Starting phenix.real_space_refine on Mon May 12 08:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j21_35941/05_2025/8j21_35941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j21_35941/05_2025/8j21_35941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j21_35941/05_2025/8j21_35941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j21_35941/05_2025/8j21_35941.map" model { file = "/net/cci-nas-00/data/ceres_data/8j21_35941/05_2025/8j21_35941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j21_35941/05_2025/8j21_35941.cif" } resolution = 3.3 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= 0.001 sd= 0.020 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 58 5.16 5 C 5612 2.51 5 N 1495 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1775 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2188 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BUA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.93, per 1000 atoms: 0.56 Number of scatterers: 8803 At special positions: 0 Unit cell: (114.4, 109.2, 121.68, 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 58 16.00 O 1638 8.00 N 1495 7.00 C 5612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 169 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 948.3 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 12 sheets defined 38.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 14 through 36 removed outlier: 4.371A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.510A pdb=" N ILE A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.761A pdb=" N SER B 69 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 94 removed outlier: 3.919A pdb=" N GLY B 94 " --> pdb=" O SER B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.665A pdb=" N THR B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 removed outlier: 3.731A pdb=" N SER C 6 " --> pdb=" O CYS C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.536A pdb=" N GLU C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.764A pdb=" N ILE C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.752A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.564A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.794A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.940A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 14 through 46 removed outlier: 4.126A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Proline residue: D 30 - end of helix Processing helix chain 'D' and resid 48 through 73 removed outlier: 3.828A pdb=" N VAL D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Proline residue: D 69 - end of helix Processing helix chain 'D' and resid 86 through 119 removed outlier: 4.133A pdb=" N LEU D 90 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 128 through 154 removed outlier: 3.686A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 151 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 192 removed outlier: 3.540A pdb=" N ILE D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Proline residue: D 183 - end of helix Processing helix chain 'D' and resid 193 through 213 removed outlier: 4.298A pdb=" N ARG D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 207 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL D 208 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 213 " --> pdb=" O TRP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 252 removed outlier: 3.514A pdb=" N ARG D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Proline residue: D 240 - end of helix removed outlier: 3.594A pdb=" N TYR D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 278 removed outlier: 3.781A pdb=" N LEU D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Proline residue: D 273 - end of helix Processing helix chain 'D' and resid 280 through 291 Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.609A pdb=" N GLN E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.084A pdb=" N LEU A 90 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 103 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 92 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 removed outlier: 3.851A pdb=" N GLY A 126 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY A 127 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN A 136 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 146 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.151A pdb=" N CYS A 160 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 169 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP A 181 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN A 187 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.555A pdb=" N PHE A 210 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 223 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.426A pdb=" N GLY A 255 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 243 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 253 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 256 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS A 261 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR A 274 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 263 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 289 removed outlier: 5.099A pdb=" N SER A 286 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 299 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS A 305 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL A 318 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 307 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 45 Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.575A pdb=" N ALA B 87 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG B 76 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TRP B 85 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 185 removed outlier: 6.514A pdb=" N LEU B 212 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR B 228 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP B 214 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 196 through 200 removed outlier: 6.357A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1164 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: 2.63 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2840 1.35 - 1.47: 2243 1.47 - 1.59: 3825 1.59 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 8990 Sorted by residual: bond pdb=" CB MET A 72 " pdb=" CG MET A 72 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN B 269 " pdb=" CG GLN B 269 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C TYR B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.08e+00 bond pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 1.803 1.828 -0.025 2.50e-02 1.60e+03 9.75e-01 bond pdb=" CA TRP D 81 " pdb=" CB TRP D 81 " ideal model delta sigma weight residual 1.530 1.516 0.013 1.38e-02 5.25e+03 9.33e-01 ... (remaining 8985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 12059 2.34 - 4.69: 93 4.69 - 7.03: 17 7.03 - 9.37: 5 9.37 - 11.72: 6 Bond angle restraints: 12180 Sorted by residual: angle pdb=" C ALA A 71 " pdb=" N MET A 72 " pdb=" CA MET A 72 " ideal model delta sigma weight residual 122.08 132.69 -10.61 1.84e+00 2.95e-01 3.33e+01 angle pdb=" CA MET A 72 " pdb=" CB MET A 72 " pdb=" CG MET A 72 " ideal model delta sigma weight residual 114.10 124.74 -10.64 2.00e+00 2.50e-01 2.83e+01 angle pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta sigma weight residual 121.80 132.93 -11.13 2.44e+00 1.68e-01 2.08e+01 angle pdb=" CB MET A 72 " pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 112.70 124.42 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CB MET D 79 " pdb=" CG MET D 79 " pdb=" SD MET D 79 " ideal model delta sigma weight residual 112.70 122.13 -9.43 3.00e+00 1.11e-01 9.88e+00 ... (remaining 12175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4438 17.78 - 35.56: 649 35.56 - 53.34: 195 53.34 - 71.13: 27 71.13 - 88.91: 5 Dihedral angle restraints: 5314 sinusoidal: 2064 harmonic: 3250 Sorted by residual: dihedral pdb=" CA ARG A 161 " pdb=" C ARG A 161 " pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 246 " pdb=" C PHE A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta harmonic sigma weight residual 180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU B 272 " pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1035 0.042 - 0.083: 264 0.083 - 0.125: 76 0.125 - 0.166: 5 0.166 - 0.208: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA TYR B 273 " pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CB TYR B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 284 " pdb=" N ILE A 284 " pdb=" C ILE A 284 " pdb=" CB ILE A 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CG LEU D 181 " pdb=" CB LEU D 181 " pdb=" CD1 LEU D 181 " pdb=" CD2 LEU D 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1378 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 273 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO B 274 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 71 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ALA A 71 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA A 71 " 0.017 2.00e-02 2.50e+03 pdb=" N MET A 72 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 140 " 0.013 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" CG TRP D 140 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 140 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 140 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 140 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 140 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 140 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 140 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 140 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 140 " 0.002 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 255 2.69 - 3.24: 8335 3.24 - 3.80: 13973 3.80 - 4.35: 17941 4.35 - 4.90: 30022 Nonbonded interactions: 70526 Sorted by model distance: nonbonded pdb=" O ILE A 69 " pdb=" OG SER A 327 " model vdw 2.140 3.040 nonbonded pdb=" O LEU D 263 " pdb=" OG1 THR D 266 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR B 211 " pdb=" OG SER C 6 " model vdw 2.185 3.040 nonbonded pdb=" OG SER A 342 " pdb=" OD1 ASP A 344 " model vdw 2.193 3.040 nonbonded pdb=" O GLN A 86 " pdb=" OG SER A 109 " model vdw 2.220 3.040 ... (remaining 70521 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=0.01 max=1.00 mean=0.98 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: 1.810 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8993 Z= 0.111 Angle : 0.618 11.718 12186 Z= 0.310 Chirality : 0.040 0.208 1381 Planarity : 0.004 0.106 1540 Dihedral : 17.794 88.907 3213 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.70 % Favored : 94.76 % Rotamer: Outliers : 0.42 % Allowed : 36.11 % Favored : 63.48 % 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: 0.09 (0.25), residues: 1107 helix: 1.33 (0.27), residues: 388 sheet: 0.68 (0.33), residues: 245 loop : -1.38 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 140 HIS 0.004 0.001 HIS D 245 PHE 0.016 0.001 PHE B 241 TYR 0.019 0.001 TYR D 276 ARG 0.005 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.14688 ( 411) hydrogen bonds : angle 6.23304 ( 1164) SS BOND : bond 0.00474 ( 3) SS BOND : angle 1.07173 ( 6) covalent geometry : bond 0.00227 ( 8990) covalent geometry : angle 0.61816 (12180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.6730 (mtt90) cc_final: 0.6339 (mtt90) REVERT: A 338 VAL cc_start: 0.8515 (t) cc_final: 0.8208 (p) REVERT: C 198 MET cc_start: 0.7561 (tpp) cc_final: 0.7224 (tpp) outliers start: 4 outliers final: 2 residues processed: 220 average time/residue: 0.2446 time to fit residues: 70.4717 Evaluate side-chains 221 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain D residue 274 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN D 14 HIS E 18 GLN E 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127690 restraints weight = 13342.354| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.16 r_work: 0.3472 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8993 Z= 0.252 Angle : 0.702 12.163 12186 Z= 0.359 Chirality : 0.047 0.298 1381 Planarity : 0.005 0.084 1540 Dihedral : 4.865 43.412 1225 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.23 % Favored : 93.32 % Rotamer: Outliers : 6.97 % Allowed : 29.97 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1107 helix: 1.03 (0.26), residues: 405 sheet: 0.23 (0.32), residues: 262 loop : -1.52 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.009 0.002 HIS D 245 PHE 0.016 0.002 PHE A 210 TYR 0.018 0.002 TYR A 70 ARG 0.009 0.001 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 411) hydrogen bonds : angle 5.10981 ( 1164) SS BOND : bond 0.00740 ( 3) SS BOND : angle 1.39945 ( 6) covalent geometry : bond 0.00572 ( 8990) covalent geometry : angle 0.70136 (12180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7405 (mtt90) REVERT: A 266 LEU cc_start: 0.7911 (mt) cc_final: 0.7662 (mt) REVERT: A 288 SER cc_start: 0.8460 (p) cc_final: 0.8218 (m) REVERT: A 338 VAL cc_start: 0.8626 (t) cc_final: 0.8319 (p) REVERT: A 346 PHE cc_start: 0.7957 (m-80) cc_final: 0.7690 (m-80) REVERT: B 97 TYR cc_start: 0.8094 (m-80) cc_final: 0.7740 (m-80) REVERT: B 107 THR cc_start: 0.7783 (t) cc_final: 0.7569 (m) REVERT: C 186 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6313 (mt-10) REVERT: C 197 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7885 (mmtm) REVERT: C 240 MET cc_start: 0.3660 (ttp) cc_final: 0.3249 (ttp) REVERT: C 243 MET cc_start: 0.7572 (ttm) cc_final: 0.7343 (ttm) REVERT: D 29 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7972 (mt) REVERT: D 46 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6335 (ptt90) REVERT: D 151 TYR cc_start: 0.3554 (p90) cc_final: 0.2933 (p90) outliers start: 67 outliers final: 45 residues processed: 278 average time/residue: 0.2388 time to fit residues: 88.2913 Evaluate side-chains 267 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN B 180 GLN D 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128571 restraints weight = 13421.000| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.20 r_work: 0.3440 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8993 Z= 0.151 Angle : 0.615 11.227 12186 Z= 0.311 Chirality : 0.043 0.204 1381 Planarity : 0.004 0.061 1540 Dihedral : 4.430 23.296 1221 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.97 % Favored : 94.67 % Rotamer: Outliers : 7.08 % Allowed : 30.59 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1107 helix: 1.04 (0.26), residues: 407 sheet: 0.27 (0.32), residues: 253 loop : -1.64 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.009 0.001 HIS D 14 PHE 0.025 0.002 PHE C 189 TYR 0.017 0.001 TYR B 273 ARG 0.006 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 411) hydrogen bonds : angle 4.85108 ( 1164) SS BOND : bond 0.00538 ( 3) SS BOND : angle 1.01572 ( 6) covalent geometry : bond 0.00341 ( 8990) covalent geometry : angle 0.61477 (12180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 231 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.6686 (p0) REVERT: A 98 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7729 (p) REVERT: A 107 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7282 (mtt90) REVERT: A 122 TYR cc_start: 0.8242 (m-80) cc_final: 0.7647 (m-80) REVERT: A 239 ASP cc_start: 0.8034 (p0) cc_final: 0.7619 (p0) REVERT: A 266 LEU cc_start: 0.7796 (mt) cc_final: 0.7527 (mt) REVERT: A 288 SER cc_start: 0.8468 (p) cc_final: 0.8208 (m) REVERT: A 338 VAL cc_start: 0.8646 (t) cc_final: 0.8318 (p) REVERT: B 107 THR cc_start: 0.7876 (OUTLIER) cc_final: 0.7666 (m) REVERT: B 203 LEU cc_start: 0.7903 (mt) cc_final: 0.7684 (mp) REVERT: C 35 LYS cc_start: 0.8388 (mttp) cc_final: 0.8115 (mtmm) REVERT: C 231 ASP cc_start: 0.7767 (t0) cc_final: 0.7481 (t0) REVERT: C 240 MET cc_start: 0.3629 (ttp) cc_final: 0.3160 (ttp) REVERT: C 243 MET cc_start: 0.7490 (ttm) cc_final: 0.7262 (ttm) REVERT: D 29 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7908 (mt) REVERT: D 46 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.6270 (ptt90) REVERT: D 109 VAL cc_start: 0.8285 (m) cc_final: 0.7879 (p) REVERT: D 151 TYR cc_start: 0.3641 (p90) cc_final: 0.2972 (p90) outliers start: 68 outliers final: 41 residues processed: 270 average time/residue: 0.2385 time to fit residues: 84.7077 Evaluate side-chains 269 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.129906 restraints weight = 13295.816| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.17 r_work: 0.3437 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8993 Z= 0.155 Angle : 0.611 11.444 12186 Z= 0.311 Chirality : 0.043 0.182 1381 Planarity : 0.005 0.067 1540 Dihedral : 4.465 24.303 1221 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.60 % Favored : 94.04 % Rotamer: Outliers : 8.12 % Allowed : 29.55 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1107 helix: 1.10 (0.26), residues: 403 sheet: 0.29 (0.33), residues: 247 loop : -1.74 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 180 HIS 0.009 0.001 HIS D 14 PHE 0.023 0.002 PHE D 234 TYR 0.014 0.001 TYR D 202 ARG 0.008 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 411) hydrogen bonds : angle 4.80951 ( 1164) SS BOND : bond 0.00579 ( 3) SS BOND : angle 0.99507 ( 6) covalent geometry : bond 0.00354 ( 8990) covalent geometry : angle 0.61096 (12180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 222 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7551 (mtt90) cc_final: 0.7174 (mtt90) REVERT: A 122 TYR cc_start: 0.8249 (m-80) cc_final: 0.7701 (m-80) REVERT: A 239 ASP cc_start: 0.8016 (p0) cc_final: 0.7616 (p0) REVERT: A 266 LEU cc_start: 0.7768 (mt) cc_final: 0.7513 (mt) REVERT: A 288 SER cc_start: 0.8455 (p) cc_final: 0.8185 (m) REVERT: A 301 ASP cc_start: 0.7168 (m-30) cc_final: 0.6962 (m-30) REVERT: A 338 VAL cc_start: 0.8634 (t) cc_final: 0.8320 (p) REVERT: B 70 PHE cc_start: 0.8303 (m-80) cc_final: 0.8005 (m-80) REVERT: B 107 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7575 (m) REVERT: B 203 LEU cc_start: 0.7910 (mt) cc_final: 0.7690 (mp) REVERT: C 35 LYS cc_start: 0.8366 (mttp) cc_final: 0.8042 (mtmm) REVERT: C 36 LEU cc_start: 0.8571 (mt) cc_final: 0.8309 (mp) REVERT: C 231 ASP cc_start: 0.7819 (t0) cc_final: 0.7523 (t0) REVERT: C 240 MET cc_start: 0.3616 (ttp) cc_final: 0.3165 (ttp) REVERT: C 261 ASP cc_start: 0.7739 (t0) cc_final: 0.7388 (t0) REVERT: D 29 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7872 (mt) REVERT: D 46 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.6350 (ptt90) REVERT: D 151 TYR cc_start: 0.3698 (p90) cc_final: 0.2912 (p90) outliers start: 78 outliers final: 53 residues processed: 270 average time/residue: 0.2287 time to fit residues: 81.6721 Evaluate side-chains 282 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 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 270 GLN C 331 ASN D 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.148259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128513 restraints weight = 13252.667| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.17 r_work: 0.3395 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8993 Z= 0.210 Angle : 0.660 13.363 12186 Z= 0.336 Chirality : 0.044 0.188 1381 Planarity : 0.005 0.066 1540 Dihedral : 4.728 29.266 1221 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.60 % Favored : 94.04 % Rotamer: Outliers : 7.28 % Allowed : 30.91 % Favored : 61.81 % 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: -0.49 (0.25), residues: 1107 helix: 0.97 (0.27), residues: 403 sheet: -0.06 (0.32), residues: 262 loop : -1.71 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 15 HIS 0.014 0.002 HIS D 14 PHE 0.026 0.002 PHE D 234 TYR 0.019 0.002 TYR A 70 ARG 0.005 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 411) hydrogen bonds : angle 4.86467 ( 1164) SS BOND : bond 0.00578 ( 3) SS BOND : angle 0.93687 ( 6) covalent geometry : bond 0.00480 ( 8990) covalent geometry : angle 0.65961 (12180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.7834 (p) REVERT: A 107 ARG cc_start: 0.7577 (mtt90) cc_final: 0.7204 (mtt90) REVERT: A 182 ILE cc_start: 0.7952 (mm) cc_final: 0.7667 (mm) REVERT: A 239 ASP cc_start: 0.8046 (p0) cc_final: 0.7641 (p0) REVERT: A 266 LEU cc_start: 0.7753 (mt) cc_final: 0.7521 (mt) REVERT: A 288 SER cc_start: 0.8398 (p) cc_final: 0.8139 (m) REVERT: A 301 ASP cc_start: 0.7227 (m-30) cc_final: 0.6985 (m-30) REVERT: A 338 VAL cc_start: 0.8670 (t) cc_final: 0.8353 (p) REVERT: B 203 LEU cc_start: 0.7866 (mt) cc_final: 0.7630 (mp) REVERT: B 250 PHE cc_start: 0.8316 (m-80) cc_final: 0.7702 (m-80) REVERT: C 35 LYS cc_start: 0.8384 (mttp) cc_final: 0.8069 (mtmm) REVERT: C 36 LEU cc_start: 0.8582 (mt) cc_final: 0.8191 (mt) REVERT: C 186 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6478 (mt-10) REVERT: C 231 ASP cc_start: 0.7936 (t0) cc_final: 0.7665 (t0) REVERT: C 240 MET cc_start: 0.3659 (ttp) cc_final: 0.3310 (ttp) REVERT: C 261 ASP cc_start: 0.7817 (t0) cc_final: 0.7464 (t0) REVERT: C 309 ASP cc_start: 0.7618 (m-30) cc_final: 0.7231 (m-30) REVERT: D 29 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7893 (mt) REVERT: D 126 ARG cc_start: 0.6943 (mtm-85) cc_final: 0.6392 (mtm-85) REVERT: D 151 TYR cc_start: 0.3851 (OUTLIER) cc_final: 0.2979 (p90) outliers start: 70 outliers final: 53 residues processed: 269 average time/residue: 0.2355 time to fit residues: 83.5378 Evaluate side-chains 287 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 18 optimal weight: 0.0370 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN D 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129167 restraints weight = 13272.455| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.19 r_work: 0.3422 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 67 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8993 Z= 0.153 Angle : 0.630 13.188 12186 Z= 0.321 Chirality : 0.043 0.177 1381 Planarity : 0.005 0.068 1540 Dihedral : 4.589 28.668 1221 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.15 % Favored : 94.49 % Rotamer: Outliers : 7.80 % Allowed : 30.07 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1107 helix: 1.07 (0.27), residues: 403 sheet: -0.10 (0.32), residues: 263 loop : -1.68 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.013 0.001 HIS D 14 PHE 0.027 0.002 PHE D 234 TYR 0.018 0.001 TYR D 202 ARG 0.005 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 411) hydrogen bonds : angle 4.79342 ( 1164) SS BOND : bond 0.00605 ( 3) SS BOND : angle 1.08105 ( 6) covalent geometry : bond 0.00346 ( 8990) covalent geometry : angle 0.62995 (12180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 220 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7821 (p) REVERT: A 107 ARG cc_start: 0.7609 (mtt90) cc_final: 0.7246 (mtt90) REVERT: A 182 ILE cc_start: 0.7808 (mm) cc_final: 0.7541 (mm) REVERT: A 239 ASP cc_start: 0.8047 (p0) cc_final: 0.7628 (p0) REVERT: A 266 LEU cc_start: 0.7715 (mt) cc_final: 0.7456 (mt) REVERT: A 288 SER cc_start: 0.8386 (p) cc_final: 0.8150 (m) REVERT: A 301 ASP cc_start: 0.7143 (m-30) cc_final: 0.6935 (m-30) REVERT: A 315 ARG cc_start: 0.7943 (ttm170) cc_final: 0.7396 (ttm170) REVERT: A 338 VAL cc_start: 0.8679 (t) cc_final: 0.8369 (p) REVERT: B 70 PHE cc_start: 0.8315 (m-80) cc_final: 0.8046 (m-80) REVERT: B 202 SER cc_start: 0.7157 (t) cc_final: 0.6911 (p) REVERT: C 35 LYS cc_start: 0.8409 (mttp) cc_final: 0.8132 (mtmm) REVERT: C 231 ASP cc_start: 0.7954 (t0) cc_final: 0.7666 (t0) REVERT: C 240 MET cc_start: 0.3666 (ttp) cc_final: 0.3326 (ttp) REVERT: C 247 MET cc_start: 0.7994 (mmm) cc_final: 0.7711 (mtt) REVERT: C 261 ASP cc_start: 0.7801 (t0) cc_final: 0.7440 (t0) REVERT: C 309 ASP cc_start: 0.7582 (m-30) cc_final: 0.7205 (m-30) REVERT: D 15 TRP cc_start: 0.6663 (OUTLIER) cc_final: 0.5677 (p90) REVERT: D 29 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7846 (mt) REVERT: D 126 ARG cc_start: 0.6970 (mtm-85) cc_final: 0.6468 (mtm-85) REVERT: D 151 TYR cc_start: 0.3769 (OUTLIER) cc_final: 0.2873 (p90) REVERT: D 207 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7801 (tp) outliers start: 75 outliers final: 59 residues processed: 269 average time/residue: 0.2383 time to fit residues: 84.1265 Evaluate side-chains 285 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 221 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.149227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128988 restraints weight = 13358.515| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.18 r_work: 0.3436 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 66 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8993 Z= 0.148 Angle : 0.627 14.153 12186 Z= 0.317 Chirality : 0.043 0.183 1381 Planarity : 0.005 0.067 1540 Dihedral : 4.551 28.257 1221 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 8.22 % Allowed : 29.97 % Favored : 61.81 % 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: -0.39 (0.26), residues: 1107 helix: 1.14 (0.27), residues: 402 sheet: -0.11 (0.32), residues: 263 loop : -1.67 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.014 0.001 HIS D 14 PHE 0.028 0.002 PHE D 234 TYR 0.020 0.001 TYR D 202 ARG 0.004 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 411) hydrogen bonds : angle 4.77013 ( 1164) SS BOND : bond 0.00634 ( 3) SS BOND : angle 1.15128 ( 6) covalent geometry : bond 0.00333 ( 8990) covalent geometry : angle 0.62628 (12180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 218 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.6757 (p0) REVERT: A 60 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7342 (mmt180) REVERT: A 98 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.7857 (p) REVERT: A 107 ARG cc_start: 0.7595 (mtt90) cc_final: 0.7221 (mtt90) REVERT: A 226 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: A 239 ASP cc_start: 0.8034 (p0) cc_final: 0.7728 (p0) REVERT: A 266 LEU cc_start: 0.7666 (mt) cc_final: 0.7373 (mt) REVERT: A 288 SER cc_start: 0.8475 (p) cc_final: 0.8111 (m) REVERT: A 301 ASP cc_start: 0.7122 (m-30) cc_final: 0.6908 (m-30) REVERT: A 315 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7444 (ttm170) REVERT: A 338 VAL cc_start: 0.8677 (t) cc_final: 0.8373 (p) REVERT: B 70 PHE cc_start: 0.8316 (m-80) cc_final: 0.8044 (m-80) REVERT: B 202 SER cc_start: 0.7105 (t) cc_final: 0.6875 (p) REVERT: B 227 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8412 (pt) REVERT: C 35 LYS cc_start: 0.8427 (mttp) cc_final: 0.8145 (mtmm) REVERT: C 231 ASP cc_start: 0.7982 (t0) cc_final: 0.7689 (t0) REVERT: C 240 MET cc_start: 0.3773 (ttp) cc_final: 0.3457 (ttp) REVERT: C 247 MET cc_start: 0.8021 (mmm) cc_final: 0.7713 (mtt) REVERT: C 261 ASP cc_start: 0.7735 (t0) cc_final: 0.7307 (t0) REVERT: C 309 ASP cc_start: 0.7581 (m-30) cc_final: 0.7203 (m-30) REVERT: D 29 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7836 (mt) REVERT: D 113 ARG cc_start: 0.8319 (mtt180) cc_final: 0.8101 (mtt180) REVERT: D 126 ARG cc_start: 0.7054 (mtm-85) cc_final: 0.6442 (mtm-85) REVERT: D 151 TYR cc_start: 0.4083 (OUTLIER) cc_final: 0.3189 (p90) REVERT: D 207 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7803 (tp) outliers start: 79 outliers final: 63 residues processed: 267 average time/residue: 0.2329 time to fit residues: 82.2108 Evaluate side-chains 293 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 222 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.129410 restraints weight = 13493.238| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.20 r_work: 0.3418 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8993 Z= 0.168 Angle : 0.633 10.472 12186 Z= 0.322 Chirality : 0.044 0.235 1381 Planarity : 0.005 0.067 1540 Dihedral : 4.603 28.521 1221 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.51 % Favored : 94.13 % Rotamer: Outliers : 8.01 % Allowed : 30.07 % Favored : 61.91 % 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: -0.43 (0.26), residues: 1107 helix: 1.10 (0.27), residues: 402 sheet: -0.16 (0.32), residues: 267 loop : -1.67 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.015 0.001 HIS D 14 PHE 0.029 0.002 PHE D 234 TYR 0.021 0.002 TYR D 202 ARG 0.013 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 411) hydrogen bonds : angle 4.80542 ( 1164) SS BOND : bond 0.00669 ( 3) SS BOND : angle 1.17682 ( 6) covalent geometry : bond 0.00381 ( 8990) covalent geometry : angle 0.63306 (12180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 221 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.6845 (p0) REVERT: A 98 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7752 (p) REVERT: A 107 ARG cc_start: 0.7607 (mtt90) cc_final: 0.7234 (mtt90) REVERT: A 226 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: A 239 ASP cc_start: 0.8026 (p0) cc_final: 0.7629 (p0) REVERT: A 266 LEU cc_start: 0.7651 (mt) cc_final: 0.7385 (mt) REVERT: A 273 MET cc_start: 0.7504 (ppp) cc_final: 0.7117 (ppp) REVERT: A 288 SER cc_start: 0.8499 (p) cc_final: 0.8022 (m) REVERT: A 315 ARG cc_start: 0.8048 (ttm170) cc_final: 0.7523 (ttm170) REVERT: A 338 VAL cc_start: 0.8672 (t) cc_final: 0.8380 (p) REVERT: B 70 PHE cc_start: 0.8335 (m-80) cc_final: 0.8055 (m-80) REVERT: B 97 TYR cc_start: 0.8159 (m-80) cc_final: 0.7684 (m-80) REVERT: B 202 SER cc_start: 0.7089 (t) cc_final: 0.6865 (p) REVERT: B 227 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8429 (pt) REVERT: B 250 PHE cc_start: 0.8293 (m-80) cc_final: 0.7588 (m-80) REVERT: C 35 LYS cc_start: 0.8378 (mttp) cc_final: 0.8051 (mtmm) REVERT: C 36 LEU cc_start: 0.8566 (mt) cc_final: 0.8292 (mp) REVERT: C 197 LYS cc_start: 0.8075 (mttm) cc_final: 0.7764 (mmtt) REVERT: C 231 ASP cc_start: 0.8000 (t0) cc_final: 0.7726 (t0) REVERT: C 240 MET cc_start: 0.3807 (ttp) cc_final: 0.3519 (ttp) REVERT: C 247 MET cc_start: 0.8052 (mmm) cc_final: 0.7800 (mtt) REVERT: C 261 ASP cc_start: 0.7732 (t0) cc_final: 0.7327 (t0) REVERT: C 309 ASP cc_start: 0.7613 (m-30) cc_final: 0.7214 (m-30) REVERT: D 29 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7860 (mt) REVERT: D 126 ARG cc_start: 0.6957 (mtm-85) cc_final: 0.6327 (mtm-85) REVERT: D 151 TYR cc_start: 0.3942 (OUTLIER) cc_final: 0.3018 (p90) REVERT: D 207 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7829 (tp) outliers start: 77 outliers final: 63 residues processed: 271 average time/residue: 0.2339 time to fit residues: 83.7963 Evaluate side-chains 288 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.148095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.127994 restraints weight = 13373.140| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.20 r_work: 0.3391 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8993 Z= 0.195 Angle : 0.659 9.515 12186 Z= 0.337 Chirality : 0.045 0.206 1381 Planarity : 0.005 0.065 1540 Dihedral : 4.778 29.249 1221 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.78 % Favored : 93.86 % Rotamer: Outliers : 8.12 % Allowed : 30.28 % Favored : 61.60 % 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: -0.55 (0.25), residues: 1107 helix: 1.01 (0.27), residues: 402 sheet: -0.24 (0.32), residues: 265 loop : -1.74 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 180 HIS 0.006 0.001 HIS C 188 PHE 0.024 0.002 PHE B 277 TYR 0.019 0.002 TYR D 202 ARG 0.014 0.001 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 411) hydrogen bonds : angle 4.90559 ( 1164) SS BOND : bond 0.00818 ( 3) SS BOND : angle 1.50715 ( 6) covalent geometry : bond 0.00450 ( 8990) covalent geometry : angle 0.65839 (12180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 213 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.6908 (p0) REVERT: A 60 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7381 (mmt180) REVERT: A 98 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7831 (p) REVERT: A 107 ARG cc_start: 0.7578 (mtt90) cc_final: 0.7208 (mtt90) REVERT: A 226 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6645 (mp0) REVERT: A 239 ASP cc_start: 0.8053 (p0) cc_final: 0.7623 (p0) REVERT: A 266 LEU cc_start: 0.7621 (mt) cc_final: 0.7367 (mt) REVERT: A 273 MET cc_start: 0.7573 (ppp) cc_final: 0.7262 (ppp) REVERT: A 288 SER cc_start: 0.8509 (p) cc_final: 0.7949 (m) REVERT: A 338 VAL cc_start: 0.8661 (t) cc_final: 0.8356 (p) REVERT: B 97 TYR cc_start: 0.8248 (m-80) cc_final: 0.7824 (m-80) REVERT: B 202 SER cc_start: 0.7093 (t) cc_final: 0.6884 (p) REVERT: B 227 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8456 (pt) REVERT: B 250 PHE cc_start: 0.8143 (m-80) cc_final: 0.7645 (m-80) REVERT: C 197 LYS cc_start: 0.8149 (mttm) cc_final: 0.7785 (mmtm) REVERT: C 198 MET cc_start: 0.8257 (mtp) cc_final: 0.8054 (ttm) REVERT: C 231 ASP cc_start: 0.8000 (t0) cc_final: 0.7685 (t0) REVERT: C 240 MET cc_start: 0.3805 (ttp) cc_final: 0.3580 (ttp) REVERT: C 245 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 247 MET cc_start: 0.8119 (mmm) cc_final: 0.7768 (mtt) REVERT: C 248 LYS cc_start: 0.7909 (ptpp) cc_final: 0.7575 (mttm) REVERT: C 261 ASP cc_start: 0.7781 (t0) cc_final: 0.7374 (t0) REVERT: C 309 ASP cc_start: 0.7621 (m-30) cc_final: 0.7215 (m-30) REVERT: D 15 TRP cc_start: 0.6874 (OUTLIER) cc_final: 0.6182 (p90) REVERT: D 29 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7815 (mt) REVERT: D 126 ARG cc_start: 0.6903 (mtm-85) cc_final: 0.6279 (mtm-85) REVERT: D 151 TYR cc_start: 0.3989 (OUTLIER) cc_final: 0.3005 (p90) REVERT: D 207 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7932 (tp) outliers start: 78 outliers final: 61 residues processed: 263 average time/residue: 0.2297 time to fit residues: 80.3245 Evaluate side-chains 286 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.129457 restraints weight = 13347.415| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.21 r_work: 0.3418 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 70 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8993 Z= 0.141 Angle : 0.642 11.013 12186 Z= 0.327 Chirality : 0.043 0.225 1381 Planarity : 0.005 0.065 1540 Dihedral : 4.623 25.232 1221 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.60 % Favored : 94.04 % Rotamer: Outliers : 6.76 % Allowed : 31.74 % Favored : 61.50 % 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: -0.44 (0.25), residues: 1107 helix: 1.20 (0.27), residues: 396 sheet: -0.21 (0.31), residues: 262 loop : -1.71 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 140 HIS 0.005 0.001 HIS D 245 PHE 0.027 0.002 PHE B 277 TYR 0.021 0.001 TYR A 70 ARG 0.007 0.000 ARG D 113 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 411) hydrogen bonds : angle 4.78709 ( 1164) SS BOND : bond 0.00788 ( 3) SS BOND : angle 1.51598 ( 6) covalent geometry : bond 0.00320 ( 8990) covalent geometry : angle 0.64168 (12180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 225 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7627 (mmt180) REVERT: A 63 ARG cc_start: 0.7503 (ptp90) cc_final: 0.7292 (ptp-170) REVERT: A 107 ARG cc_start: 0.7574 (mtt90) cc_final: 0.7190 (mtt90) REVERT: A 226 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: A 239 ASP cc_start: 0.8011 (p0) cc_final: 0.7526 (p0) REVERT: A 267 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7444 (mtm180) REVERT: A 273 MET cc_start: 0.7483 (ppp) cc_final: 0.7184 (ppp) REVERT: A 288 SER cc_start: 0.8496 (p) cc_final: 0.8014 (m) REVERT: A 315 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7593 (ttm170) REVERT: A 338 VAL cc_start: 0.8678 (t) cc_final: 0.8399 (p) REVERT: B 97 TYR cc_start: 0.8238 (m-80) cc_final: 0.7759 (m-80) REVERT: B 227 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8402 (pt) REVERT: B 250 PHE cc_start: 0.8112 (m-80) cc_final: 0.7854 (m-80) REVERT: C 197 LYS cc_start: 0.8105 (mttm) cc_final: 0.7688 (mmtt) REVERT: C 198 MET cc_start: 0.8275 (mtp) cc_final: 0.8028 (ttm) REVERT: C 231 ASP cc_start: 0.7972 (t0) cc_final: 0.7653 (t0) REVERT: C 240 MET cc_start: 0.3862 (ttp) cc_final: 0.3625 (ttp) REVERT: C 247 MET cc_start: 0.8087 (mmm) cc_final: 0.7763 (mtt) REVERT: C 261 ASP cc_start: 0.7706 (t0) cc_final: 0.7267 (t0) REVERT: C 309 ASP cc_start: 0.7593 (m-30) cc_final: 0.7178 (m-30) REVERT: D 15 TRP cc_start: 0.6840 (OUTLIER) cc_final: 0.6121 (p90) REVERT: D 29 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7781 (mt) REVERT: D 126 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6274 (mtm-85) REVERT: D 151 TYR cc_start: 0.4101 (OUTLIER) cc_final: 0.3184 (p90) outliers start: 65 outliers final: 55 residues processed: 270 average time/residue: 0.2814 time to fit residues: 100.1567 Evaluate side-chains 280 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125160 restraints weight = 13442.738| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.18 r_work: 0.3406 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 70 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 73 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8993 Z= 0.164 Angle : 0.662 13.866 12186 Z= 0.335 Chirality : 0.044 0.241 1381 Planarity : 0.005 0.066 1540 Dihedral : 4.675 26.341 1221 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.78 % Favored : 93.86 % Rotamer: Outliers : 6.35 % Allowed : 32.57 % Favored : 61.08 % 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: -0.47 (0.25), residues: 1107 helix: 1.12 (0.27), residues: 401 sheet: -0.07 (0.32), residues: 257 loop : -1.80 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 180 HIS 0.005 0.001 HIS C 188 PHE 0.028 0.002 PHE D 234 TYR 0.021 0.001 TYR A 70 ARG 0.008 0.001 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 411) hydrogen bonds : angle 4.81065 ( 1164) SS BOND : bond 0.00809 ( 3) SS BOND : angle 1.46206 ( 6) covalent geometry : bond 0.00375 ( 8990) covalent geometry : angle 0.66127 (12180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5248.22 seconds wall clock time: 91 minutes 38.17 seconds (5498.17 seconds total)