Starting phenix.real_space_refine on Thu Mar 13 13:10:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iul_35725/03_2025/8iul_35725_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iul_35725/03_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_35725/03_2025/8iul_35725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iul_35725/03_2025/8iul_35725.map" model { file = "/net/cci-nas-00/data/ceres_data/8iul_35725/03_2025/8iul_35725_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iul_35725/03_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.57, per 1000 atoms: 0.62 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.18 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: 2.45 Time building geometry restraints manager: 2.53 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: 1.060 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- 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 9195 Z= 0.378 Angle : 0.659 15.725 12435 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 *********************** 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 : 1.002 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: 1.0976 time to fit residues: 377.5850 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 : 1.045 ------------------------------------------------------------------------------- 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 9195 Z= 0.179 Angle : 0.552 7.070 12435 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 *********************** 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 : 0.951 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: 1.0872 time to fit residues: 244.3489 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 : 0.843 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.9982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.161720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123812 restraints weight = 10513.363| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.29 r_work: 0.3409 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9195 Z= 0.185 Angle : 0.524 6.672 12435 Z= 0.275 Chirality : 0.041 0.150 1411 Planarity : 0.004 0.075 1572 Dihedral : 6.082 115.857 1276 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 1.01 (0.25), residues: 1129 helix: 2.17 (0.26), residues: 410 sheet: 0.29 (0.30), residues: 277 loop : -0.48 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 174 HIS 0.006 0.001 HIS A 324 PHE 0.026 0.002 PHE R 101 TYR 0.013 0.002 TYR E 190 ARG 0.008 0.000 ARG B 139 *********************** 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 : 1.010 Fit side-chains revert: symmetry clash REVERT: A 188 LYS cc_start: 0.8476 (tttm) cc_final: 0.7775 (tptm) REVERT: A 281 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7451 (mt-10) REVERT: A 314 ASP cc_start: 0.7895 (m-30) cc_final: 0.7571 (m-30) REVERT: E 75 LYS cc_start: 0.7836 (mtmm) cc_final: 0.7510 (mtmm) REVERT: E 160 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7349 (mtm110) REVERT: E 183 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7124 (mm-40) REVERT: E 219 LEU cc_start: 0.8648 (tt) cc_final: 0.8335 (tm) REVERT: E 245 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7046 (mp) REVERT: G 20 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6628 (mtt) REVERT: R 53 LYS cc_start: 0.7580 (ttpt) cc_final: 0.7054 (tptp) REVERT: R 148 THR cc_start: 0.7653 (m) cc_final: 0.7316 (p) outliers start: 29 outliers final: 14 residues processed: 180 average time/residue: 1.2165 time to fit residues: 234.7909 Evaluate side-chains 158 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 43 ASN 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 G residue 20 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: 5.9990 chunk 26 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.0770 chunk 101 optimal weight: 5.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN B 225 GLN B 235 ASN B 264 GLN B 273 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124589 restraints weight = 10433.046| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.29 r_work: 0.3413 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9195 Z= 0.154 Angle : 0.495 6.133 12435 Z= 0.259 Chirality : 0.040 0.139 1411 Planarity : 0.004 0.066 1572 Dihedral : 5.944 110.544 1274 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.75 % Allowed : 18.51 % Favored : 78.74 % 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: 1.24 (0.26), residues: 1129 helix: 2.31 (0.26), residues: 416 sheet: 0.40 (0.31), residues: 275 loop : -0.31 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 344 HIS 0.005 0.001 HIS B 188 PHE 0.023 0.001 PHE R 207 TYR 0.010 0.001 TYR R 177 ARG 0.009 0.000 ARG B 139 *********************** 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 183 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ARG cc_start: 0.8155 (ptp-110) cc_final: 0.7772 (ptp-170) REVERT: A 276 GLU cc_start: 0.7588 (tp30) cc_final: 0.7291 (tp30) REVERT: A 281 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 310 LYS cc_start: 0.8140 (tppt) cc_final: 0.7715 (tppt) REVERT: A 314 ASP cc_start: 0.7899 (m-30) cc_final: 0.7472 (m-30) REVERT: E 160 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7357 (mtm110) REVERT: E 183 GLN cc_start: 0.7347 (mm-40) cc_final: 0.7091 (mm-40) REVERT: E 245 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7011 (mp) REVERT: G 20 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6736 (mtt) REVERT: R 53 LYS cc_start: 0.7498 (ttpt) cc_final: 0.6971 (tptp) REVERT: R 139 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7843 (mtpp) outliers start: 27 outliers final: 19 residues processed: 169 average time/residue: 1.1475 time to fit residues: 207.6437 Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN 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 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 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 G residue 20 MET Chi-restraints excluded: chain R residue 252 LEU 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: 0.6980 chunk 45 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN B 235 ASN B 264 GLN B 273 ASN R 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.161456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123719 restraints weight = 10444.734| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.29 r_work: 0.3407 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9195 Z= 0.150 Angle : 0.488 8.336 12435 Z= 0.256 Chirality : 0.040 0.135 1411 Planarity : 0.004 0.060 1572 Dihedral : 5.774 109.641 1274 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.15 % Allowed : 18.31 % Favored : 78.54 % 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: 1.36 (0.26), residues: 1129 helix: 2.38 (0.26), residues: 416 sheet: 0.42 (0.31), residues: 276 loop : -0.16 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.004 0.001 HIS A 197 PHE 0.025 0.001 PHE R 207 TYR 0.009 0.001 TYR E 190 ARG 0.010 0.000 ARG B 139 *********************** 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 178 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7701 (p) REVERT: A 197 HIS cc_start: 0.8504 (m-70) cc_final: 0.7776 (t-90) REVERT: A 250 ARG cc_start: 0.8187 (ptp-110) cc_final: 0.7905 (ptp-170) REVERT: A 276 GLU cc_start: 0.7560 (tp30) cc_final: 0.7314 (tp30) REVERT: A 281 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 310 LYS cc_start: 0.8108 (tppt) cc_final: 0.7716 (tppt) REVERT: A 314 ASP cc_start: 0.7901 (m-30) cc_final: 0.7479 (m-30) REVERT: E 160 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7387 (mtm110) REVERT: E 183 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7073 (mm-40) REVERT: E 219 LEU cc_start: 0.8658 (tt) cc_final: 0.8350 (tm) REVERT: G 20 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6664 (mtt) REVERT: R 53 LYS cc_start: 0.7489 (ttpt) cc_final: 0.6954 (tptp) REVERT: R 139 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7847 (mtpp) REVERT: R 148 THR cc_start: 0.7557 (m) cc_final: 0.7282 (p) outliers start: 31 outliers final: 17 residues processed: 166 average time/residue: 1.1538 time to fit residues: 205.7420 Evaluate side-chains 151 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 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 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 116 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain R residue 252 LEU 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: 10.0000 chunk 28 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 0.0370 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 overall best weight: 1.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN B 235 ASN B 264 GLN B 273 ASN G 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.156577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.118845 restraints weight = 10564.769| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.36 r_work: 0.3319 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9195 Z= 0.226 Angle : 0.548 6.892 12435 Z= 0.289 Chirality : 0.042 0.144 1411 Planarity : 0.004 0.058 1572 Dihedral : 5.909 110.657 1274 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.05 % Allowed : 19.33 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1129 helix: 2.34 (0.26), residues: 413 sheet: 0.38 (0.31), residues: 276 loop : -0.20 (0.30), residues: 440 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 0.002 PHE R 207 TYR 0.014 0.001 TYR E 190 ARG 0.012 0.001 ARG B 139 *********************** 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 178 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 182 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7603 (p) REVERT: A 188 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8303 (mmmt) REVERT: A 235 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 247 ARG cc_start: 0.8128 (ptm160) cc_final: 0.7622 (ttt180) REVERT: A 276 GLU cc_start: 0.7629 (tp30) cc_final: 0.7389 (tp30) REVERT: A 310 LYS cc_start: 0.8265 (tppt) cc_final: 0.7956 (tppt) REVERT: A 314 ASP cc_start: 0.8010 (m-30) cc_final: 0.7622 (m-30) REVERT: E 58 TYR cc_start: 0.8149 (m-10) cc_final: 0.7859 (m-10) REVERT: E 75 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7658 (mtmm) REVERT: E 160 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7405 (mtm110) REVERT: E 183 GLN cc_start: 0.7376 (mm-40) cc_final: 0.7081 (mm-40) REVERT: E 219 LEU cc_start: 0.8667 (tt) cc_final: 0.8383 (tm) REVERT: R 52 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.5838 (mtm) REVERT: R 53 LYS cc_start: 0.7740 (ttpt) cc_final: 0.7131 (tptp) REVERT: R 148 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.7399 (p) outliers start: 30 outliers final: 17 residues processed: 164 average time/residue: 1.2451 time to fit residues: 217.7979 Evaluate side-chains 157 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 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 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 116 LEU Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 148 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.155170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117273 restraints weight = 10630.702| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.23 r_work: 0.3311 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9195 Z= 0.226 Angle : 0.551 6.643 12435 Z= 0.291 Chirality : 0.042 0.184 1411 Planarity : 0.004 0.054 1572 Dihedral : 5.992 110.529 1274 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.26 % Allowed : 19.33 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1129 helix: 2.27 (0.26), residues: 413 sheet: 0.36 (0.31), residues: 274 loop : -0.18 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.006 0.001 HIS A 324 PHE 0.027 0.002 PHE R 207 TYR 0.013 0.001 TYR E 190 ARG 0.010 0.000 ARG B 139 *********************** 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 176 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.049 Fit side-chains REVERT: A 182 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7588 (p) REVERT: A 188 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8292 (mmmt) REVERT: A 197 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.7984 (t-90) REVERT: A 235 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 247 ARG cc_start: 0.8163 (ptm160) cc_final: 0.7665 (ttt180) REVERT: A 276 GLU cc_start: 0.7527 (tp30) cc_final: 0.7267 (tp30) REVERT: E 58 TYR cc_start: 0.8164 (m-10) cc_final: 0.7872 (m-10) REVERT: E 75 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7655 (mtmm) REVERT: E 160 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7374 (mtm110) REVERT: E 183 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7152 (mm-40) REVERT: R 52 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.5952 (mtm) REVERT: R 53 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7151 (tptp) outliers start: 32 outliers final: 20 residues processed: 164 average time/residue: 1.2405 time to fit residues: 216.7577 Evaluate side-chains 157 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 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 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 233 LEU Chi-restraints excluded: chain R residue 52 MET 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: 3.9990 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.156145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118224 restraints weight = 10631.966| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.25 r_work: 0.3340 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9195 Z= 0.180 Angle : 0.538 8.720 12435 Z= 0.280 Chirality : 0.041 0.176 1411 Planarity : 0.004 0.056 1572 Dihedral : 5.854 107.589 1274 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.64 % Allowed : 20.75 % Favored : 76.60 % 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: 1.34 (0.26), residues: 1129 helix: 2.35 (0.26), residues: 416 sheet: 0.40 (0.31), residues: 274 loop : -0.16 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.005 0.001 HIS B 188 PHE 0.025 0.001 PHE R 207 TYR 0.010 0.001 TYR E 190 ARG 0.014 0.000 ARG B 139 *********************** 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 164 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.095 Fit side-chains REVERT: A 182 SER cc_start: 0.8005 (OUTLIER) cc_final: 0.7529 (p) REVERT: A 188 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8185 (mmmt) REVERT: A 197 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.7989 (t-90) REVERT: A 235 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 247 ARG cc_start: 0.8128 (ptm160) cc_final: 0.7612 (ttt180) REVERT: A 276 GLU cc_start: 0.7431 (tp30) cc_final: 0.7165 (tp30) REVERT: E 58 TYR cc_start: 0.8080 (m-10) cc_final: 0.7755 (m-10) REVERT: E 75 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7623 (mtmm) REVERT: E 160 ARG cc_start: 0.8189 (mmm160) cc_final: 0.7368 (mtm110) REVERT: E 219 LEU cc_start: 0.8681 (tt) cc_final: 0.8414 (tm) REVERT: E 234 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: G 20 MET cc_start: 0.7228 (tmm) cc_final: 0.6961 (mtt) REVERT: R 53 LYS cc_start: 0.7680 (ttpt) cc_final: 0.7108 (tptp) outliers start: 26 outliers final: 17 residues processed: 154 average time/residue: 1.3294 time to fit residues: 218.1307 Evaluate side-chains 150 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 36 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3900 r_free = 0.3900 target = 0.155148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117029 restraints weight = 10462.728| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.23 r_work: 0.3324 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9195 Z= 0.199 Angle : 0.549 9.037 12435 Z= 0.286 Chirality : 0.042 0.176 1411 Planarity : 0.004 0.051 1572 Dihedral : 5.875 106.757 1274 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.46 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: 1.33 (0.26), residues: 1129 helix: 2.33 (0.26), residues: 414 sheet: 0.45 (0.31), residues: 272 loop : -0.18 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.006 0.001 HIS B 188 PHE 0.025 0.001 PHE R 207 TYR 0.012 0.001 TYR E 190 ARG 0.009 0.000 ARG B 139 *********************** 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 161 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.039 Fit side-chains REVERT: A 182 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7507 (p) REVERT: A 188 LYS cc_start: 0.8524 (mttm) cc_final: 0.8258 (mmmt) REVERT: A 235 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7451 (mt-10) REVERT: A 247 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7635 (ttt180) REVERT: A 276 GLU cc_start: 0.7454 (tp30) cc_final: 0.7185 (tp30) REVERT: E 58 TYR cc_start: 0.8105 (m-10) cc_final: 0.7782 (m-10) REVERT: E 75 LYS cc_start: 0.7926 (mtmm) cc_final: 0.7654 (mtmm) REVERT: E 160 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7364 (mtm110) REVERT: E 219 LEU cc_start: 0.8676 (tt) cc_final: 0.8422 (tm) REVERT: E 234 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7211 (mt-10) REVERT: G 20 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6951 (mtt) REVERT: R 53 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7160 (tptp) outliers start: 27 outliers final: 20 residues processed: 148 average time/residue: 1.2770 time to fit residues: 201.3804 Evaluate side-chains 150 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 233 LEU 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 233 LEU 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 Chi-restraints excluded: chain R residue 292 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 104 optimal weight: 0.0770 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.156436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118473 restraints weight = 10540.156| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.24 r_work: 0.3340 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9195 Z= 0.176 Angle : 0.535 8.954 12435 Z= 0.278 Chirality : 0.041 0.177 1411 Planarity : 0.004 0.057 1572 Dihedral : 5.806 104.121 1274 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.85 % Allowed : 20.75 % Favored : 76.40 % 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: 1.38 (0.26), residues: 1129 helix: 2.34 (0.26), residues: 417 sheet: 0.50 (0.31), residues: 272 loop : -0.14 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.005 0.001 HIS B 188 PHE 0.026 0.001 PHE R 207 TYR 0.012 0.001 TYR R 177 ARG 0.014 0.000 ARG B 139 ********************** 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 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.192 Fit side-chains REVERT: A 182 SER cc_start: 0.7950 (OUTLIER) cc_final: 0.7473 (p) REVERT: A 188 LYS cc_start: 0.8478 (mttm) cc_final: 0.8236 (mmmt) REVERT: A 235 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7376 (mt-10) REVERT: A 247 ARG cc_start: 0.8150 (ptm160) cc_final: 0.7635 (ttt180) REVERT: A 276 GLU cc_start: 0.7378 (tp30) cc_final: 0.7074 (tp30) REVERT: B 219 ARG cc_start: 0.7783 (mmt-90) cc_final: 0.7520 (mtp85) REVERT: E 58 TYR cc_start: 0.8055 (m-10) cc_final: 0.7738 (m-10) REVERT: E 75 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7635 (mtmm) REVERT: E 160 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7286 (mtm110) REVERT: E 220 GLU cc_start: 0.7681 (mp0) cc_final: 0.7478 (mp0) REVERT: E 234 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: G 20 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6856 (mtt) REVERT: R 53 LYS cc_start: 0.7681 (ttpt) cc_final: 0.7112 (tptp) outliers start: 28 outliers final: 20 residues processed: 150 average time/residue: 1.4410 time to fit residues: 230.5116 Evaluate side-chains 151 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 233 LEU 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 233 LEU 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: 3.9990 chunk 112 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- 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 273 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.157080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119081 restraints weight = 10469.075| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.23 r_work: 0.3347 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9195 Z= 0.169 Angle : 0.531 8.964 12435 Z= 0.275 Chirality : 0.041 0.176 1411 Planarity : 0.004 0.049 1572 Dihedral : 5.761 102.584 1274 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.44 % Allowed : 21.57 % Favored : 75.99 % 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: 1.42 (0.26), residues: 1129 helix: 2.35 (0.26), residues: 418 sheet: 0.53 (0.31), residues: 272 loop : -0.13 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 216 HIS 0.005 0.001 HIS B 188 PHE 0.026 0.001 PHE R 207 TYR 0.018 0.001 TYR R 177 ARG 0.007 0.000 ARG B 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8336.24 seconds wall clock time: 144 minutes 58.17 seconds (8698.17 seconds total)