Starting phenix.real_space_refine on Thu Mar 13 11:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j21_35941/03_2025/8j21_35941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j21_35941/03_2025/8j21_35941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j21_35941/03_2025/8j21_35941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j21_35941/03_2025/8j21_35941.map" model { file = "/net/cci-nas-00/data/ceres_data/8j21_35941/03_2025/8j21_35941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j21_35941/03_2025/8j21_35941.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5612 2.51 5 N 1495 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1775 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2188 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BUA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.72, per 1000 atoms: 0.65 Number of scatterers: 8803 At special positions: 0 Unit cell: (114.4, 109.2, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1638 8.00 N 1495 7.00 C 5612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 169 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 14 through 36 removed outlier: 4.371A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.510A pdb=" N ILE A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 70 removed outlier: 3.761A pdb=" N SER B 69 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 94 removed outlier: 3.919A pdb=" N GLY B 94 " --> pdb=" O SER B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.665A pdb=" N THR B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 removed outlier: 3.731A pdb=" N SER C 6 " --> pdb=" O CYS C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.536A pdb=" N GLU C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.764A pdb=" N ILE C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.752A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.564A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.794A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.940A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 14 through 46 removed outlier: 4.126A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) Proline residue: D 30 - end of helix Processing helix chain 'D' and resid 48 through 73 removed outlier: 3.828A pdb=" N VAL D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Proline residue: D 69 - end of helix Processing helix chain 'D' and resid 86 through 119 removed outlier: 4.133A pdb=" N LEU D 90 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 128 through 154 removed outlier: 3.686A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 151 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 192 removed outlier: 3.540A pdb=" N ILE D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Proline residue: D 183 - end of helix Processing helix chain 'D' and resid 193 through 213 removed outlier: 4.298A pdb=" N ARG D 206 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 207 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL D 208 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 213 " --> pdb=" O TRP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 252 removed outlier: 3.514A pdb=" N ARG D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Proline residue: D 240 - end of helix removed outlier: 3.594A pdb=" N TYR D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 278 removed outlier: 3.781A pdb=" N LEU D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Proline residue: D 273 - end of helix Processing helix chain 'D' and resid 280 through 291 Processing helix chain 'E' and resid 7 through 22 removed outlier: 3.609A pdb=" N GLN E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.084A pdb=" N LEU A 90 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 103 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 92 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 removed outlier: 3.851A pdb=" N GLY A 126 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY A 127 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN A 136 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL A 146 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.151A pdb=" N CYS A 160 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 169 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP A 181 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLN A 187 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.555A pdb=" N PHE A 210 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 223 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.426A pdb=" N GLY A 255 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 243 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA A 253 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 256 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS A 261 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR A 274 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 263 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 289 removed outlier: 5.099A pdb=" N SER A 286 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A 299 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS A 305 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL A 318 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL A 307 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 41 through 45 Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.575A pdb=" N ALA B 87 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ARG B 76 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TRP B 85 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 185 removed outlier: 6.514A pdb=" N LEU B 212 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR B 228 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP B 214 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 196 through 200 removed outlier: 6.357A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.44 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2840 1.35 - 1.47: 2243 1.47 - 1.59: 3825 1.59 - 1.71: 0 1.71 - 1.83: 82 Bond restraints: 8990 Sorted by residual: bond pdb=" CB MET A 72 " pdb=" CG MET A 72 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB GLN B 269 " pdb=" CG GLN B 269 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C TYR B 273 " pdb=" N PRO B 274 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.08e+00 bond pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 1.803 1.828 -0.025 2.50e-02 1.60e+03 9.75e-01 bond pdb=" CA TRP D 81 " pdb=" CB TRP D 81 " ideal model delta sigma weight residual 1.530 1.516 0.013 1.38e-02 5.25e+03 9.33e-01 ... (remaining 8985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 12059 2.34 - 4.69: 93 4.69 - 7.03: 17 7.03 - 9.37: 5 9.37 - 11.72: 6 Bond angle restraints: 12180 Sorted by residual: angle pdb=" C ALA A 71 " pdb=" N MET A 72 " pdb=" CA MET A 72 " ideal model delta sigma weight residual 122.08 132.69 -10.61 1.84e+00 2.95e-01 3.33e+01 angle pdb=" CA MET A 72 " pdb=" CB MET A 72 " pdb=" CG MET A 72 " ideal model delta sigma weight residual 114.10 124.74 -10.64 2.00e+00 2.50e-01 2.83e+01 angle pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta sigma weight residual 121.80 132.93 -11.13 2.44e+00 1.68e-01 2.08e+01 angle pdb=" CB MET A 72 " pdb=" CG MET A 72 " pdb=" SD MET A 72 " ideal model delta sigma weight residual 112.70 124.42 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CB MET D 79 " pdb=" CG MET D 79 " pdb=" SD MET D 79 " ideal model delta sigma weight residual 112.70 122.13 -9.43 3.00e+00 1.11e-01 9.88e+00 ... (remaining 12175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4438 17.78 - 35.56: 649 35.56 - 53.34: 195 53.34 - 71.13: 27 71.13 - 88.91: 5 Dihedral angle restraints: 5314 sinusoidal: 2064 harmonic: 3250 Sorted by residual: dihedral pdb=" CA ARG A 161 " pdb=" C ARG A 161 " pdb=" N PHE A 162 " pdb=" CA PHE A 162 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 246 " pdb=" C PHE A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta harmonic sigma weight residual 180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA GLU B 272 " pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1035 0.042 - 0.083: 264 0.083 - 0.125: 76 0.125 - 0.166: 5 0.166 - 0.208: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA TYR B 273 " pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CB TYR B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 284 " pdb=" N ILE A 284 " pdb=" C ILE A 284 " pdb=" CB ILE A 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CG LEU D 181 " pdb=" CB LEU D 181 " pdb=" CD1 LEU D 181 " pdb=" CD2 LEU D 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1378 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 273 " -0.070 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO B 274 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 71 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C ALA A 71 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA A 71 " 0.017 2.00e-02 2.50e+03 pdb=" N MET A 72 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 140 " 0.013 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" CG TRP D 140 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP D 140 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 140 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 140 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 140 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 140 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 140 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 140 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 140 " 0.002 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 255 2.69 - 3.24: 8335 3.24 - 3.80: 13973 3.80 - 4.35: 17941 4.35 - 4.90: 30022 Nonbonded interactions: 70526 Sorted by model distance: nonbonded pdb=" O ILE A 69 " pdb=" OG SER A 327 " model vdw 2.140 3.040 nonbonded pdb=" O LEU D 263 " pdb=" OG1 THR D 266 " model vdw 2.172 3.040 nonbonded pdb=" OH TYR B 211 " pdb=" OG SER C 6 " model vdw 2.185 3.040 nonbonded pdb=" OG SER A 342 " pdb=" OD1 ASP A 344 " model vdw 2.193 3.040 nonbonded pdb=" O GLN A 86 " pdb=" OG SER A 109 " model vdw 2.220 3.040 ... (remaining 70521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.920 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- 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 8990 Z= 0.146 Angle : 0.618 11.718 12180 Z= 0.310 Chirality : 0.040 0.208 1381 Planarity : 0.004 0.106 1540 Dihedral : 17.794 88.907 3213 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.70 % Favored : 94.76 % Rotamer: Outliers : 0.42 % Allowed : 36.11 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.25), residues: 1107 helix: 1.33 (0.27), residues: 388 sheet: 0.68 (0.33), residues: 245 loop : -1.38 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 140 HIS 0.004 0.001 HIS D 245 PHE 0.016 0.001 PHE B 241 TYR 0.019 0.001 TYR D 276 ARG 0.005 0.000 ARG A 145 *********************** 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 : 0.909 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: 0.2515 time to fit residues: 72.6551 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 : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain D residue 274 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN D 14 HIS E 18 GLN E 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127705 restraints weight = 13342.354| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.15 r_work: 0.3469 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 8990 Z= 0.375 Angle : 0.701 12.163 12180 Z= 0.359 Chirality : 0.047 0.298 1381 Planarity : 0.005 0.084 1540 Dihedral : 4.865 43.412 1225 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.23 % Favored : 93.32 % Rotamer: Outliers : 6.97 % Allowed : 29.97 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1107 helix: 1.03 (0.26), residues: 405 sheet: 0.23 (0.32), residues: 262 loop : -1.52 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.009 0.002 HIS D 245 PHE 0.016 0.002 PHE A 210 TYR 0.018 0.002 TYR A 70 ARG 0.009 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7399 (mtt90) REVERT: A 266 LEU cc_start: 0.7913 (mt) cc_final: 0.7663 (mt) REVERT: A 288 SER cc_start: 0.8461 (p) cc_final: 0.8221 (m) REVERT: A 338 VAL cc_start: 0.8622 (t) cc_final: 0.8316 (p) REVERT: A 346 PHE cc_start: 0.7959 (m-80) cc_final: 0.7692 (m-80) REVERT: B 97 TYR cc_start: 0.8094 (m-80) cc_final: 0.7742 (m-80) REVERT: B 107 THR cc_start: 0.7785 (t) cc_final: 0.7572 (m) REVERT: C 186 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6311 (mt-10) REVERT: C 197 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7890 (mmtm) REVERT: C 240 MET cc_start: 0.3661 (ttp) cc_final: 0.3249 (ttp) REVERT: C 243 MET cc_start: 0.7569 (ttm) cc_final: 0.7340 (ttm) REVERT: D 29 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7971 (mt) REVERT: D 46 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.6335 (ptt90) REVERT: D 151 TYR cc_start: 0.3549 (p90) cc_final: 0.2930 (p90) outliers start: 67 outliers final: 45 residues processed: 278 average time/residue: 0.2366 time to fit residues: 87.2319 Evaluate side-chains 267 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 220 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN B 180 GLN D 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.152341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.132114 restraints weight = 13413.535| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.22 r_work: 0.3431 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8990 Z= 0.238 Angle : 0.622 11.427 12180 Z= 0.315 Chirality : 0.043 0.204 1381 Planarity : 0.004 0.062 1540 Dihedral : 4.460 23.260 1221 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.06 % Favored : 94.58 % Rotamer: Outliers : 7.18 % Allowed : 30.39 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1107 helix: 1.03 (0.26), residues: 407 sheet: 0.26 (0.32), residues: 259 loop : -1.63 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.009 0.001 HIS D 14 PHE 0.024 0.002 PHE C 189 TYR 0.015 0.001 TYR B 273 ARG 0.007 0.000 ARG A 262 *********************** 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 305 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 236 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7731 (p) REVERT: A 107 ARG cc_start: 0.7638 (mtt90) cc_final: 0.7259 (mtt90) REVERT: A 122 TYR cc_start: 0.8240 (m-80) cc_final: 0.7660 (m-80) REVERT: A 239 ASP cc_start: 0.8048 (p0) cc_final: 0.7624 (p0) REVERT: A 266 LEU cc_start: 0.7790 (mt) cc_final: 0.7529 (mt) REVERT: A 288 SER cc_start: 0.8462 (p) cc_final: 0.8211 (m) REVERT: A 338 VAL cc_start: 0.8651 (t) cc_final: 0.8330 (p) REVERT: B 107 THR cc_start: 0.7869 (OUTLIER) cc_final: 0.7665 (m) REVERT: B 203 LEU cc_start: 0.7908 (mt) cc_final: 0.7691 (mp) REVERT: C 35 LYS cc_start: 0.8380 (mttp) cc_final: 0.8110 (mtmm) REVERT: C 231 ASP cc_start: 0.7759 (t0) cc_final: 0.7473 (t0) REVERT: C 240 MET cc_start: 0.3632 (ttp) cc_final: 0.3158 (ttp) REVERT: C 243 MET cc_start: 0.7502 (ttm) cc_final: 0.7276 (ttm) REVERT: D 29 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7914 (mt) REVERT: D 46 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.6270 (ptt90) REVERT: D 109 VAL cc_start: 0.8287 (m) cc_final: 0.7876 (p) REVERT: D 151 TYR cc_start: 0.3659 (p90) cc_final: 0.2983 (p90) outliers start: 69 outliers final: 43 residues processed: 275 average time/residue: 0.2497 time to fit residues: 90.7611 Evaluate side-chains 275 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN C 331 ASN D 14 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.148334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128107 restraints weight = 13308.054| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.22 r_work: 0.3403 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8990 Z= 0.291 Angle : 0.643 12.472 12180 Z= 0.328 Chirality : 0.044 0.201 1381 Planarity : 0.005 0.067 1540 Dihedral : 4.648 25.337 1221 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.69 % Favored : 93.95 % Rotamer: Outliers : 8.53 % Allowed : 29.24 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1107 helix: 0.99 (0.26), residues: 403 sheet: 0.12 (0.32), residues: 257 loop : -1.73 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 180 HIS 0.009 0.001 HIS D 14 PHE 0.024 0.002 PHE D 234 TYR 0.016 0.002 TYR A 70 ARG 0.009 0.001 ARG A 63 *********************** 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 306 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 224 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ARG cc_start: 0.7573 (mtt90) cc_final: 0.7214 (mtt90) REVERT: A 122 TYR cc_start: 0.8270 (m-80) cc_final: 0.7799 (m-80) REVERT: A 182 ILE cc_start: 0.7919 (mm) cc_final: 0.7716 (mm) REVERT: A 239 ASP cc_start: 0.8050 (p0) cc_final: 0.7594 (p0) REVERT: A 266 LEU cc_start: 0.7801 (mt) cc_final: 0.7560 (mt) REVERT: A 301 ASP cc_start: 0.7241 (m-30) cc_final: 0.7037 (m-30) REVERT: A 338 VAL cc_start: 0.8652 (t) cc_final: 0.8331 (p) REVERT: B 107 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7615 (m) REVERT: B 203 LEU cc_start: 0.7897 (mt) cc_final: 0.7680 (mp) REVERT: B 250 PHE cc_start: 0.8345 (m-80) cc_final: 0.7680 (m-80) REVERT: C 35 LYS cc_start: 0.8370 (mttp) cc_final: 0.8041 (mtmm) REVERT: C 36 LEU cc_start: 0.8580 (mt) cc_final: 0.8311 (mp) REVERT: C 231 ASP cc_start: 0.7895 (t0) cc_final: 0.7612 (t0) REVERT: C 240 MET cc_start: 0.3645 (ttp) cc_final: 0.3208 (ttp) REVERT: C 261 ASP cc_start: 0.7832 (t0) cc_final: 0.7476 (t0) REVERT: C 309 ASP cc_start: 0.7649 (m-30) cc_final: 0.7280 (m-30) REVERT: D 29 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7895 (mt) REVERT: D 46 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6306 (ptt90) REVERT: D 109 VAL cc_start: 0.8266 (m) cc_final: 0.7868 (p) REVERT: D 151 TYR cc_start: 0.3778 (p90) cc_final: 0.2956 (p90) outliers start: 82 outliers final: 51 residues processed: 277 average time/residue: 0.2855 time to fit residues: 105.3269 Evaluate side-chains 279 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 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 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 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 201 SER Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN D 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.148133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.127983 restraints weight = 13314.224| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.19 r_work: 0.3401 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8990 Z= 0.295 Angle : 0.654 13.542 12180 Z= 0.332 Chirality : 0.044 0.188 1381 Planarity : 0.005 0.072 1540 Dihedral : 4.726 30.721 1221 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.87 % Favored : 93.77 % Rotamer: Outliers : 7.91 % Allowed : 29.97 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1107 helix: 0.98 (0.27), residues: 403 sheet: -0.12 (0.32), residues: 263 loop : -1.73 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 180 HIS 0.005 0.001 HIS D 14 PHE 0.026 0.002 PHE D 234 TYR 0.018 0.002 TYR D 202 ARG 0.006 0.000 ARG A 63 *********************** 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 305 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 229 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7700 (p) REVERT: A 107 ARG cc_start: 0.7577 (mtt90) cc_final: 0.7215 (mtt90) REVERT: A 182 ILE cc_start: 0.7937 (mm) cc_final: 0.7704 (mm) REVERT: A 226 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: A 239 ASP cc_start: 0.8056 (p0) cc_final: 0.7742 (p0) REVERT: A 266 LEU cc_start: 0.7721 (mt) cc_final: 0.7483 (mt) REVERT: A 301 ASP cc_start: 0.7181 (m-30) cc_final: 0.6936 (m-30) REVERT: A 338 VAL cc_start: 0.8685 (t) cc_final: 0.8371 (p) REVERT: B 97 TYR cc_start: 0.8146 (m-80) cc_final: 0.7672 (m-80) REVERT: B 202 SER cc_start: 0.7175 (t) cc_final: 0.6928 (p) REVERT: C 35 LYS cc_start: 0.8378 (mttp) cc_final: 0.8068 (mtmm) REVERT: C 36 LEU cc_start: 0.8577 (mt) cc_final: 0.8182 (mt) REVERT: C 186 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6497 (mt-10) REVERT: C 231 ASP cc_start: 0.7935 (t0) cc_final: 0.7665 (t0) REVERT: C 240 MET cc_start: 0.3705 (ttp) cc_final: 0.3366 (ttp) REVERT: C 247 MET cc_start: 0.8075 (mmm) cc_final: 0.7805 (mtt) REVERT: C 261 ASP cc_start: 0.7842 (t0) cc_final: 0.7452 (t0) REVERT: C 309 ASP cc_start: 0.7613 (m-30) cc_final: 0.7219 (m-30) REVERT: D 15 TRP cc_start: 0.6851 (OUTLIER) cc_final: 0.6350 (p90) REVERT: D 29 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7895 (mt) REVERT: D 46 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6396 (ptt90) REVERT: D 126 ARG cc_start: 0.6965 (mtm-85) cc_final: 0.6409 (mtm-85) REVERT: D 151 TYR cc_start: 0.3831 (OUTLIER) cc_final: 0.2937 (p90) outliers start: 76 outliers final: 57 residues processed: 277 average time/residue: 0.2554 time to fit residues: 93.0378 Evaluate side-chains 287 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.147726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127258 restraints weight = 13137.414| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.17 r_work: 0.3418 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8990 Z= 0.256 Angle : 0.646 13.634 12180 Z= 0.328 Chirality : 0.043 0.175 1381 Planarity : 0.005 0.070 1540 Dihedral : 4.663 30.014 1221 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.60 % Favored : 94.04 % Rotamer: Outliers : 8.12 % Allowed : 29.55 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1107 helix: 1.01 (0.27), residues: 403 sheet: -0.18 (0.32), residues: 263 loop : -1.72 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 180 HIS 0.014 0.001 HIS D 14 PHE 0.027 0.002 PHE D 234 TYR 0.018 0.002 TYR D 202 ARG 0.005 0.000 ARG D 206 *********************** 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 300 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 222 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7717 (p) REVERT: A 107 ARG cc_start: 0.7598 (mtt90) cc_final: 0.7215 (mtt90) REVERT: A 161 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7794 (mmt180) REVERT: A 182 ILE cc_start: 0.8009 (mm) cc_final: 0.7786 (mm) REVERT: A 226 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: A 239 ASP cc_start: 0.8066 (p0) cc_final: 0.7647 (p0) REVERT: A 266 LEU cc_start: 0.7734 (mt) cc_final: 0.7486 (mt) REVERT: A 288 SER cc_start: 0.8407 (p) cc_final: 0.8130 (m) REVERT: A 301 ASP cc_start: 0.7165 (m-30) cc_final: 0.6958 (m-30) REVERT: A 315 ARG cc_start: 0.7983 (ttm170) cc_final: 0.7427 (ttm170) REVERT: A 338 VAL cc_start: 0.8684 (t) cc_final: 0.8371 (p) REVERT: B 70 PHE cc_start: 0.8312 (m-80) cc_final: 0.8054 (m-80) REVERT: B 97 TYR cc_start: 0.8184 (m-80) cc_final: 0.7735 (m-80) REVERT: B 202 SER cc_start: 0.7134 (t) cc_final: 0.6908 (p) REVERT: B 227 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8431 (pt) REVERT: C 35 LYS cc_start: 0.8393 (mttp) cc_final: 0.8074 (mtmm) REVERT: C 36 LEU cc_start: 0.8569 (mt) cc_final: 0.8317 (mp) REVERT: C 186 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6660 (mt-10) REVERT: C 231 ASP cc_start: 0.7948 (t0) cc_final: 0.7671 (t0) REVERT: C 240 MET cc_start: 0.3758 (ttp) cc_final: 0.3435 (ttp) REVERT: C 247 MET cc_start: 0.8057 (mmm) cc_final: 0.7786 (mtt) REVERT: C 261 ASP cc_start: 0.7798 (t0) cc_final: 0.7384 (t0) REVERT: C 309 ASP cc_start: 0.7570 (m-30) cc_final: 0.7198 (m-30) REVERT: D 15 TRP cc_start: 0.6889 (OUTLIER) cc_final: 0.6217 (p90) REVERT: D 29 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7870 (mt) REVERT: D 46 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6413 (ptt90) REVERT: D 126 ARG cc_start: 0.6943 (mtm-85) cc_final: 0.6399 (mtm-85) REVERT: D 151 TYR cc_start: 0.3932 (OUTLIER) cc_final: 0.3010 (p90) REVERT: D 207 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7552 (tp) outliers start: 78 outliers final: 58 residues processed: 276 average time/residue: 0.2496 time to fit residues: 90.5148 Evaluate side-chains 285 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 219 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 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 55 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 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 48 optimal weight: 0.0370 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN 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 = 0.3839 r_free = 0.3839 target = 0.148279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.127889 restraints weight = 13328.779| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.19 r_work: 0.3432 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 74 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8990 Z= 0.198 Angle : 0.619 13.911 12180 Z= 0.312 Chirality : 0.042 0.181 1381 Planarity : 0.004 0.072 1540 Dihedral : 4.497 27.848 1221 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 7.70 % Allowed : 30.39 % Favored : 61.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.26), residues: 1107 helix: 1.12 (0.27), residues: 403 sheet: -0.04 (0.32), residues: 258 loop : -1.71 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.009 0.001 HIS D 14 PHE 0.028 0.002 PHE D 234 TYR 0.015 0.001 TYR A 70 ARG 0.004 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 223 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.6734 (p0) REVERT: A 98 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7849 (p) REVERT: A 107 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7158 (mtt90) REVERT: A 226 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: A 239 ASP cc_start: 0.7970 (p0) cc_final: 0.7522 (p0) REVERT: A 288 SER cc_start: 0.8429 (p) cc_final: 0.8134 (m) REVERT: A 301 ASP cc_start: 0.7133 (m-30) cc_final: 0.6894 (m-30) REVERT: A 315 ARG cc_start: 0.7907 (ttm170) cc_final: 0.7399 (ttm170) REVERT: A 338 VAL cc_start: 0.8682 (t) cc_final: 0.8377 (p) REVERT: B 70 PHE cc_start: 0.8312 (m-80) cc_final: 0.8002 (m-80) REVERT: B 202 SER cc_start: 0.7060 (t) cc_final: 0.6841 (p) REVERT: B 227 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8408 (pt) REVERT: C 35 LYS cc_start: 0.8438 (mttp) cc_final: 0.8168 (mtmm) REVERT: C 197 LYS cc_start: 0.7938 (mttm) cc_final: 0.7671 (mmtt) REVERT: C 231 ASP cc_start: 0.7962 (t0) cc_final: 0.7685 (t0) REVERT: C 240 MET cc_start: 0.3811 (ttp) cc_final: 0.3520 (ttp) REVERT: C 247 MET cc_start: 0.8026 (mmm) cc_final: 0.7650 (mtt) REVERT: C 261 ASP cc_start: 0.7724 (t0) cc_final: 0.7304 (t0) REVERT: C 309 ASP cc_start: 0.7596 (m-30) cc_final: 0.7190 (m-30) REVERT: D 29 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7860 (mt) REVERT: D 113 ARG cc_start: 0.8372 (mtt180) cc_final: 0.8077 (mtt180) REVERT: D 126 ARG cc_start: 0.6941 (mtm-85) cc_final: 0.6330 (mtm-85) REVERT: D 151 TYR cc_start: 0.4080 (OUTLIER) cc_final: 0.3172 (p90) outliers start: 74 outliers final: 54 residues processed: 267 average time/residue: 0.2430 time to fit residues: 85.5429 Evaluate side-chains 279 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 219 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 TRP Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 14 HIS Chi-restraints excluded: chain D residue 24 THR 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 71 ARG Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN 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 = 0.3815 r_free = 0.3815 target = 0.146391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126324 restraints weight = 13491.507| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.18 r_work: 0.3395 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8990 Z= 0.264 Angle : 0.636 10.141 12180 Z= 0.324 Chirality : 0.044 0.218 1381 Planarity : 0.005 0.070 1540 Dihedral : 4.591 28.127 1221 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.60 % Favored : 94.04 % Rotamer: Outliers : 8.01 % Allowed : 30.39 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 1107 helix: 1.08 (0.27), residues: 403 sheet: -0.18 (0.32), residues: 262 loop : -1.68 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 180 HIS 0.019 0.002 HIS D 14 PHE 0.031 0.002 PHE C 334 TYR 0.020 0.002 TYR D 202 ARG 0.013 0.000 ARG A 145 *********************** 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 302 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 225 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7770 (p) REVERT: A 107 ARG cc_start: 0.7572 (mtt90) cc_final: 0.7179 (mtt90) REVERT: A 182 ILE cc_start: 0.7876 (mm) cc_final: 0.7620 (mm) REVERT: A 226 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: A 239 ASP cc_start: 0.8021 (p0) cc_final: 0.7612 (p0) REVERT: A 288 SER cc_start: 0.8495 (p) cc_final: 0.7930 (m) REVERT: A 301 ASP cc_start: 0.7181 (m-30) cc_final: 0.6959 (m-30) REVERT: A 315 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7407 (ttm170) REVERT: A 338 VAL cc_start: 0.8674 (t) cc_final: 0.8375 (p) REVERT: B 202 SER cc_start: 0.7087 (t) cc_final: 0.6866 (p) REVERT: B 227 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8444 (pt) REVERT: C 35 LYS cc_start: 0.8397 (mttp) cc_final: 0.8095 (mtmm) REVERT: C 36 LEU cc_start: 0.8511 (mt) cc_final: 0.8096 (mt) REVERT: C 197 LYS cc_start: 0.8045 (mttm) cc_final: 0.7663 (mmtt) REVERT: C 231 ASP cc_start: 0.7952 (t0) cc_final: 0.7691 (t0) REVERT: C 240 MET cc_start: 0.3836 (ttp) cc_final: 0.3560 (ttp) REVERT: C 247 MET cc_start: 0.8120 (mmm) cc_final: 0.7783 (mtt) REVERT: C 261 ASP cc_start: 0.7714 (t0) cc_final: 0.7287 (t0) REVERT: C 309 ASP cc_start: 0.7517 (m-30) cc_final: 0.7106 (m-30) REVERT: D 15 TRP cc_start: 0.6910 (OUTLIER) cc_final: 0.6270 (p90) REVERT: D 29 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7859 (mt) REVERT: D 126 ARG cc_start: 0.6943 (mtm-85) cc_final: 0.6331 (mtm-85) REVERT: D 151 TYR cc_start: 0.3955 (OUTLIER) cc_final: 0.2996 (p90) REVERT: D 207 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7795 (tp) outliers start: 77 outliers final: 59 residues processed: 275 average time/residue: 0.2403 time to fit residues: 87.3947 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 : 0.971 ------------------------------------------------------------------------------- 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 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 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 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 HIS D 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.147946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127721 restraints weight = 13364.154| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.22 r_work: 0.3376 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 87 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8990 Z= 0.276 Angle : 0.649 9.544 12180 Z= 0.333 Chirality : 0.044 0.186 1381 Planarity : 0.005 0.071 1540 Dihedral : 4.718 28.197 1221 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.87 % Favored : 93.77 % Rotamer: Outliers : 8.01 % Allowed : 30.18 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1107 helix: 1.02 (0.27), residues: 403 sheet: -0.29 (0.32), residues: 262 loop : -1.73 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 180 HIS 0.005 0.001 HIS C 188 PHE 0.023 0.002 PHE C 334 TYR 0.018 0.002 TYR D 202 ARG 0.014 0.001 ARG A 145 *********************** 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 301 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 224 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7259 (p0) REVERT: A 98 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7826 (p) REVERT: A 107 ARG cc_start: 0.7546 (mtt90) cc_final: 0.7166 (mtt90) REVERT: A 122 TYR cc_start: 0.8370 (m-80) cc_final: 0.7690 (m-80) REVERT: A 226 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: A 239 ASP cc_start: 0.8033 (p0) cc_final: 0.7593 (p0) REVERT: A 250 ASN cc_start: 0.7942 (m-40) cc_final: 0.7617 (m110) REVERT: A 273 MET cc_start: 0.7617 (ppp) cc_final: 0.7213 (ppp) REVERT: A 301 ASP cc_start: 0.7287 (m-30) cc_final: 0.6988 (m-30) REVERT: A 338 VAL cc_start: 0.8683 (t) cc_final: 0.8367 (p) REVERT: B 202 SER cc_start: 0.7118 (t) cc_final: 0.6901 (p) REVERT: C 35 LYS cc_start: 0.8387 (mttp) cc_final: 0.8082 (mtmm) REVERT: C 36 LEU cc_start: 0.8555 (mt) cc_final: 0.8179 (mt) REVERT: C 198 MET cc_start: 0.8162 (mtp) cc_final: 0.7926 (ttm) REVERT: C 231 ASP cc_start: 0.7964 (t0) cc_final: 0.7675 (t0) REVERT: C 240 MET cc_start: 0.3843 (ttp) cc_final: 0.3603 (ttp) REVERT: C 247 MET cc_start: 0.8114 (mmm) cc_final: 0.7764 (mtt) REVERT: C 261 ASP cc_start: 0.7811 (t0) cc_final: 0.7392 (t0) REVERT: C 309 ASP cc_start: 0.7603 (m-30) cc_final: 0.7190 (m-30) REVERT: D 15 TRP cc_start: 0.6916 (OUTLIER) cc_final: 0.6348 (p90) REVERT: D 29 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7834 (mt) REVERT: D 112 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: D 126 ARG cc_start: 0.6932 (mtm-85) cc_final: 0.6340 (mtm-85) REVERT: D 151 TYR cc_start: 0.3938 (OUTLIER) cc_final: 0.2969 (p90) REVERT: D 171 LEU cc_start: 0.5994 (OUTLIER) cc_final: 0.5774 (mm) REVERT: D 207 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7921 (tp) outliers start: 77 outliers final: 61 residues processed: 275 average time/residue: 0.2443 time to fit residues: 88.9531 Evaluate side-chains 293 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU 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 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.146555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126729 restraints weight = 13368.717| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.20 r_work: 0.3384 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8990 Z= 0.256 Angle : 0.651 10.769 12180 Z= 0.331 Chirality : 0.044 0.175 1381 Planarity : 0.005 0.069 1540 Dihedral : 4.712 26.166 1221 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.96 % Favored : 93.68 % Rotamer: Outliers : 7.39 % Allowed : 31.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1107 helix: 1.06 (0.27), residues: 403 sheet: -0.25 (0.32), residues: 260 loop : -1.76 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 180 HIS 0.005 0.001 HIS D 245 PHE 0.034 0.002 PHE B 277 TYR 0.021 0.002 TYR A 70 ARG 0.008 0.000 ARG A 145 ********************** 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 302 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 231 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7207 (p0) REVERT: A 98 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7820 (p) REVERT: A 107 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7097 (mtt90) REVERT: A 122 TYR cc_start: 0.8355 (m-80) cc_final: 0.7797 (m-80) REVERT: A 161 ARG cc_start: 0.8037 (mmt180) cc_final: 0.7823 (mmt180) REVERT: A 226 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: A 239 ASP cc_start: 0.8005 (p0) cc_final: 0.7576 (p0) REVERT: A 250 ASN cc_start: 0.7915 (m-40) cc_final: 0.7591 (m110) REVERT: A 301 ASP cc_start: 0.7242 (m-30) cc_final: 0.6931 (m-30) REVERT: A 338 VAL cc_start: 0.8682 (t) cc_final: 0.8345 (p) REVERT: B 202 SER cc_start: 0.7048 (t) cc_final: 0.6825 (p) REVERT: C 35 LYS cc_start: 0.8373 (mttp) cc_final: 0.8102 (mtmm) REVERT: C 197 LYS cc_start: 0.8106 (mttm) cc_final: 0.7737 (mmtt) REVERT: C 231 ASP cc_start: 0.7984 (t0) cc_final: 0.7675 (t0) REVERT: C 240 MET cc_start: 0.3900 (ttp) cc_final: 0.3683 (ttp) REVERT: C 245 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7338 (tm-30) REVERT: C 261 ASP cc_start: 0.7773 (t0) cc_final: 0.7357 (t0) REVERT: C 309 ASP cc_start: 0.7598 (m-30) cc_final: 0.7202 (m-30) REVERT: D 15 TRP cc_start: 0.6932 (OUTLIER) cc_final: 0.6391 (p90) REVERT: D 29 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7801 (mt) REVERT: D 112 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: D 151 TYR cc_start: 0.3852 (OUTLIER) cc_final: 0.2880 (p90) REVERT: D 207 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7931 (tp) REVERT: D 258 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.7569 (ttm170) outliers start: 71 outliers final: 59 residues processed: 276 average time/residue: 0.2541 time to fit residues: 90.9110 Evaluate side-chains 297 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 230 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 36 CYS Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 230 MET 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 246 SER Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 15 TRP Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 257 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 278 PHE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 47 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.146582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126801 restraints weight = 13453.190| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.21 r_work: 0.3400 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-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: 86 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8990 Z= 0.241 Angle : 0.670 15.553 12180 Z= 0.336 Chirality : 0.044 0.173 1381 Planarity : 0.005 0.070 1540 Dihedral : 4.740 26.701 1221 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.96 % Favored : 93.68 % Rotamer: Outliers : 7.18 % Allowed : 31.95 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1107 helix: 1.02 (0.27), residues: 408 sheet: -0.26 (0.31), residues: 261 loop : -1.83 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 180 HIS 0.004 0.001 HIS D 245 PHE 0.052 0.002 PHE C 334 TYR 0.021 0.001 TYR A 70 ARG 0.009 0.001 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5437.83 seconds wall clock time: 94 minutes 51.79 seconds (5691.79 seconds total)