1410 Planarity : 0.004 0.052 1559 Dihedral : 6.499 57.506 1312 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.24 % Allowed : 16.32 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.34 (0.25), residues: 1124 helix: -0.83 (0.27), residues: 369 sheet: -0.34 (0.31), residues: 269 loop : -1.11 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS R 85 PHE 0.015 0.001 PHE A 334 TYR 0.011 0.001 TYR G 40 ARG 0.006 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 395) hydrogen bonds : angle 4.94793 ( 1104) SS BOND : bond 0.00283 ( 4) SS BOND : angle 0.81257 ( 8) covalent geometry : bond 0.00379 ( 9131) covalent geometry : angle 0.60644 (12375) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5823 (mtt180) cc_final: 0.5149 (tpp80) REVERT: R 316 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7022 (tttm) REVERT: R 344 ARG cc_start: 0.7461 (mtm110) cc_final: 0.7203 (mtm110) REVERT: R 373 MET cc_start: 0.7914 (mmp) cc_final: 0.7710 (mmp) REVERT: R 376 GLN cc_start: 0.7994 (mp10) cc_final: 0.7591 (mm-40) REVERT: A 298 GLU cc_start: 0.8296 (tp30) cc_final: 0.7470 (tm-30) REVERT: B 42 ARG cc_start: 0.7538 (tpt170) cc_final: 0.7187 (tpp-160) REVERT: B 46 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7045 (mmt180) REVERT: B 175 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: B 214 ARG cc_start: 0.6555 (mmp-170) cc_final: 0.5713 (mmm160) REVERT: E 17 SER cc_start: 0.8229 (m) cc_final: 0.7931 (p) outliers start: 41 outliers final: 27 residues processed: 181 average time/residue: 1.1019 time to fit residues: 213.9875 Evaluate side-chains 178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN A 306 GLN A 311 ASN B 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.161468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122488 restraints weight = 10600.994| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.20 r_work: 0.3237 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9135 Z= 0.154 Angle : 0.593 8.062 12383 Z= 0.303 Chirality : 0.043 0.135 1410 Planarity : 0.004 0.039 1559 Dihedral : 6.306 58.520 1312 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.03 % Allowed : 17.87 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1124 helix: -0.49 (0.28), residues: 370 sheet: -0.29 (0.31), residues: 269 loop : -1.03 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 85 PHE 0.013 0.001 PHE A 334 TYR 0.010 0.001 TYR B 105 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 395) hydrogen bonds : angle 4.80750 ( 1104) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.23206 ( 8) covalent geometry : bond 0.00358 ( 9131) covalent geometry : angle 0.59263 (12375) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5823 (mtt180) cc_final: 0.5191 (tpp80) REVERT: R 316 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7162 (tttm) REVERT: R 344 ARG cc_start: 0.7534 (mtm110) cc_final: 0.7133 (mtm110) REVERT: R 376 GLN cc_start: 0.8060 (mp10) cc_final: 0.7691 (mm-40) REVERT: A 204 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7002 (mm-40) REVERT: A 298 GLU cc_start: 0.8291 (tp30) cc_final: 0.7479 (tm-30) REVERT: B 42 ARG cc_start: 0.7523 (tpt170) cc_final: 0.7120 (tpp-160) REVERT: B 46 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7087 (mmt180) REVERT: B 175 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: B 214 ARG cc_start: 0.6589 (mmp-170) cc_final: 0.5778 (mmm-85) REVERT: B 290 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6315 (m-30) REVERT: B 338 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8316 (mm) REVERT: E 17 SER cc_start: 0.8240 (m) cc_final: 0.7998 (p) REVERT: E 218 ARG cc_start: 0.7093 (mmp-170) cc_final: 0.6615 (mtm-85) REVERT: G 42 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6854 (tm-30) outliers start: 39 outliers final: 23 residues processed: 181 average time/residue: 1.1596 time to fit residues: 224.2543 Evaluate side-chains 174 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN A 311 ASN B 16 ASN B 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.163735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125672 restraints weight = 10556.284| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.17 r_work: 0.3275 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9135 Z= 0.111 Angle : 0.558 7.896 12383 Z= 0.285 Chirality : 0.041 0.139 1410 Planarity : 0.003 0.038 1559 Dihedral : 5.967 58.028 1312 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.72 % Allowed : 19.01 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.77 (0.25), residues: 1124 helix: -0.11 (0.28), residues: 365 sheet: -0.18 (0.31), residues: 272 loop : -0.89 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 334 TYR 0.008 0.001 TYR E 190 ARG 0.004 0.000 ARG R 176 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 395) hydrogen bonds : angle 4.51903 ( 1104) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.86105 ( 8) covalent geometry : bond 0.00250 ( 9131) covalent geometry : angle 0.55780 (12375) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5757 (mtt180) cc_final: 0.5185 (tpp80) REVERT: R 316 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7275 (tttm) REVERT: R 344 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7124 (mtm110) REVERT: R 376 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7706 (mm-40) REVERT: A 53 MET cc_start: 0.6170 (mtm) cc_final: 0.5969 (mtp) REVERT: A 204 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6818 (mm-40) REVERT: A 276 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7462 (mm-30) REVERT: A 298 GLU cc_start: 0.8247 (tp30) cc_final: 0.7504 (tm-30) REVERT: A 306 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7749 (mm110) REVERT: B 46 ARG cc_start: 0.7933 (mtp-110) cc_final: 0.7087 (mmt180) REVERT: B 198 LEU cc_start: 0.7977 (mt) cc_final: 0.7770 (mt) REVERT: B 214 ARG cc_start: 0.6612 (mmp-170) cc_final: 0.5794 (mmm-85) REVERT: B 303 ASP cc_start: 0.7869 (m-30) cc_final: 0.7660 (m-30) REVERT: B 338 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8297 (mm) REVERT: E 17 SER cc_start: 0.8104 (m) cc_final: 0.7854 (p) REVERT: E 46 GLU cc_start: 0.7781 (pt0) cc_final: 0.7448 (pt0) REVERT: E 87 ARG cc_start: 0.7389 (mtp180) cc_final: 0.7162 (mtm-85) REVERT: G 21 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7441 (tmt) REVERT: G 27 ARG cc_start: 0.8117 (mtt90) cc_final: 0.7558 (mpt180) REVERT: G 42 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6946 (tm-30) outliers start: 36 outliers final: 20 residues processed: 183 average time/residue: 1.2056 time to fit residues: 235.8046 Evaluate side-chains 173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 376 GLN Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 0.0980 chunk 24 optimal weight: 0.3980 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 HIS R 357 ASN R 379 GLN A 204 GLN A 241 ASN A 256 ASN B 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.162257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123242 restraints weight = 10504.584| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.20 r_work: 0.3250 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9135 Z= 0.147 Angle : 0.589 8.877 12383 Z= 0.301 Chirality : 0.043 0.169 1410 Planarity : 0.004 0.063 1559 Dihedral : 5.749 55.845 1311 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.34 % Allowed : 18.70 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.71 (0.25), residues: 1124 helix: -0.16 (0.28), residues: 371 sheet: -0.07 (0.31), residues: 270 loop : -0.82 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 332 HIS 0.004 0.001 HIS R 85 PHE 0.022 0.001 PHE R 92 TYR 0.010 0.001 TYR E 190 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 395) hydrogen bonds : angle 4.60431 ( 1104) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.80901 ( 8) covalent geometry : bond 0.00341 ( 9131) covalent geometry : angle 0.58920 (12375) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5759 (mtt180) cc_final: 0.5183 (tpp80) REVERT: R 316 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7239 (tttm) REVERT: R 344 ARG cc_start: 0.7558 (mtm110) cc_final: 0.6903 (mtm110) REVERT: R 376 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7756 (mm-40) REVERT: A 204 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6857 (mm-40) REVERT: A 273 LEU cc_start: 0.8415 (mt) cc_final: 0.8213 (mt) REVERT: A 276 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 298 GLU cc_start: 0.8264 (tp30) cc_final: 0.7522 (tm-30) REVERT: B 46 ARG cc_start: 0.7992 (mtp-110) cc_final: 0.7145 (mmt180) REVERT: B 175 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: B 214 ARG cc_start: 0.6576 (mmp-170) cc_final: 0.5761 (mmm-85) REVERT: B 338 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8307 (mm) REVERT: E 46 GLU cc_start: 0.7815 (pt0) cc_final: 0.7499 (pt0) REVERT: E 191 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7855 (mtt180) REVERT: E 218 ARG cc_start: 0.6975 (mmp-170) cc_final: 0.6671 (mmp-170) REVERT: G 27 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7564 (mpt180) outliers start: 42 outliers final: 24 residues processed: 176 average time/residue: 1.1854 time to fit residues: 222.5877 Evaluate side-chains 174 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 376 GLN Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 61 ASN R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN A 311 ASN B 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.162597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123991 restraints weight = 10660.629| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.20 r_work: 0.3248 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9135 Z= 0.140 Angle : 0.598 10.134 12383 Z= 0.303 Chirality : 0.042 0.180 1410 Planarity : 0.004 0.054 1559 Dihedral : 5.628 56.083 1311 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.44 % Allowed : 18.80 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.62 (0.25), residues: 1124 helix: -0.09 (0.28), residues: 371 sheet: -0.00 (0.31), residues: 270 loop : -0.77 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 332 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE A 334 TYR 0.010 0.001 TYR E 190 ARG 0.008 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 395) hydrogen bonds : angle 4.59538 ( 1104) SS BOND : bond 0.00222 ( 4) SS BOND : angle 1.69116 ( 8) covalent geometry : bond 0.00324 ( 9131) covalent geometry : angle 0.59702 (12375) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5741 (mtt180) cc_final: 0.5152 (tpp80) REVERT: R 316 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7146 (tttm) REVERT: R 344 ARG cc_start: 0.7596 (mtm110) cc_final: 0.7010 (mtm110) REVERT: R 376 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7707 (mm-40) REVERT: A 204 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6872 (mm-40) REVERT: A 276 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 298 GLU cc_start: 0.8266 (tp30) cc_final: 0.7512 (tm-30) REVERT: B 46 ARG cc_start: 0.7958 (mtp-110) cc_final: 0.7072 (mmt180) REVERT: B 175 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: B 214 ARG cc_start: 0.6568 (mmp-170) cc_final: 0.5741 (mmm-85) REVERT: B 338 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8305 (mm) REVERT: E 46 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: E 178 LEU cc_start: 0.8867 (tt) cc_final: 0.8666 (tt) REVERT: E 191 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7841 (mtt180) REVERT: E 218 ARG cc_start: 0.6947 (mmp-170) cc_final: 0.6621 (mmp-170) outliers start: 43 outliers final: 27 residues processed: 174 average time/residue: 1.2170 time to fit residues: 226.2322 Evaluate side-chains 176 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 376 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.163624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126129 restraints weight = 10712.595| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.18 r_work: 0.3275 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9135 Z= 0.121 Angle : 0.579 11.652 12383 Z= 0.293 Chirality : 0.042 0.143 1410 Planarity : 0.004 0.059 1559 Dihedral : 5.485 55.362 1311 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.31 % Allowed : 20.14 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.46 (0.25), residues: 1124 helix: 0.07 (0.28), residues: 371 sheet: 0.04 (0.31), residues: 276 loop : -0.67 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 332 HIS 0.003 0.001 HIS R 85 PHE 0.026 0.001 PHE R 92 TYR 0.009 0.001 TYR E 190 ARG 0.009 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 395) hydrogen bonds : angle 4.47615 ( 1104) SS BOND : bond 0.00246 ( 4) SS BOND : angle 1.28337 ( 8) covalent geometry : bond 0.00276 ( 9131) covalent geometry : angle 0.57841 (12375) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5768 (mtt180) cc_final: 0.5080 (ttm110) REVERT: R 316 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7232 (tttm) REVERT: R 344 ARG cc_start: 0.7556 (mtm110) cc_final: 0.7055 (mtm110) REVERT: R 376 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7723 (mm-40) REVERT: A 204 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.6798 (mm-40) REVERT: A 276 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7551 (mm-30) REVERT: A 298 GLU cc_start: 0.8247 (tp30) cc_final: 0.7520 (tm-30) REVERT: B 46 ARG cc_start: 0.7967 (mtp-110) cc_final: 0.7121 (mmt180) REVERT: B 214 ARG cc_start: 0.6584 (mmp-170) cc_final: 0.5786 (mmm-85) REVERT: B 338 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8372 (mm) REVERT: E 46 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: E 191 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8042 (mpp80) REVERT: E 218 ARG cc_start: 0.7030 (mmp-170) cc_final: 0.6695 (mmp-170) outliers start: 32 outliers final: 22 residues processed: 178 average time/residue: 1.1482 time to fit residues: 218.8934 Evaluate side-chains 173 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 376 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 HIS R 379 GLN A 241 ASN A 256 ASN A 306 GLN A 311 ASN B 75 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.164105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126140 restraints weight = 10611.681| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.16 r_work: 0.3291 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9135 Z= 0.122 Angle : 0.600 12.721 12383 Z= 0.303 Chirality : 0.042 0.136 1410 Planarity : 0.004 0.044 1559 Dihedral : 5.421 55.238 1311 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.31 % Allowed : 20.66 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.32 (0.25), residues: 1124 helix: 0.24 (0.28), residues: 365 sheet: 0.07 (0.31), residues: 276 loop : -0.61 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 332 HIS 0.004 0.001 HIS R 85 PHE 0.011 0.001 PHE A 334 TYR 0.009 0.001 TYR E 190 ARG 0.005 0.000 ARG R 375 Details of bonding type rmsd hydrogen bonds : bond 0.03045 ( 395) hydrogen bonds : angle 4.47713 ( 1104) SS BOND : bond 0.00181 ( 4) SS BOND : angle 1.14610 ( 8) covalent geometry : bond 0.00281 ( 9131) covalent geometry : angle 0.59993 (12375) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5750 (mtt180) cc_final: 0.5060 (ttm110) REVERT: R 316 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7214 (tttm) REVERT: R 344 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7380 (mtm110) REVERT: R 376 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7734 (mm-40) REVERT: A 204 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6693 (mm-40) REVERT: A 209 LYS cc_start: 0.8278 (tptm) cc_final: 0.7367 (mmpt) REVERT: A 276 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 298 GLU cc_start: 0.8265 (tp30) cc_final: 0.7538 (tm-30) REVERT: B 46 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7149 (mmt180) REVERT: B 214 ARG cc_start: 0.6583 (mmp-170) cc_final: 0.5790 (mmm-85) REVERT: B 338 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8368 (mm) REVERT: E 18 ARG cc_start: 0.6982 (ttt90) cc_final: 0.6572 (mtp85) REVERT: E 46 GLU cc_start: 0.7774 (pt0) cc_final: 0.7413 (pt0) REVERT: E 191 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8045 (mpp80) REVERT: E 218 ARG cc_start: 0.7010 (mmp-170) cc_final: 0.6567 (mmp-170) REVERT: G 27 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7506 (mpt180) outliers start: 32 outliers final: 20 residues processed: 171 average time/residue: 1.2886 time to fit residues: 234.7944 Evaluate side-chains 171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 376 GLN Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN A 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.164095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126224 restraints weight = 10639.661| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.18 r_work: 0.3294 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9135 Z= 0.122 Angle : 0.611 13.235 12383 Z= 0.307 Chirality : 0.042 0.135 1410 Planarity : 0.003 0.038 1559 Dihedral : 5.381 55.251 1311 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.79 % Allowed : 21.18 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.25 (0.26), residues: 1124 helix: 0.35 (0.28), residues: 366 sheet: 0.19 (0.31), residues: 277 loop : -0.68 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 332 HIS 0.005 0.001 HIS R 85 PHE 0.032 0.001 PHE R 92 TYR 0.009 0.001 TYR E 190 ARG 0.005 0.000 ARG R 375 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 395) hydrogen bonds : angle 4.44276 ( 1104) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.08762 ( 8) covalent geometry : bond 0.00278 ( 9131) covalent geometry : angle 0.61022 (12375) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5724 (mtt180) cc_final: 0.5058 (ttm110) REVERT: R 316 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7204 (tttm) REVERT: R 344 ARG cc_start: 0.7454 (mtm110) cc_final: 0.7221 (mtm110) REVERT: R 376 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7692 (mm-40) REVERT: A 209 LYS cc_start: 0.8192 (tptm) cc_final: 0.7302 (mmpt) REVERT: A 252 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 276 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 298 GLU cc_start: 0.8290 (tp30) cc_final: 0.7554 (tm-30) REVERT: B 46 ARG cc_start: 0.8042 (mtp-110) cc_final: 0.7169 (mmt180) REVERT: B 175 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: B 214 ARG cc_start: 0.6614 (mmp-170) cc_final: 0.5805 (mmm-85) REVERT: B 338 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8356 (mm) REVERT: E 178 LEU cc_start: 0.8897 (tt) cc_final: 0.8687 (tt) REVERT: E 191 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8036 (mpp80) REVERT: E 218 ARG cc_start: 0.6973 (mmp-170) cc_final: 0.6506 (mmp-170) outliers start: 27 outliers final: 19 residues processed: 171 average time/residue: 1.3010 time to fit residues: 236.8923 Evaluate side-chains 168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 376 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 191 ARG Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 85 HIS R 379 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 256 ASN A 304 GLN A 311 ASN B 156 GLN E 231 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120676 restraints weight = 10872.615| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.21 r_work: 0.3202 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9135 Z= 0.272 Angle : 0.730 13.612 12383 Z= 0.371 Chirality : 0.048 0.303 1410 Planarity : 0.004 0.034 1559 Dihedral : 5.948 61.487 1311 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.31 % Allowed : 21.07 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.68 (0.25), residues: 1124 helix: -0.08 (0.28), residues: 364 sheet: 0.04 (0.30), residues: 282 loop : -0.93 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 332 HIS 0.005 0.001 HIS R 85 PHE 0.019 0.002 PHE B 199 TYR 0.014 0.002 TYR R 69 ARG 0.009 0.001 ARG R 375 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 395) hydrogen bonds : angle 5.06378 ( 1104) SS BOND : bond 0.00202 ( 4) SS BOND : angle 1.38000 ( 8) covalent geometry : bond 0.00640 ( 9131) covalent geometry : angle 0.72952 (12375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7925.50 seconds wall clock time: 137 minutes 6.05 seconds (8226.05 seconds total)