Starting phenix.real_space_refine on Fri Nov 15 13:08:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/11_2024/8g05_29645_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/11_2024/8g05_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/11_2024/8g05_29645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/11_2024/8g05_29645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/11_2024/8g05_29645_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g05_29645/11_2024/8g05_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-5513/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: 5.28, per 1000 atoms: 0.59 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 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: 1.08 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: 2.47 Time building geometry restraints manager: 2.62 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.240 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- 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 9131 Z= 0.418 Angle : 0.908 17.165 12375 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 *********************** 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 : 1.000 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: 1.2322 time to fit residues: 264.9360 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 : 1.064 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.1302 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9131 Z= 0.212 Angle : 0.599 8.739 12375 Z= 0.312 Chirality : 0.043 0.163 1410 Planarity : 0.004 0.046 1559 Dihedral : 6.964 59.794 1314 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.10 % Allowed : 14.36 % Favored : 82.54 % 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: -1.88 (0.24), residues: 1124 helix: -1.54 (0.25), residues: 368 sheet: -0.61 (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 0.015 0.001 PHE A 334 TYR 0.011 0.001 TYR E 94 ARG 0.005 0.000 ARG B 150 *********************** 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 195 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.915 Fit side-chains REVERT: R 94 ARG cc_start: 0.5780 (mtt180) cc_final: 0.5569 (tpp80) REVERT: R 316 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7311 (tttm) REVERT: R 344 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7321 (mtm110) REVERT: R 376 GLN cc_start: 0.7996 (mp10) cc_final: 0.7493 (mm-40) REVERT: A 204 GLN cc_start: 0.7676 (mt0) cc_final: 0.7323 (mm-40) REVERT: A 298 GLU cc_start: 0.7469 (tp30) cc_final: 0.7110 (tm-30) REVERT: B 10 GLU cc_start: 0.8375 (tp30) cc_final: 0.7951 (tp30) REVERT: B 16 ASN cc_start: 0.7822 (m110) cc_final: 0.7501 (m110) REVERT: B 42 ARG cc_start: 0.7203 (tpt170) cc_final: 0.6923 (tpp-160) REVERT: B 46 ARG cc_start: 0.6908 (mtp-110) cc_final: 0.6588 (mmt180) REVERT: B 214 ARG cc_start: 0.6516 (mmp-170) cc_final: 0.5856 (mmm160) REVERT: E 17 SER cc_start: 0.8077 (m) cc_final: 0.7703 (p) outliers start: 30 outliers final: 12 residues processed: 184 average time/residue: 1.1979 time to fit residues: 235.5243 Evaluate side-chains 159 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 100 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 B 16 ASN B 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9131 Z= 0.162 Angle : 0.565 7.928 12375 Z= 0.290 Chirality : 0.041 0.133 1410 Planarity : 0.004 0.045 1559 Dihedral : 6.335 57.758 1312 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.20 % Allowed : 16.84 % Favored : 79.96 % 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: -1.24 (0.25), residues: 1124 helix: -0.69 (0.27), residues: 369 sheet: -0.37 (0.30), residues: 280 loop : -1.04 (0.29), residues: 475 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 0.014 0.001 PHE A 334 TYR 0.010 0.001 TYR R 186 ARG 0.004 0.000 ARG R 375 *********************** 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 192 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5604 (mtt180) cc_final: 0.5340 (tpp80) REVERT: R 316 LYS cc_start: 0.7892 (mtmm) cc_final: 0.7269 (tttm) REVERT: R 344 ARG cc_start: 0.7397 (mtm110) cc_final: 0.7196 (mtm110) REVERT: R 376 GLN cc_start: 0.8052 (mp10) cc_final: 0.7603 (mm-40) REVERT: A 306 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7493 (mm110) REVERT: B 42 ARG cc_start: 0.7155 (tpt170) cc_final: 0.6858 (tpp-160) REVERT: B 46 ARG cc_start: 0.6812 (mtp-110) cc_final: 0.6557 (mmt180) REVERT: B 198 LEU cc_start: 0.8054 (mt) cc_final: 0.7825 (mt) REVERT: B 214 ARG cc_start: 0.6540 (mmp-170) cc_final: 0.5885 (mmm-85) outliers start: 31 outliers final: 20 residues processed: 186 average time/residue: 1.0561 time to fit residues: 211.5434 Evaluate side-chains 168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 149 VAL Chi-restraints excluded: chain R residue 169 SER 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 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.3980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 A 311 ASN B 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9131 Z= 0.169 Angle : 0.546 7.018 12375 Z= 0.281 Chirality : 0.041 0.156 1410 Planarity : 0.003 0.037 1559 Dihedral : 6.112 58.787 1312 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.20 % Allowed : 18.60 % Favored : 78.20 % 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: -0.88 (0.25), residues: 1124 helix: -0.31 (0.28), residues: 372 sheet: -0.16 (0.30), residues: 275 loop : -0.93 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 85 PHE 0.012 0.001 PHE A 334 TYR 0.010 0.001 TYR E 190 ARG 0.004 0.000 ARG B 314 *********************** 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 188 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5618 (mtt180) cc_final: 0.5407 (tpp80) REVERT: R 316 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7302 (tttm) REVERT: R 344 ARG cc_start: 0.7394 (mtm110) cc_final: 0.7131 (mtm110) REVERT: R 376 GLN cc_start: 0.8115 (mp10) cc_final: 0.7743 (mm-40) REVERT: A 204 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6871 (mm-40) REVERT: B 42 ARG cc_start: 0.7152 (tpt170) cc_final: 0.6873 (tpp-160) REVERT: B 46 ARG cc_start: 0.6867 (mtp-110) cc_final: 0.6583 (mmt180) REVERT: B 198 LEU cc_start: 0.8056 (mt) cc_final: 0.7805 (mt) REVERT: B 214 ARG cc_start: 0.6518 (mmp-170) cc_final: 0.5902 (mmm-85) REVERT: B 338 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8216 (mm) REVERT: E 191 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7978 (mpp80) REVERT: G 27 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7819 (mpt180) outliers start: 31 outliers final: 20 residues processed: 178 average time/residue: 1.1762 time to fit residues: 223.9196 Evaluate side-chains 170 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL 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 307 PHE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 13 GLN 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 338 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 149 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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 256 ASN A 311 ASN B 156 GLN E 231 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 9131 Z= 0.505 Angle : 0.734 10.690 12375 Z= 0.378 Chirality : 0.050 0.267 1410 Planarity : 0.005 0.046 1559 Dihedral : 6.615 64.193 1311 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.27 % Allowed : 17.56 % Favored : 77.17 % 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: -1.19 (0.25), residues: 1124 helix: -0.65 (0.27), residues: 370 sheet: -0.33 (0.30), residues: 286 loop : -1.05 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.003 PHE B 199 TYR 0.017 0.002 TYR B 59 ARG 0.011 0.001 ARG B 150 *********************** 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 205 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 154 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5698 (mtt180) cc_final: 0.5385 (tpp80) REVERT: R 143 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8618 (m) REVERT: R 186 TYR cc_start: 0.7299 (m-80) cc_final: 0.7001 (m-80) REVERT: R 344 ARG cc_start: 0.7401 (mtm110) cc_final: 0.6873 (mtm110) REVERT: R 376 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7844 (mm-40) REVERT: A 53 MET cc_start: 0.6158 (mtm) cc_final: 0.5948 (mtp) REVERT: A 204 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: A 298 GLU cc_start: 0.7903 (tp30) cc_final: 0.7425 (tm-30) REVERT: B 43 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.9046 (mp) REVERT: B 46 ARG cc_start: 0.7121 (mtp-110) cc_final: 0.6699 (mmt180) REVERT: B 175 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7707 (mt0) REVERT: B 214 ARG cc_start: 0.6497 (mmp-170) cc_final: 0.5835 (mmm160) REVERT: G 27 ARG cc_start: 0.8309 (mtt90) cc_final: 0.7828 (mpt180) outliers start: 51 outliers final: 34 residues processed: 182 average time/residue: 1.1697 time to fit residues: 227.9005 Evaluate side-chains 179 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 143 SER 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 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 227 LEU 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 B residue 30 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE 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 B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 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 Chi-restraints excluded: chain E residue 231 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 30.0000 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 B 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9131 Z= 0.213 Angle : 0.590 7.999 12375 Z= 0.303 Chirality : 0.043 0.143 1410 Planarity : 0.003 0.038 1559 Dihedral : 5.949 57.677 1311 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.34 % Allowed : 19.94 % Favored : 75.72 % 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: -0.82 (0.25), residues: 1124 helix: -0.30 (0.28), residues: 370 sheet: -0.09 (0.31), residues: 270 loop : -0.86 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.000 ARG R 176 *********************** 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 193 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5572 (mtt180) cc_final: 0.5366 (tpp80) REVERT: R 186 TYR cc_start: 0.7037 (m-80) cc_final: 0.6751 (m-80) REVERT: R 316 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7278 (tttm) REVERT: R 344 ARG cc_start: 0.7482 (mtm110) cc_final: 0.7213 (mtm110) REVERT: R 376 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7813 (mm-40) REVERT: A 204 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6843 (mm-40) REVERT: A 298 GLU cc_start: 0.7857 (tp30) cc_final: 0.7413 (tm-30) REVERT: B 46 ARG cc_start: 0.6899 (mtp-110) cc_final: 0.6597 (mmt180) REVERT: B 175 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: B 214 ARG cc_start: 0.6412 (mmp-170) cc_final: 0.5698 (mmm-85) REVERT: B 338 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8215 (mm) REVERT: E 218 ARG cc_start: 0.6989 (mmp-170) cc_final: 0.6726 (mmp-170) outliers start: 42 outliers final: 20 residues processed: 176 average time/residue: 1.2318 time to fit residues: 232.1893 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 : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 88 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 254 CYS 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 219 ARG 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 84 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9131 Z= 0.222 Angle : 0.594 8.489 12375 Z= 0.303 Chirality : 0.043 0.140 1410 Planarity : 0.003 0.038 1559 Dihedral : 5.802 58.413 1311 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.62 % Allowed : 19.94 % Favored : 76.45 % 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: -0.20 (0.28), residues: 373 sheet: -0.01 (0.30), residues: 274 loop : -0.78 (0.29), residues: 477 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 B 199 TYR 0.009 0.001 TYR G 40 ARG 0.004 0.000 ARG R 176 *********************** 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 181 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 ARG cc_start: 0.5541 (mtt180) cc_final: 0.5331 (tpp80) REVERT: R 186 TYR cc_start: 0.7014 (m-80) cc_final: 0.6716 (m-80) REVERT: R 316 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7239 (tttm) REVERT: R 344 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7082 (mtm110) REVERT: R 376 GLN cc_start: 0.8185 (mp10) cc_final: 0.7823 (mm-40) REVERT: A 204 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6919 (mm-40) REVERT: A 298 GLU cc_start: 0.7856 (tp30) cc_final: 0.7437 (tm-30) REVERT: B 46 ARG cc_start: 0.6899 (mtp-110) cc_final: 0.6605 (mmt180) REVERT: B 175 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: B 214 ARG cc_start: 0.6382 (mmp-170) cc_final: 0.5680 (mmm-85) REVERT: B 338 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8225 (mm) REVERT: E 178 LEU cc_start: 0.8574 (tt) cc_final: 0.8332 (tt) REVERT: E 218 ARG cc_start: 0.6923 (mmp-170) cc_final: 0.6649 (mmp-170) REVERT: G 19 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8140 (mp) outliers start: 35 outliers final: 21 residues processed: 167 average time/residue: 1.2252 time to fit residues: 218.8791 Evaluate side-chains 168 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 88 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 A residue 50 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 254 CYS 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 219 ARG 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 84 THR Chi-restraints excluded: chain E residue 119 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 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 68 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 HIS R 379 GLN A 204 GLN A 241 ASN A 256 ASN B 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9131 Z= 0.215 Angle : 0.589 8.553 12375 Z= 0.300 Chirality : 0.043 0.165 1410 Planarity : 0.004 0.037 1559 Dihedral : 5.726 58.174 1311 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.24 % Allowed : 19.94 % Favored : 75.83 % 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: -0.60 (0.25), residues: 1124 helix: -0.12 (0.28), residues: 374 sheet: 0.09 (0.30), residues: 279 loop : -0.79 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.030 0.002 PHE R 92 TYR 0.009 0.001 TYR E 190 ARG 0.004 0.000 ARG B 314 *********************** 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 189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: R 186 TYR cc_start: 0.6933 (m-80) cc_final: 0.6726 (m-80) REVERT: R 316 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7234 (tttm) REVERT: R 344 ARG cc_start: 0.7468 (mtm110) cc_final: 0.6872 (mtm110) REVERT: R 376 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7840 (mm-40) REVERT: A 204 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6936 (mm-40) REVERT: A 298 GLU cc_start: 0.7852 (tp30) cc_final: 0.7447 (tm-30) REVERT: B 46 ARG cc_start: 0.6904 (mtp-110) cc_final: 0.6609 (mmt180) REVERT: B 175 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: B 198 LEU cc_start: 0.8061 (mt) cc_final: 0.7810 (mt) REVERT: B 214 ARG cc_start: 0.6382 (mmp-170) cc_final: 0.5773 (mmm-85) REVERT: B 338 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8222 (mm) REVERT: E 178 LEU cc_start: 0.8583 (tt) cc_final: 0.8346 (tt) REVERT: G 19 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8159 (mp) outliers start: 41 outliers final: 24 residues processed: 174 average time/residue: 1.2227 time to fit residues: 227.3522 Evaluate side-chains 171 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 219 ARG 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 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 119 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 19 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 241 ASN A 256 ASN A 306 GLN A 311 ASN B 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9131 Z= 0.212 Angle : 0.600 8.571 12375 Z= 0.308 Chirality : 0.043 0.155 1410 Planarity : 0.004 0.040 1559 Dihedral : 5.650 58.005 1311 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.41 % Allowed : 21.07 % Favored : 75.52 % 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: -0.55 (0.25), residues: 1124 helix: -0.10 (0.28), residues: 374 sheet: 0.07 (0.30), residues: 284 loop : -0.71 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 332 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 199 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.000 ARG R 375 *********************** 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 182 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: R 316 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7221 (tttm) REVERT: R 344 ARG cc_start: 0.7490 (mtm110) cc_final: 0.7037 (mtm110) REVERT: R 376 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: A 204 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6721 (mm-40) REVERT: A 298 GLU cc_start: 0.7849 (tp30) cc_final: 0.7448 (tm-30) REVERT: B 46 ARG cc_start: 0.6901 (mtp-110) cc_final: 0.6610 (mmt180) REVERT: B 175 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7669 (mt0) REVERT: B 198 LEU cc_start: 0.8056 (mt) cc_final: 0.7796 (mt) REVERT: B 214 ARG cc_start: 0.6376 (mmp-170) cc_final: 0.5774 (mmm-85) REVERT: E 178 LEU cc_start: 0.8601 (tt) cc_final: 0.8358 (tt) REVERT: E 218 ARG cc_start: 0.6933 (mmp-170) cc_final: 0.6567 (mmp-170) REVERT: G 19 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8171 (mp) outliers start: 33 outliers final: 22 residues processed: 169 average time/residue: 1.2090 time to fit residues: 218.6636 Evaluate side-chains 172 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 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 50 VAL Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 219 ARG 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 E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 119 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 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 B 75 GLN B 156 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9131 Z= 0.164 Angle : 0.588 10.888 12375 Z= 0.301 Chirality : 0.042 0.142 1410 Planarity : 0.003 0.036 1559 Dihedral : 5.411 54.273 1311 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.10 % Allowed : 21.69 % Favored : 75.21 % 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: -0.29 (0.26), residues: 1124 helix: 0.21 (0.28), residues: 368 sheet: 0.11 (0.30), residues: 287 loop : -0.57 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 332 HIS 0.003 0.001 HIS E 35 PHE 0.035 0.001 PHE R 92 TYR 0.014 0.001 TYR B 59 ARG 0.004 0.000 ARG R 375 ********************** 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 178 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 316 LYS cc_start: 0.7886 (mtmm) cc_final: 0.7216 (tttm) REVERT: R 344 ARG cc_start: 0.7514 (mtm110) cc_final: 0.7064 (mtm110) REVERT: R 376 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7781 (mt0) REVERT: A 209 LYS cc_start: 0.7893 (tptm) cc_final: 0.7269 (mmpt) REVERT: A 252 SER cc_start: 0.8742 (m) cc_final: 0.8172 (p) REVERT: A 298 GLU cc_start: 0.7854 (tp30) cc_final: 0.7451 (tm-30) REVERT: B 46 ARG cc_start: 0.6955 (mtp-110) cc_final: 0.6645 (mmt180) REVERT: B 198 LEU cc_start: 0.8052 (mt) cc_final: 0.7776 (mt) REVERT: B 214 ARG cc_start: 0.6339 (mmp-170) cc_final: 0.5783 (mmm-85) REVERT: E 178 LEU cc_start: 0.8571 (tt) cc_final: 0.8310 (tt) REVERT: G 19 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8185 (mp) REVERT: G 27 ARG cc_start: 0.8201 (mtt90) cc_final: 0.7671 (mtt180) outliers start: 30 outliers final: 22 residues processed: 170 average time/residue: 1.1963 time to fit residues: 219.1710 Evaluate side-chains 166 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 376 GLN Chi-restraints excluded: chain A residue 50 VAL 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 219 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 119 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 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 241 ASN A 256 ASN A 311 ASN B 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126606 restraints weight = 10512.803| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.17 r_work: 0.3295 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9131 Z= 0.183 Angle : 0.601 8.973 12375 Z= 0.308 Chirality : 0.042 0.149 1410 Planarity : 0.003 0.036 1559 Dihedral : 5.358 53.403 1311 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.89 % Allowed : 21.90 % Favored : 75.21 % 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: -0.20 (0.26), residues: 1124 helix: 0.32 (0.28), residues: 369 sheet: 0.14 (0.30), residues: 288 loop : -0.55 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 332 HIS 0.005 0.001 HIS R 85 PHE 0.010 0.001 PHE B 199 TYR 0.008 0.001 TYR E 190 ARG 0.005 0.000 ARG R 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4019.66 seconds wall clock time: 72 minutes 36.60 seconds (4356.60 seconds total)