Starting phenix.real_space_refine on Tue Apr 29 21:07:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iul_35725/04_2025/8iul_35725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iul_35725/04_2025/8iul_35725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iul_35725/04_2025/8iul_35725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iul_35725/04_2025/8iul_35725.map" model { file = "/net/cci-nas-00/data/ceres_data/8iul_35725/04_2025/8iul_35725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iul_35725/04_2025/8iul_35725_neut.cif" } resolution = 2.78 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= 0.004 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 64 5.16 5 C 5725 2.51 5 N 1551 2.21 5 O 1676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9016 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2314 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 5, 'TRANS': 287} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7WT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.58 Number of scatterers: 9016 At special positions: 0 Unit cell: (122.776, 92.288, 128.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1676 8.00 N 1551 7.00 C 5725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 978.8 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.7% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.625A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.594A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.576A pdb=" N PHE A 282 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.591A pdb=" N ALA A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 360 Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.564A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 removed outlier: 3.720A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.561A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.693A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.695A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 removed outlier: 3.951A pdb=" N ASP G 47 " --> pdb=" O ALA G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 47' Processing helix chain 'G' and resid 54 through 58 Processing helix chain 'R' and resid 30 through 59 removed outlier: 3.585A pdb=" N VAL R 39 " --> pdb=" O ILE R 35 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY R 40 " --> pdb=" O PHE R 36 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 93 removed outlier: 3.578A pdb=" N GLY R 85 " --> pdb=" O HIS R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 102 Processing helix chain 'R' and resid 106 through 139 removed outlier: 4.470A pdb=" N MET R 115 " --> pdb=" O PHE R 111 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER R 118 " --> pdb=" O CYS R 114 " (cutoff:3.500A) Proline residue: R 122 - end of helix removed outlier: 4.028A pdb=" N GLY R 126 " --> pdb=" O PRO R 122 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA R 130 " --> pdb=" O GLY R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 148 through 169 Processing helix chain 'R' and resid 170 through 174 removed outlier: 3.889A pdb=" N HIS R 174 " --> pdb=" O ILE R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 233 removed outlier: 3.944A pdb=" N ARG R 199 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 276 removed outlier: 3.587A pdb=" N CYS R 259 " --> pdb=" O MET R 255 " (cutoff:3.500A) Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 282 through 294 removed outlier: 3.545A pdb=" N THR R 286 " --> pdb=" O THR R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 305 removed outlier: 3.877A pdb=" N ILE R 305 " --> pdb=" O PRO R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 323 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.525A pdb=" N LEU A 34 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.533A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.665A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.838A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N THR B 184 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 180 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.841A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.856A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.666A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.688A pdb=" N ARG E 17 " --> pdb=" O MET E 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.072A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.566A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.911A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 178 through 179 removed outlier: 3.585A pdb=" N PHE R 187 " --> pdb=" O LYS R 178 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1272 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: 2.51 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1481 1.31 - 1.44: 2528 1.44 - 1.56: 5090 1.56 - 1.69: 4 1.69 - 1.81: 92 Bond restraints: 9195 Sorted by residual: bond pdb=" C02 7WT R 401 " pdb=" C06 7WT R 401 " ideal model delta sigma weight residual 1.525 1.339 0.186 2.00e-02 2.50e+03 8.66e+01 bond pdb=" C03 7WT R 401 " pdb=" C04 7WT R 401 " ideal model delta sigma weight residual 1.538 1.372 0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C02 7WT R 401 " pdb=" C03 7WT R 401 " ideal model delta sigma weight residual 1.527 1.662 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" CA VAL R 30 " pdb=" C VAL R 30 " ideal model delta sigma weight residual 1.523 1.441 0.082 1.27e-02 6.20e+03 4.20e+01 bond pdb=" N PHE R 31 " pdb=" CA PHE R 31 " ideal model delta sigma weight residual 1.459 1.399 0.060 1.23e-02 6.61e+03 2.41e+01 ... (remaining 9190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 12334 3.14 - 6.29: 78 6.29 - 9.43: 18 9.43 - 12.58: 3 12.58 - 15.72: 2 Bond angle restraints: 12435 Sorted by residual: angle pdb=" N ILE R 298 " pdb=" CA ILE R 298 " pdb=" C ILE R 298 " ideal model delta sigma weight residual 111.67 98.24 13.43 9.50e-01 1.11e+00 2.00e+02 angle pdb=" N ASN R 296 " pdb=" CA ASN R 296 " pdb=" C ASN R 296 " ideal model delta sigma weight residual 113.97 98.25 15.72 1.28e+00 6.10e-01 1.51e+02 angle pdb=" N PHE R 111 " pdb=" CA PHE R 111 " pdb=" C PHE R 111 " ideal model delta sigma weight residual 112.97 102.86 10.11 1.06e+00 8.90e-01 9.09e+01 angle pdb=" N TYR R 92 " pdb=" CA TYR R 92 " pdb=" C TYR R 92 " ideal model delta sigma weight residual 113.50 103.29 10.21 1.23e+00 6.61e-01 6.89e+01 angle pdb=" N LEU R 290 " pdb=" CA LEU R 290 " pdb=" C LEU R 290 " ideal model delta sigma weight residual 111.36 103.15 8.21 1.09e+00 8.42e-01 5.68e+01 ... (remaining 12430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.41: 5392 25.41 - 50.81: 77 50.81 - 76.22: 14 76.22 - 101.63: 2 101.63 - 127.03: 4 Dihedral angle restraints: 5489 sinusoidal: 2170 harmonic: 3319 Sorted by residual: dihedral pdb=" CD ARG A 209 " pdb=" NE ARG A 209 " pdb=" CZ ARG A 209 " pdb=" NH1 ARG A 209 " ideal model delta sinusoidal sigma weight residual 0.00 86.80 -86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" C LEU R 120 " pdb=" N LEU R 120 " pdb=" CA LEU R 120 " pdb=" CB LEU R 120 " ideal model delta harmonic sigma weight residual -122.60 -133.86 11.26 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CA LEU R 120 " pdb=" CB LEU R 120 " ideal model delta harmonic sigma weight residual 122.80 133.92 -11.12 0 2.50e+00 1.60e-01 1.98e+01 ... (remaining 5486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1335 0.108 - 0.216: 56 0.216 - 0.324: 11 0.324 - 0.432: 6 0.432 - 0.540: 3 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CA LEU R 120 " pdb=" N LEU R 120 " pdb=" C LEU R 120 " pdb=" CB LEU R 120 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CA PRO R 122 " pdb=" N PRO R 122 " pdb=" C PRO R 122 " pdb=" CB PRO R 122 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CA CYS R 114 " pdb=" N CYS R 114 " pdb=" C CYS R 114 " pdb=" CB CYS R 114 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 1408 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 209 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 209 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 209 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 209 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 121 " 0.104 5.00e-02 4.00e+02 1.51e-01 3.67e+01 pdb=" N PRO R 122 " -0.261 5.00e-02 4.00e+02 pdb=" CA PRO R 122 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO R 122 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 300 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.70e+01 pdb=" N PRO R 301 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " 0.059 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 189 2.67 - 3.23: 8854 3.23 - 3.79: 13642 3.79 - 4.34: 18934 4.34 - 4.90: 31663 Nonbonded interactions: 73282 Sorted by model distance: nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.116 3.040 nonbonded pdb=" OD1 ASP A 226 " pdb=" OG SER A 228 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASN A 216 " pdb=" NZ LYS B 62 " model vdw 2.146 3.120 nonbonded pdb=" ND2 ASN E 169 " pdb=" OD1 ASN E 171 " model vdw 2.190 3.120 nonbonded pdb=" O ALA A 318 " pdb=" OG SER A 319 " model vdw 2.238 3.040 ... (remaining 73277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.760 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: 0.000 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.006 0.186 9196 Z= 0.370 Angle : 0.659 15.725 12437 Z= 0.433 Chirality : 0.058 0.540 1411 Planarity : 0.014 0.492 1572 Dihedral : 9.740 127.032 3342 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.61 % Allowed : 4.48 % Favored : 94.91 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1129 helix: 0.07 (0.25), residues: 418 sheet: -0.53 (0.30), residues: 257 loop : -1.51 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 302 HIS 0.004 0.000 HIS R 81 PHE 0.011 0.001 PHE R 117 TYR 0.005 0.000 TYR R 92 ARG 0.002 0.000 ARG R 291 Details of bonding type rmsd hydrogen bonds : bond 0.18501 ( 453) hydrogen bonds : angle 6.83273 ( 1272) SS BOND : bond 0.00011 ( 1) SS BOND : angle 0.78256 ( 2) covalent geometry : bond 0.00571 ( 9195) covalent geometry : angle 0.65893 (12435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 317 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7006 (m-40) cc_final: 0.6643 (m-40) REVERT: A 227 SER cc_start: 0.7758 (p) cc_final: 0.7519 (p) REVERT: A 298 ASP cc_start: 0.7698 (t0) cc_final: 0.7469 (t0) REVERT: A 310 LYS cc_start: 0.7746 (tptt) cc_final: 0.7331 (tptt) REVERT: A 314 ASP cc_start: 0.6837 (m-30) cc_final: 0.6590 (m-30) REVERT: B 42 ILE cc_start: 0.7703 (tt) cc_final: 0.7459 (pt) REVERT: B 252 ASP cc_start: 0.6133 (t0) cc_final: 0.4766 (t0) REVERT: B 306 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6773 (mmmm) REVERT: E 230 MET cc_start: 0.8471 (ttp) cc_final: 0.8259 (ttt) outliers start: 6 outliers final: 2 residues processed: 321 average time/residue: 1.1459 time to fit residues: 394.0600 Evaluate side-chains 173 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain R residue 294 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN B 161 GLN B 225 GLN B 273 ASN B 298 ASN E 12 GLN E 34 HIS ** E 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN R 297 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.173457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137991 restraints weight = 10272.134| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.23 r_work: 0.3587 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9196 Z= 0.124 Angle : 0.552 7.070 12437 Z= 0.287 Chirality : 0.041 0.144 1411 Planarity : 0.005 0.073 1572 Dihedral : 6.245 101.719 1277 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.26 % Allowed : 14.34 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1129 helix: 1.68 (0.26), residues: 409 sheet: 0.12 (0.30), residues: 269 loop : -0.82 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 174 HIS 0.005 0.001 HIS A 324 PHE 0.021 0.002 PHE R 207 TYR 0.014 0.002 TYR R 92 ARG 0.007 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 453) hydrogen bonds : angle 4.56687 ( 1272) SS BOND : bond 0.00344 ( 1) SS BOND : angle 0.91452 ( 2) covalent geometry : bond 0.00272 ( 9195) covalent geometry : angle 0.55164 (12435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7192 (mt) cc_final: 0.6923 (mp) REVERT: A 182 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7639 (p) REVERT: A 281 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 310 LYS cc_start: 0.7889 (tptt) cc_final: 0.7617 (tppt) REVERT: A 314 ASP cc_start: 0.7733 (m-30) cc_final: 0.7291 (m-30) REVERT: B 42 ILE cc_start: 0.7510 (tt) cc_final: 0.7280 (pt) REVERT: B 64 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: B 233 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: E 89 ASP cc_start: 0.6690 (m-30) cc_final: 0.6440 (m-30) REVERT: E 183 GLN cc_start: 0.7356 (mm-40) cc_final: 0.7154 (mm-40) REVERT: E 219 LEU cc_start: 0.8423 (tt) cc_final: 0.8180 (tm) REVERT: E 245 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7354 (mp) REVERT: R 53 LYS cc_start: 0.7348 (ttpt) cc_final: 0.6925 (tptp) REVERT: R 148 THR cc_start: 0.7714 (m) cc_final: 0.7456 (p) outliers start: 32 outliers final: 12 residues processed: 208 average time/residue: 1.0358 time to fit residues: 231.7644 Evaluate side-chains 169 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 271 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN B 273 ASN E 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124855 restraints weight = 10533.075| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.28 r_work: 0.3422 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9196 Z= 0.129 Angle : 0.526 6.630 12437 Z= 0.275 Chirality : 0.041 0.151 1411 Planarity : 0.004 0.075 1572 Dihedral : 6.035 112.484 1276 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.95 % Allowed : 17.09 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1129 helix: 2.13 (0.26), residues: 410 sheet: 0.22 (0.30), residues: 279 loop : -0.54 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS A 197 PHE 0.025 0.002 PHE R 101 TYR 0.012 0.002 TYR E 190 ARG 0.008 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 453) hydrogen bonds : angle 4.27468 ( 1272) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.51370 ( 2) covalent geometry : bond 0.00293 ( 9195) covalent geometry : angle 0.52638 (12435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.7883 (mt) cc_final: 0.7627 (mp) REVERT: A 182 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7755 (p) REVERT: A 188 LYS cc_start: 0.8485 (tttm) cc_final: 0.7850 (tptm) REVERT: A 281 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7431 (mt-10) REVERT: A 314 ASP cc_start: 0.7916 (m-30) cc_final: 0.7593 (m-30) REVERT: B 27 ARG cc_start: 0.5559 (ttm170) cc_final: 0.5321 (mtt180) REVERT: E 160 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7276 (mtm110) REVERT: E 183 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7105 (mm-40) REVERT: E 219 LEU cc_start: 0.8572 (tt) cc_final: 0.8272 (tm) REVERT: E 223 ASP cc_start: 0.8016 (m-30) cc_final: 0.7807 (m-30) REVERT: E 245 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7113 (mp) REVERT: R 53 LYS cc_start: 0.7560 (ttpt) cc_final: 0.7020 (tptp) REVERT: R 148 THR cc_start: 0.7625 (m) cc_final: 0.7307 (p) outliers start: 29 outliers final: 15 residues processed: 179 average time/residue: 1.1129 time to fit residues: 213.4752 Evaluate side-chains 160 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain R residue 115 MET Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 259 ASN A 329 HIS B 181 GLN B 225 GLN B 235 ASN B 264 GLN B 273 ASN B 298 ASN E 171 ASN G 58 ASN R 56 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.154250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115569 restraints weight = 10513.667| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.26 r_work: 0.3287 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9196 Z= 0.179 Angle : 0.585 6.955 12437 Z= 0.309 Chirality : 0.043 0.165 1411 Planarity : 0.004 0.068 1572 Dihedral : 6.231 118.466 1274 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.56 % Allowed : 17.19 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.25), residues: 1129 helix: 2.04 (0.26), residues: 412 sheet: 0.20 (0.31), residues: 278 loop : -0.42 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 35 HIS 0.009 0.002 HIS A 197 PHE 0.024 0.002 PHE R 207 TYR 0.017 0.002 TYR E 190 ARG 0.010 0.001 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 453) hydrogen bonds : angle 4.42207 ( 1272) SS BOND : bond 0.00117 ( 1) SS BOND : angle 0.74191 ( 2) covalent geometry : bond 0.00417 ( 9195) covalent geometry : angle 0.58470 (12435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 182 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 235 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7513 (mt-10) REVERT: A 247 ARG cc_start: 0.8172 (ptm160) cc_final: 0.7697 (ttt180) REVERT: A 276 GLU cc_start: 0.7691 (tp30) cc_final: 0.7452 (tp30) REVERT: A 310 LYS cc_start: 0.8373 (tppt) cc_final: 0.8079 (tppt) REVERT: A 314 ASP cc_start: 0.8056 (m-30) cc_final: 0.7773 (m-30) REVERT: B 27 ARG cc_start: 0.5671 (ttm170) cc_final: 0.5391 (mtt180) REVERT: E 18 LYS cc_start: 0.7847 (tptt) cc_final: 0.7468 (tptp) REVERT: E 58 TYR cc_start: 0.8242 (m-10) cc_final: 0.8025 (m-10) REVERT: E 75 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7623 (mtmm) REVERT: E 160 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7334 (mtm110) REVERT: E 183 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7258 (mm-40) REVERT: R 52 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.5926 (mtm) REVERT: R 53 LYS cc_start: 0.7831 (ttpt) cc_final: 0.7218 (tptp) REVERT: R 148 THR cc_start: 0.7856 (m) cc_final: 0.7569 (p) outliers start: 35 outliers final: 16 residues processed: 173 average time/residue: 1.2452 time to fit residues: 229.3815 Evaluate side-chains 156 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 0.0000 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 48 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 181 GLN B 235 ASN B 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120249 restraints weight = 10443.670| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.24 r_work: 0.3356 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9196 Z= 0.106 Angle : 0.506 8.101 12437 Z= 0.266 Chirality : 0.040 0.137 1411 Planarity : 0.004 0.059 1572 Dihedral : 5.938 112.830 1274 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.95 % Allowed : 19.02 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1129 helix: 2.28 (0.26), residues: 415 sheet: 0.43 (0.31), residues: 264 loop : -0.30 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.005 0.001 HIS B 188 PHE 0.024 0.001 PHE R 207 TYR 0.011 0.001 TYR R 177 ARG 0.010 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 453) hydrogen bonds : angle 4.12124 ( 1272) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.46287 ( 2) covalent geometry : bond 0.00234 ( 9195) covalent geometry : angle 0.50649 (12435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.046 Fit side-chains REVERT: A 182 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7613 (p) REVERT: A 188 LYS cc_start: 0.8850 (mttt) cc_final: 0.8563 (mttm) REVERT: A 276 GLU cc_start: 0.7646 (tp30) cc_final: 0.7409 (tp30) REVERT: A 310 LYS cc_start: 0.8247 (tppt) cc_final: 0.7959 (tppt) REVERT: A 314 ASP cc_start: 0.7952 (m-30) cc_final: 0.7609 (m-30) REVERT: E 18 LYS cc_start: 0.7779 (tptt) cc_final: 0.7452 (tptp) REVERT: E 58 TYR cc_start: 0.8028 (m-10) cc_final: 0.7742 (m-10) REVERT: E 75 LYS cc_start: 0.7788 (mtmm) cc_final: 0.7521 (mtmm) REVERT: E 160 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7371 (mtm110) REVERT: E 183 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7190 (mm-40) REVERT: E 219 LEU cc_start: 0.8714 (tt) cc_final: 0.8424 (tm) REVERT: G 20 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6830 (mtt) REVERT: R 53 LYS cc_start: 0.7662 (ttpt) cc_final: 0.7109 (tptp) REVERT: R 139 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7806 (mtpp) REVERT: R 148 THR cc_start: 0.7735 (m) cc_final: 0.7473 (p) outliers start: 29 outliers final: 16 residues processed: 160 average time/residue: 1.2376 time to fit residues: 211.4729 Evaluate side-chains 147 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118628 restraints weight = 10539.999| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.22 r_work: 0.3325 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9196 Z= 0.129 Angle : 0.527 6.580 12437 Z= 0.279 Chirality : 0.041 0.173 1411 Planarity : 0.004 0.054 1572 Dihedral : 5.935 112.017 1274 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.36 % Allowed : 18.51 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1129 helix: 2.31 (0.26), residues: 416 sheet: 0.38 (0.30), residues: 272 loop : -0.26 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 PHE 0.024 0.001 PHE R 207 TYR 0.013 0.001 TYR E 190 ARG 0.012 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 453) hydrogen bonds : angle 4.17580 ( 1272) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.55225 ( 2) covalent geometry : bond 0.00293 ( 9195) covalent geometry : angle 0.52725 (12435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.034 Fit side-chains REVERT: A 182 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7628 (p) REVERT: A 188 LYS cc_start: 0.8809 (mttt) cc_final: 0.8570 (mttm) REVERT: A 235 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7420 (mt-10) REVERT: A 247 ARG cc_start: 0.8131 (ptm160) cc_final: 0.7629 (ttt180) REVERT: A 276 GLU cc_start: 0.7545 (tp30) cc_final: 0.7306 (tp30) REVERT: A 310 LYS cc_start: 0.8291 (tppt) cc_final: 0.8016 (tppt) REVERT: A 314 ASP cc_start: 0.8050 (m-30) cc_final: 0.7709 (m-30) REVERT: E 58 TYR cc_start: 0.8080 (m-10) cc_final: 0.7752 (m-10) REVERT: E 75 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7508 (mtmm) REVERT: E 160 ARG cc_start: 0.8120 (mmm160) cc_final: 0.7368 (mtm110) REVERT: E 183 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7240 (mm-40) REVERT: E 234 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: R 53 LYS cc_start: 0.7742 (ttpt) cc_final: 0.7170 (tptp) REVERT: R 139 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7843 (mtpp) REVERT: R 148 THR cc_start: 0.7763 (m) cc_final: 0.7529 (p) outliers start: 33 outliers final: 19 residues processed: 169 average time/residue: 1.2723 time to fit residues: 229.1357 Evaluate side-chains 156 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 264 GLN B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.156202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.118348 restraints weight = 10610.831| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.23 r_work: 0.3323 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.128 Angle : 0.534 8.551 12437 Z= 0.279 Chirality : 0.041 0.174 1411 Planarity : 0.004 0.051 1572 Dihedral : 5.879 109.035 1274 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.26 % Allowed : 19.74 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1129 helix: 2.33 (0.26), residues: 415 sheet: 0.40 (0.31), residues: 272 loop : -0.25 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 PHE 0.025 0.001 PHE R 207 TYR 0.014 0.001 TYR R 177 ARG 0.006 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 453) hydrogen bonds : angle 4.16204 ( 1272) SS BOND : bond 0.00136 ( 1) SS BOND : angle 0.55548 ( 2) covalent geometry : bond 0.00290 ( 9195) covalent geometry : angle 0.53386 (12435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.980 Fit side-chains REVERT: A 182 SER cc_start: 0.8032 (OUTLIER) cc_final: 0.7572 (p) REVERT: A 188 LYS cc_start: 0.8798 (mttt) cc_final: 0.8544 (mttm) REVERT: A 235 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 247 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7636 (ttt180) REVERT: A 276 GLU cc_start: 0.7505 (tp30) cc_final: 0.7260 (tp30) REVERT: B 222 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8216 (ppp) REVERT: E 58 TYR cc_start: 0.8091 (m-10) cc_final: 0.7775 (m-10) REVERT: E 75 LYS cc_start: 0.7789 (mtmm) cc_final: 0.7519 (mtmm) REVERT: E 160 ARG cc_start: 0.8148 (mmm160) cc_final: 0.7378 (mtm110) REVERT: E 183 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7146 (mm-40) REVERT: E 219 LEU cc_start: 0.8691 (tt) cc_final: 0.8405 (tm) REVERT: E 234 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: G 20 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6804 (mtt) REVERT: R 53 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7149 (tptp) REVERT: R 148 THR cc_start: 0.7718 (m) cc_final: 0.7511 (p) outliers start: 32 outliers final: 22 residues processed: 156 average time/residue: 1.2582 time to fit residues: 209.2161 Evaluate side-chains 157 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 280 LEU Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN B 264 GLN B 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118416 restraints weight = 10661.732| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.26 r_work: 0.3338 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9196 Z= 0.122 Angle : 0.540 8.472 12437 Z= 0.279 Chirality : 0.041 0.175 1411 Planarity : 0.004 0.049 1572 Dihedral : 5.837 105.209 1274 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.75 % Allowed : 20.55 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1129 helix: 2.40 (0.26), residues: 415 sheet: 0.48 (0.31), residues: 272 loop : -0.26 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.005 0.001 HIS B 188 PHE 0.026 0.001 PHE R 207 TYR 0.011 0.001 TYR E 190 ARG 0.012 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 453) hydrogen bonds : angle 4.13717 ( 1272) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.52329 ( 2) covalent geometry : bond 0.00276 ( 9195) covalent geometry : angle 0.53975 (12435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.044 Fit side-chains REVERT: A 21 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7340 (mmtp) REVERT: A 188 LYS cc_start: 0.8786 (mttt) cc_final: 0.8533 (mttm) REVERT: A 247 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7638 (ttt180) REVERT: A 276 GLU cc_start: 0.7442 (tp30) cc_final: 0.7176 (tp30) REVERT: E 58 TYR cc_start: 0.8055 (m-10) cc_final: 0.7747 (m-10) REVERT: E 75 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7503 (mtmm) REVERT: E 160 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7314 (mtm110) REVERT: E 234 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: G 20 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6926 (mtt) REVERT: R 53 LYS cc_start: 0.7722 (ttpt) cc_final: 0.7157 (tptp) REVERT: R 100 ARG cc_start: 0.6066 (tmm-80) cc_final: 0.5734 (ttt90) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 1.3104 time to fit residues: 206.1637 Evaluate side-chains 152 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 225 GLN B 264 GLN B 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118361 restraints weight = 10400.170| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.23 r_work: 0.3340 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9196 Z= 0.119 Angle : 0.536 8.739 12437 Z= 0.277 Chirality : 0.041 0.175 1411 Planarity : 0.004 0.048 1572 Dihedral : 5.792 101.530 1274 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.54 % Allowed : 20.75 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1129 helix: 2.40 (0.26), residues: 416 sheet: 0.48 (0.31), residues: 273 loop : -0.23 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.005 0.001 HIS B 188 PHE 0.026 0.001 PHE R 207 TYR 0.013 0.001 TYR R 177 ARG 0.006 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 453) hydrogen bonds : angle 4.16632 ( 1272) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.52416 ( 2) covalent geometry : bond 0.00270 ( 9195) covalent geometry : angle 0.53608 (12435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.930 Fit side-chains REVERT: A 188 LYS cc_start: 0.8765 (mttt) cc_final: 0.8514 (mttm) REVERT: A 247 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7636 (ttt180) REVERT: A 276 GLU cc_start: 0.7441 (tp30) cc_final: 0.7148 (tp30) REVERT: B 139 ARG cc_start: 0.8305 (ptm160) cc_final: 0.7785 (mtm110) REVERT: B 143 GLU cc_start: 0.8294 (tt0) cc_final: 0.7896 (tt0) REVERT: E 58 TYR cc_start: 0.8038 (m-10) cc_final: 0.7734 (m-10) REVERT: E 75 LYS cc_start: 0.7803 (mtmm) cc_final: 0.7517 (mtmm) REVERT: E 160 ARG cc_start: 0.8106 (mmm160) cc_final: 0.7295 (mtm110) REVERT: E 219 LEU cc_start: 0.8682 (tt) cc_final: 0.8403 (tm) REVERT: E 220 GLU cc_start: 0.7623 (mp0) cc_final: 0.7403 (mp0) REVERT: E 234 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7151 (mt-10) REVERT: G 20 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: R 53 LYS cc_start: 0.7709 (ttpt) cc_final: 0.7142 (tptp) REVERT: R 100 ARG cc_start: 0.6087 (tmm-80) cc_final: 0.5755 (ttt90) outliers start: 25 outliers final: 19 residues processed: 147 average time/residue: 1.2997 time to fit residues: 203.2535 Evaluate side-chains 151 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 197 HIS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN B 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.155854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117522 restraints weight = 10540.080| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.25 r_work: 0.3331 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9196 Z= 0.128 Angle : 0.549 8.538 12437 Z= 0.283 Chirality : 0.041 0.176 1411 Planarity : 0.004 0.047 1572 Dihedral : 5.836 100.316 1274 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.34 % Allowed : 21.46 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.26), residues: 1129 helix: 2.38 (0.26), residues: 413 sheet: 0.54 (0.31), residues: 272 loop : -0.23 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 PHE 0.026 0.001 PHE R 207 TYR 0.013 0.001 TYR R 177 ARG 0.006 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 453) hydrogen bonds : angle 4.22002 ( 1272) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.55077 ( 2) covalent geometry : bond 0.00292 ( 9195) covalent geometry : angle 0.54879 (12435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8787 (mttt) cc_final: 0.8525 (mttm) REVERT: A 235 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 247 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7631 (ttt180) REVERT: A 276 GLU cc_start: 0.7394 (tp30) cc_final: 0.7115 (tp30) REVERT: B 139 ARG cc_start: 0.8330 (ptm160) cc_final: 0.7761 (mtm110) REVERT: B 143 GLU cc_start: 0.8395 (tt0) cc_final: 0.8017 (tt0) REVERT: B 222 MET cc_start: 0.8386 (ptm) cc_final: 0.8172 (ppp) REVERT: E 58 TYR cc_start: 0.8047 (m-10) cc_final: 0.7740 (m-10) REVERT: E 160 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7305 (mtm110) REVERT: E 219 LEU cc_start: 0.8629 (tt) cc_final: 0.8362 (tm) REVERT: E 220 GLU cc_start: 0.7688 (mp0) cc_final: 0.7451 (mp0) REVERT: E 234 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: G 20 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6971 (mtt) REVERT: R 53 LYS cc_start: 0.7723 (ttpt) cc_final: 0.7140 (tptp) REVERT: R 100 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5744 (ttt90) outliers start: 23 outliers final: 18 residues processed: 148 average time/residue: 1.2780 time to fit residues: 201.1790 Evaluate side-chains 150 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 100 ARG Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 259 CYS Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 74 optimal weight: 0.0370 chunk 69 optimal weight: 0.0030 chunk 96 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.4670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 225 GLN R 151 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122044 restraints weight = 10472.022| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.23 r_work: 0.3384 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9196 Z= 0.102 Angle : 0.518 8.274 12437 Z= 0.267 Chirality : 0.040 0.174 1411 Planarity : 0.004 0.046 1572 Dihedral : 5.725 93.123 1274 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.93 % Allowed : 21.77 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.26), residues: 1129 helix: 2.48 (0.26), residues: 416 sheet: 0.59 (0.31), residues: 274 loop : -0.09 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 211 HIS 0.004 0.001 HIS B 188 PHE 0.025 0.001 PHE R 207 TYR 0.017 0.001 TYR R 177 ARG 0.006 0.000 ARG B 139 Details of bonding type rmsd hydrogen bonds : bond 0.03051 ( 453) hydrogen bonds : angle 4.07654 ( 1272) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.40536 ( 2) covalent geometry : bond 0.00224 ( 9195) covalent geometry : angle 0.51792 (12435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8217.33 seconds wall clock time: 141 minutes 18.57 seconds (8478.57 seconds total)