Starting phenix.real_space_refine on Sat Aug 23 00:48:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j21_35941/08_2025/8j21_35941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j21_35941/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8j21_35941/08_2025/8j21_35941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j21_35941/08_2025/8j21_35941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j21_35941/08_2025/8j21_35941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j21_35941/08_2025/8j21_35941.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.70, per 1000 atoms: 0.19 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: 0.61 Conformation dependent library (CDL) restraints added in 267.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.26 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: 0.94 Time building geometry restraints manager: 0.81 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: 0.970 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.330 ------------------------------------------------------------------------------- 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 : 9.76 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A 145 TYR 0.019 0.001 TYR D 276 PHE 0.016 0.001 PHE B 241 TRP 0.031 0.001 TRP D 140 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8990) covalent geometry : angle 0.61816 (12180) SS BOND : bond 0.00474 ( 3) SS BOND : angle 1.07173 ( 6) hydrogen bonds : bond 0.14688 ( 411) hydrogen bonds : angle 6.23304 ( 1164) *********************** 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 : 0.224 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: 0.0787 time to fit residues: 23.0430 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 : 0.252 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.156665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136968 restraints weight = 13376.342| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.19 r_work: 0.3552 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 70 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8993 Z= 0.167 Angle : 0.623 11.803 12186 Z= 0.316 Chirality : 0.043 0.261 1381 Planarity : 0.004 0.085 1540 Dihedral : 4.422 43.038 1225 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.33 % Favored : 94.22 % Rotamer: Outliers : 6.66 % Allowed : 29.76 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.25), residues: 1107 helix: 1.38 (0.26), residues: 396 sheet: 0.53 (0.33), residues: 246 loop : -1.39 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 136 TYR 0.012 0.002 TYR A 70 PHE 0.013 0.002 PHE A 246 TRP 0.017 0.002 TRP A 180 HIS 0.006 0.002 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8990) covalent geometry : angle 0.62312 (12180) SS BOND : bond 0.00576 ( 3) SS BOND : angle 1.14917 ( 6) hydrogen bonds : bond 0.03910 ( 411) hydrogen bonds : angle 4.87672 ( 1164) *********************** 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 290 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 226 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.6612 (mmp80) cc_final: 0.6271 (mmp80) REVERT: A 107 ARG cc_start: 0.7605 (mtt90) cc_final: 0.7173 (mtt90) REVERT: A 239 ASP cc_start: 0.8077 (p0) cc_final: 0.7726 (p0) REVERT: A 338 VAL cc_start: 0.8616 (t) cc_final: 0.8301 (p) REVERT: A 351 ASN cc_start: 0.7574 (m-40) cc_final: 0.7336 (m-40) REVERT: B 75 VAL cc_start: 0.7917 (t) cc_final: 0.6563 (p) REVERT: C 231 ASP cc_start: 0.7488 (t0) cc_final: 0.7266 (t0) REVERT: C 243 MET cc_start: 0.7294 (ttm) cc_final: 0.7074 (ttm) REVERT: D 29 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8009 (mt) REVERT: D 46 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6196 (ptt90) REVERT: D 271 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.7588 (p) outliers start: 64 outliers final: 37 residues processed: 266 average time/residue: 0.0875 time to fit residues: 31.0375 Evaluate side-chains 254 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 245 PHE 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 158 SER Chi-restraints excluded: chain B residue 177 VAL 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 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 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 70 PHE 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 271 VAL 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 58 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.0970 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 81 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN C 188 HIS D 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130831 restraints weight = 13374.680| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.17 r_work: 0.3482 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 70 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8993 Z= 0.153 Angle : 0.604 10.700 12186 Z= 0.304 Chirality : 0.042 0.180 1381 Planarity : 0.004 0.060 1540 Dihedral : 4.233 23.524 1221 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 6.87 % Allowed : 30.28 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.25), residues: 1107 helix: 1.30 (0.26), residues: 399 sheet: 0.40 (0.33), residues: 246 loop : -1.47 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 262 TYR 0.015 0.001 TYR B 273 PHE 0.020 0.002 PHE D 234 TRP 0.017 0.001 TRP A 180 HIS 0.009 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8990) covalent geometry : angle 0.60340 (12180) SS BOND : bond 0.00519 ( 3) SS BOND : angle 0.92948 ( 6) hydrogen bonds : bond 0.03752 ( 411) hydrogen bonds : angle 4.75070 ( 1164) *********************** 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 292 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 226 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7251 (mtt90) REVERT: A 122 TYR cc_start: 0.8251 (m-80) cc_final: 0.7679 (m-80) REVERT: A 329 LEU cc_start: 0.7858 (tt) cc_final: 0.7348 (tt) REVERT: A 338 VAL cc_start: 0.8628 (t) cc_final: 0.8346 (p) REVERT: B 107 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7557 (m) REVERT: C 231 ASP cc_start: 0.7634 (t0) cc_final: 0.7397 (t0) REVERT: C 240 MET cc_start: 0.3632 (ttp) cc_final: 0.3137 (ttp) REVERT: D 29 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7948 (mt) REVERT: D 46 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.6207 (ptt90) REVERT: D 151 TYR cc_start: 0.3740 (p90) cc_final: 0.3125 (p90) REVERT: D 271 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7645 (p) outliers start: 66 outliers final: 42 residues processed: 267 average time/residue: 0.0793 time to fit residues: 28.5846 Evaluate side-chains 265 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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 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 347 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 107 THR 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 230 MET Chi-restraints excluded: chain B residue 235 SER 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 246 SER 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 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 86 ILE Chi-restraints excluded: chain D residue 106 LEU 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 271 VAL 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 100 optimal weight: 0.4980 chunk 26 optimal weight: 0.0570 chunk 102 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 0.0030 overall best weight: 0.2908 ------------------------------------------------------------------------------- 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 E 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.134851 restraints weight = 13490.416| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.21 r_work: 0.3513 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8993 Z= 0.117 Angle : 0.578 9.704 12186 Z= 0.291 Chirality : 0.041 0.168 1381 Planarity : 0.004 0.066 1540 Dihedral : 4.149 24.069 1221 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.24 % Favored : 94.40 % Rotamer: Outliers : 7.28 % Allowed : 30.18 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), residues: 1107 helix: 1.43 (0.27), residues: 391 sheet: 0.44 (0.33), residues: 241 loop : -1.49 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 262 TYR 0.011 0.001 TYR B 273 PHE 0.022 0.001 PHE D 234 TRP 0.017 0.001 TRP A 180 HIS 0.013 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8990) covalent geometry : angle 0.57772 (12180) SS BOND : bond 0.00498 ( 3) SS BOND : angle 0.92504 ( 6) hydrogen bonds : bond 0.03433 ( 411) hydrogen bonds : angle 4.61979 ( 1164) *********************** 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 280 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 210 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 98 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7857 (m) REVERT: A 107 ARG cc_start: 0.7559 (mtt90) cc_final: 0.7168 (mtt90) REVERT: A 113 THR cc_start: 0.7595 (m) cc_final: 0.7384 (m) REVERT: A 122 TYR cc_start: 0.8248 (m-80) cc_final: 0.7643 (m-80) REVERT: A 338 VAL cc_start: 0.8628 (t) cc_final: 0.8306 (p) REVERT: B 75 VAL cc_start: 0.7916 (t) cc_final: 0.6518 (p) REVERT: B 107 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7548 (m) REVERT: B 252 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (tp) REVERT: C 231 ASP cc_start: 0.7574 (t0) cc_final: 0.7321 (t0) REVERT: C 240 MET cc_start: 0.3587 (ttp) cc_final: 0.3090 (ttp) REVERT: D 29 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7904 (mt) REVERT: D 46 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.6321 (ptt90) REVERT: D 113 ARG cc_start: 0.8347 (mtt180) cc_final: 0.8049 (mtt180) REVERT: D 151 TYR cc_start: 0.3786 (p90) cc_final: 0.3126 (p90) REVERT: D 271 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7727 (p) outliers start: 70 outliers final: 45 residues processed: 255 average time/residue: 0.0874 time to fit residues: 29.7768 Evaluate side-chains 258 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 98 THR 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 221 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 287 VAL 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 237 VAL Chi-restraints excluded: chain B residue 252 LEU 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 244 HIS Chi-restraints excluded: chain C residue 246 SER 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 14 HIS Chi-restraints excluded: chain D residue 17 VAL 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 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 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 271 VAL Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 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 = 0.3883 r_free = 0.3883 target = 0.151511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131200 restraints weight = 13432.168| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.23 r_work: 0.3477 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8993 Z= 0.146 Angle : 0.606 10.640 12186 Z= 0.306 Chirality : 0.042 0.165 1381 Planarity : 0.004 0.064 1540 Dihedral : 4.285 23.725 1221 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 7.91 % Allowed : 29.34 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.26), residues: 1107 helix: 1.41 (0.27), residues: 393 sheet: 0.31 (0.33), residues: 254 loop : -1.55 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 63 TYR 0.015 0.001 TYR B 211 PHE 0.025 0.002 PHE C 334 TRP 0.018 0.002 TRP A 180 HIS 0.018 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8990) covalent geometry : angle 0.60539 (12180) SS BOND : bond 0.00571 ( 3) SS BOND : angle 0.98939 ( 6) hydrogen bonds : bond 0.03565 ( 411) hydrogen bonds : angle 4.63656 ( 1164) *********************** 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 285 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 209 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7613 (mtt90) cc_final: 0.7191 (mtt90) REVERT: A 122 TYR cc_start: 0.8243 (m-80) cc_final: 0.7674 (m-80) REVERT: A 329 LEU cc_start: 0.7684 (tt) cc_final: 0.7432 (tt) REVERT: A 338 VAL cc_start: 0.8654 (t) cc_final: 0.8350 (p) REVERT: B 107 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7545 (m) REVERT: B 203 LEU cc_start: 0.7850 (mt) cc_final: 0.7634 (mp) REVERT: B 277 PHE cc_start: 0.7429 (m-80) cc_final: 0.7188 (m-10) REVERT: C 36 LEU cc_start: 0.8502 (mt) cc_final: 0.8277 (mp) REVERT: C 186 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6324 (mt-10) REVERT: C 231 ASP cc_start: 0.7715 (t0) cc_final: 0.7425 (t0) REVERT: C 240 MET cc_start: 0.3556 (ttp) cc_final: 0.3086 (ttp) REVERT: D 29 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7909 (mt) REVERT: D 126 ARG cc_start: 0.6963 (mtm-85) cc_final: 0.6414 (mtm-85) REVERT: D 151 TYR cc_start: 0.3867 (p90) cc_final: 0.3115 (p90) outliers start: 76 outliers final: 59 residues processed: 257 average time/residue: 0.0975 time to fit residues: 33.3210 Evaluate side-chains 269 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 82 VAL 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 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 287 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 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 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 221 ILE Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 246 SER 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 17 VAL 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 60 SER 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 181 LEU Chi-restraints excluded: chain D residue 190 VAL 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 Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.129056 restraints weight = 13388.575| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.20 r_work: 0.3434 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 73 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8993 Z= 0.178 Angle : 0.630 12.061 12186 Z= 0.319 Chirality : 0.043 0.171 1381 Planarity : 0.005 0.067 1540 Dihedral : 4.434 23.368 1221 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.60 % Favored : 94.04 % Rotamer: Outliers : 7.49 % Allowed : 29.76 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.26), residues: 1107 helix: 1.20 (0.27), residues: 400 sheet: 0.27 (0.32), residues: 258 loop : -1.63 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 262 TYR 0.021 0.002 TYR D 202 PHE 0.026 0.002 PHE D 234 TRP 0.019 0.002 TRP A 180 HIS 0.016 0.002 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 8990) covalent geometry : angle 0.62935 (12180) SS BOND : bond 0.00575 ( 3) SS BOND : angle 0.89933 ( 6) hydrogen bonds : bond 0.03814 ( 411) hydrogen bonds : angle 4.71017 ( 1164) *********************** 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 291 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 219 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 98 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7757 (p) REVERT: A 107 ARG cc_start: 0.7624 (mtt90) cc_final: 0.7229 (mtt90) REVERT: A 122 TYR cc_start: 0.8275 (m-80) cc_final: 0.7775 (m-80) REVERT: A 338 VAL cc_start: 0.8661 (t) cc_final: 0.8339 (p) REVERT: A 346 PHE cc_start: 0.7954 (m-80) cc_final: 0.7602 (m-10) REVERT: B 107 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7557 (m) REVERT: B 203 LEU cc_start: 0.7871 (mt) cc_final: 0.7659 (mp) REVERT: C 36 LEU cc_start: 0.8516 (mt) cc_final: 0.8292 (mp) REVERT: C 186 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6475 (mt-10) REVERT: C 197 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7910 (mmtm) REVERT: C 231 ASP cc_start: 0.7778 (t0) cc_final: 0.7487 (t0) REVERT: C 240 MET cc_start: 0.3315 (ttp) cc_final: 0.2888 (ttp) REVERT: C 261 ASP cc_start: 0.7733 (t0) cc_final: 0.7377 (t0) REVERT: C 309 ASP cc_start: 0.7595 (m-30) cc_final: 0.7179 (m-30) REVERT: D 29 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7891 (mt) REVERT: D 109 VAL cc_start: 0.8291 (m) cc_final: 0.7911 (p) REVERT: D 126 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6354 (mtm-85) REVERT: D 151 TYR cc_start: 0.3965 (p90) cc_final: 0.3144 (p90) outliers start: 72 outliers final: 59 residues processed: 265 average time/residue: 0.1007 time to fit residues: 35.9907 Evaluate side-chains 279 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 82 VAL 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 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 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 59 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 122 THR 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 237 VAL Chi-restraints excluded: chain B residue 252 LEU 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 221 ILE Chi-restraints excluded: chain C residue 241 ASN 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 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 181 LEU Chi-restraints excluded: chain D residue 190 VAL 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 Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 0.0000 chunk 15 optimal weight: 0.9980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 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 = 0.3851 r_free = 0.3851 target = 0.148284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128005 restraints weight = 13294.470| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.17 r_work: 0.3456 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 73 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8993 Z= 0.135 Angle : 0.609 11.028 12186 Z= 0.305 Chirality : 0.042 0.172 1381 Planarity : 0.004 0.067 1540 Dihedral : 4.356 25.367 1221 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 7.91 % Allowed : 30.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.26), residues: 1107 helix: 1.25 (0.27), residues: 403 sheet: 0.35 (0.33), residues: 248 loop : -1.69 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 262 TYR 0.017 0.001 TYR D 202 PHE 0.029 0.002 PHE D 173 TRP 0.019 0.002 TRP A 180 HIS 0.010 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8990) covalent geometry : angle 0.60878 (12180) SS BOND : bond 0.00615 ( 3) SS BOND : angle 1.11290 ( 6) hydrogen bonds : bond 0.03476 ( 411) hydrogen bonds : angle 4.61483 ( 1164) *********************** 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 279 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 203 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7737 (p) REVERT: A 107 ARG cc_start: 0.7619 (mtt90) cc_final: 0.7231 (mtt90) REVERT: A 329 LEU cc_start: 0.7868 (tt) cc_final: 0.7657 (tt) REVERT: A 338 VAL cc_start: 0.8653 (t) cc_final: 0.8360 (p) REVERT: B 70 PHE cc_start: 0.8413 (m-80) cc_final: 0.8192 (m-80) REVERT: B 121 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7663 (mtm) REVERT: B 178 MET cc_start: 0.8054 (mmm) cc_final: 0.7471 (mmm) REVERT: C 35 LYS cc_start: 0.8392 (mttp) cc_final: 0.8100 (mtpp) REVERT: C 36 LEU cc_start: 0.8542 (mt) cc_final: 0.8284 (mp) REVERT: C 186 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6445 (mt-10) REVERT: C 231 ASP cc_start: 0.7767 (t0) cc_final: 0.7467 (t0) REVERT: C 240 MET cc_start: 0.3429 (ttp) cc_final: 0.3032 (ttp) REVERT: C 261 ASP cc_start: 0.7739 (t0) cc_final: 0.7379 (t0) REVERT: C 309 ASP cc_start: 0.7589 (m-30) cc_final: 0.7185 (m-30) REVERT: D 29 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7854 (mt) REVERT: D 113 ARG cc_start: 0.8368 (mtt180) cc_final: 0.7631 (mtt180) REVERT: D 126 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6395 (mtm-85) REVERT: D 151 TYR cc_start: 0.3916 (OUTLIER) cc_final: 0.3053 (p90) REVERT: D 207 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7719 (tp) REVERT: D 222 ARG cc_start: 0.8306 (tpt-90) cc_final: 0.8081 (tpt-90) REVERT: D 271 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7873 (p) outliers start: 76 outliers final: 60 residues processed: 252 average time/residue: 0.0833 time to fit residues: 28.4702 Evaluate side-chains 273 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 207 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 82 VAL 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 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 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 55 SER Chi-restraints excluded: chain B residue 59 SER 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 121 MET 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 230 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 252 LEU 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 221 ILE Chi-restraints excluded: chain C residue 244 HIS 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 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 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 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 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 188 HIS C 244 HIS D 14 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.148613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128352 restraints weight = 13423.312| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.24 r_work: 0.3403 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8993 Z= 0.209 Angle : 0.667 13.848 12186 Z= 0.338 Chirality : 0.045 0.204 1381 Planarity : 0.005 0.067 1540 Dihedral : 4.591 24.356 1221 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.69 % Favored : 93.95 % Rotamer: Outliers : 7.39 % Allowed : 30.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.26), residues: 1107 helix: 1.06 (0.27), residues: 403 sheet: -0.06 (0.32), residues: 267 loop : -1.62 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 145 TYR 0.022 0.002 TYR D 202 PHE 0.030 0.002 PHE D 234 TRP 0.027 0.002 TRP D 15 HIS 0.016 0.002 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 8990) covalent geometry : angle 0.66723 (12180) SS BOND : bond 0.00679 ( 3) SS BOND : angle 1.07969 ( 6) hydrogen bonds : bond 0.03945 ( 411) hydrogen bonds : angle 4.78876 ( 1164) *********************** 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 289 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 218 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7845 (p) REVERT: A 107 ARG cc_start: 0.7682 (mtt90) cc_final: 0.7319 (mtt90) REVERT: A 226 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: A 301 ASP cc_start: 0.7280 (m-30) cc_final: 0.7072 (m-30) REVERT: A 338 VAL cc_start: 0.8676 (t) cc_final: 0.8346 (p) REVERT: B 97 TYR cc_start: 0.8163 (m-80) cc_final: 0.7733 (m-80) REVERT: B 178 MET cc_start: 0.8041 (mmm) cc_final: 0.7492 (mmm) REVERT: B 250 PHE cc_start: 0.8314 (m-80) cc_final: 0.7712 (m-80) REVERT: C 36 LEU cc_start: 0.8550 (mt) cc_final: 0.8322 (mp) REVERT: C 209 LYS cc_start: 0.8429 (ptpp) cc_final: 0.8172 (ptpp) REVERT: C 231 ASP cc_start: 0.7820 (t0) cc_final: 0.7526 (t0) REVERT: C 240 MET cc_start: 0.3494 (ttp) cc_final: 0.3144 (ttp) REVERT: C 247 MET cc_start: 0.7936 (mmm) cc_final: 0.7632 (mtt) REVERT: C 261 ASP cc_start: 0.7843 (t0) cc_final: 0.7486 (t0) REVERT: C 309 ASP cc_start: 0.7596 (m-30) cc_final: 0.7211 (m-30) REVERT: D 29 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7894 (mt) REVERT: D 126 ARG cc_start: 0.7054 (mtm-85) cc_final: 0.6391 (mtm-85) REVERT: D 151 TYR cc_start: 0.3903 (OUTLIER) cc_final: 0.2988 (p90) REVERT: D 207 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7769 (tp) REVERT: D 222 ARG cc_start: 0.8328 (tpt-90) cc_final: 0.8103 (tpt-90) outliers start: 71 outliers final: 57 residues processed: 264 average time/residue: 0.0989 time to fit residues: 34.7586 Evaluate side-chains 277 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER 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 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 59 SER 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 224 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 252 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 244 HIS 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 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 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 207 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 Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 76 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 108 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.150520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130196 restraints weight = 13325.792| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.22 r_work: 0.3427 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 0.032 8993 Z= 0.152 Angle : 0.645 9.650 12186 Z= 0.327 Chirality : 0.043 0.179 1381 Planarity : 0.005 0.067 1540 Dihedral : 4.504 25.433 1221 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.24 % Favored : 94.40 % Rotamer: Outliers : 7.60 % Allowed : 31.11 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.26), residues: 1107 helix: 1.09 (0.27), residues: 403 sheet: -0.10 (0.32), residues: 268 loop : -1.58 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 145 TYR 0.022 0.002 TYR D 202 PHE 0.018 0.002 PHE D 234 TRP 0.018 0.002 TRP A 180 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8990) covalent geometry : angle 0.64508 (12180) SS BOND : bond 0.00625 ( 3) SS BOND : angle 1.16964 ( 6) hydrogen bonds : bond 0.03684 ( 411) hydrogen bonds : angle 4.76638 ( 1164) *********************** 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 297 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 224 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7834 (p) REVERT: A 107 ARG cc_start: 0.7636 (mtt90) cc_final: 0.7262 (mtt90) REVERT: A 226 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: A 239 ASP cc_start: 0.8031 (p0) cc_final: 0.7600 (p0) REVERT: A 329 LEU cc_start: 0.7984 (tt) cc_final: 0.7532 (tt) REVERT: A 338 VAL cc_start: 0.8660 (t) cc_final: 0.8371 (p) REVERT: B 97 TYR cc_start: 0.8158 (m-80) cc_final: 0.7647 (m-80) REVERT: B 250 PHE cc_start: 0.8298 (m-80) cc_final: 0.7677 (m-80) REVERT: C 33 GLU cc_start: 0.7449 (tt0) cc_final: 0.7248 (tt0) REVERT: C 36 LEU cc_start: 0.8556 (mt) cc_final: 0.8292 (mp) REVERT: C 197 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7744 (mmtt) REVERT: C 231 ASP cc_start: 0.7829 (t0) cc_final: 0.7526 (t0) REVERT: C 240 MET cc_start: 0.3320 (ttp) cc_final: 0.2954 (ttp) REVERT: C 247 MET cc_start: 0.7877 (mmm) cc_final: 0.7572 (mtt) REVERT: C 261 ASP cc_start: 0.7734 (t0) cc_final: 0.7376 (t0) REVERT: C 309 ASP cc_start: 0.7601 (m-30) cc_final: 0.7198 (m-30) REVERT: D 29 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7851 (mt) REVERT: D 113 ARG cc_start: 0.8383 (mtt180) cc_final: 0.8094 (mtt180) REVERT: D 126 ARG cc_start: 0.7027 (mtm-85) cc_final: 0.6336 (mtm-85) REVERT: D 151 TYR cc_start: 0.3894 (OUTLIER) cc_final: 0.2977 (p90) REVERT: D 171 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5728 (mm) REVERT: D 206 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7312 (mtm180) REVERT: D 207 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7785 (tp) REVERT: D 222 ARG cc_start: 0.8318 (tpt-90) cc_final: 0.8093 (tpt-90) outliers start: 73 outliers final: 60 residues processed: 273 average time/residue: 0.0994 time to fit residues: 36.0056 Evaluate side-chains 288 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER 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 351 ASN Chi-restraints excluded: chain B residue 59 SER 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 177 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 252 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 244 HIS 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 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 171 LEU 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 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 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.125757 restraints weight = 13374.884| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.18 r_work: 0.3415 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8993 Z= 0.175 Angle : 0.667 9.638 12186 Z= 0.338 Chirality : 0.044 0.186 1381 Planarity : 0.005 0.066 1540 Dihedral : 4.581 24.259 1221 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.96 % Favored : 93.68 % Rotamer: Outliers : 7.18 % Allowed : 31.53 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.26), residues: 1107 helix: 1.04 (0.27), residues: 403 sheet: -0.11 (0.32), residues: 257 loop : -1.65 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 145 TYR 0.021 0.002 TYR D 202 PHE 0.051 0.002 PHE C 334 TRP 0.018 0.002 TRP A 180 HIS 0.009 0.001 HIS C 244 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8990) covalent geometry : angle 0.66612 (12180) SS BOND : bond 0.00699 ( 3) SS BOND : angle 1.27913 ( 6) hydrogen bonds : bond 0.03792 ( 411) hydrogen bonds : angle 4.82443 ( 1164) ********************** 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 287 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 218 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7334 (mmt180) REVERT: A 98 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7828 (p) REVERT: A 107 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7241 (mtt90) REVERT: A 239 ASP cc_start: 0.7999 (p0) cc_final: 0.7623 (p0) REVERT: A 329 LEU cc_start: 0.7973 (tt) cc_final: 0.7556 (tt) REVERT: A 338 VAL cc_start: 0.8665 (t) cc_final: 0.8365 (p) REVERT: B 97 TYR cc_start: 0.8201 (m-80) cc_final: 0.7756 (m-80) REVERT: B 202 SER cc_start: 0.7017 (t) cc_final: 0.6782 (p) REVERT: B 250 PHE cc_start: 0.8280 (m-80) cc_final: 0.7618 (m-80) REVERT: C 33 GLU cc_start: 0.7499 (tt0) cc_final: 0.7231 (tt0) REVERT: C 36 LEU cc_start: 0.8532 (mt) cc_final: 0.8283 (mp) REVERT: C 186 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6534 (mt-10) REVERT: C 231 ASP cc_start: 0.7876 (t0) cc_final: 0.7577 (t0) REVERT: C 240 MET cc_start: 0.3703 (ttp) cc_final: 0.3340 (ttp) REVERT: C 247 MET cc_start: 0.7891 (mmm) cc_final: 0.7577 (mtt) REVERT: C 261 ASP cc_start: 0.7680 (t0) cc_final: 0.7312 (t0) REVERT: C 309 ASP cc_start: 0.7543 (m-30) cc_final: 0.7145 (m-30) REVERT: C 334 PHE cc_start: 0.8006 (t80) cc_final: 0.7611 (t80) REVERT: D 29 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7831 (mt) REVERT: D 113 ARG cc_start: 0.8402 (mtt180) cc_final: 0.8108 (mtt180) REVERT: D 151 TYR cc_start: 0.3938 (OUTLIER) cc_final: 0.2980 (p90) REVERT: D 171 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5829 (mm) REVERT: D 206 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7330 (mtm180) REVERT: D 207 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7863 (tp) REVERT: D 222 ARG cc_start: 0.8329 (tpt-90) cc_final: 0.8103 (tpt-90) outliers start: 69 outliers final: 59 residues processed: 267 average time/residue: 0.0908 time to fit residues: 32.3078 Evaluate side-chains 284 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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 82 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER 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 59 SER 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 177 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 252 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 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 171 LEU 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 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 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 108 optimal weight: 0.0040 chunk 68 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125850 restraints weight = 13264.889| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.16 r_work: 0.3412 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 83 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 84 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8993 Z= 0.159 Angle : 0.656 11.924 12186 Z= 0.331 Chirality : 0.043 0.176 1381 Planarity : 0.005 0.066 1540 Dihedral : 4.544 24.246 1221 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.96 % Favored : 93.68 % Rotamer: Outliers : 7.60 % Allowed : 31.01 % Favored : 61.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.26), residues: 1107 helix: 1.08 (0.27), residues: 403 sheet: -0.14 (0.32), residues: 263 loop : -1.61 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 145 TYR 0.020 0.002 TYR D 202 PHE 0.045 0.002 PHE C 334 TRP 0.018 0.002 TRP A 180 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8990) covalent geometry : angle 0.65558 (12180) SS BOND : bond 0.00735 ( 3) SS BOND : angle 1.40678 ( 6) hydrogen bonds : bond 0.03639 ( 411) hydrogen bonds : angle 4.79823 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.90 seconds wall clock time: 38 minutes 27.97 seconds (2307.97 seconds total)