Starting phenix.real_space_refine on Thu Jul 2 07:27:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8x_37360/07_2026/8w8x_37360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8x_37360/07_2026/8w8x_37360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w8x_37360/07_2026/8w8x_37360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8x_37360/07_2026/8w8x_37360.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8x_37360/07_2026/8w8x_37360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8x_37360/07_2026/8w8x_37360.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 61 5.16 5 C 4847 2.51 5 N 1316 2.21 5 O 1383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7608 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "A" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1482 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 181} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "R" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2030 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 104 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.31, per 1000 atoms: 0.17 Number of scatterers: 7608 At special positions: 0 Unit cell: (78.2, 100.3, 131.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 61 16.00 O 1383 8.00 N 1316 7.00 C 4847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.32 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.20 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 393.3 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 10 sheets defined 40.4% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.626A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.545A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.846A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.589A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.910A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.592A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.570A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.729A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 39 removed outlier: 3.593A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.758A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.591A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.746A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.833A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 66 removed outlier: 4.207A pdb=" N PHE R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 101 removed outlier: 3.742A pdb=" N PHE R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE R 76 " --> pdb=" O PRO R 72 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 148 removed outlier: 3.908A pdb=" N ILE R 119 " --> pdb=" O HIS R 115 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 120 " --> pdb=" O MET R 116 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL R 129 " --> pdb=" O CYS R 125 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 182 removed outlier: 3.835A pdb=" N ILE R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 223 removed outlier: 4.084A pdb=" N CYS R 191 " --> pdb=" O MET R 187 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET R 195 " --> pdb=" O CYS R 191 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU R 216 " --> pdb=" O LEU R 212 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS R 217 " --> pdb=" O PHE R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 268 Proline residue: R 257 - end of helix removed outlier: 3.602A pdb=" N ILE R 265 " --> pdb=" O HIS R 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 279 removed outlier: 3.650A pdb=" N ALA R 279 " --> pdb=" O CYS R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 299 removed outlier: 3.600A pdb=" N TYR R 284 " --> pdb=" O HIS R 280 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU R 285 " --> pdb=" O PHE R 281 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 310 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.867A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.909A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.842A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.783A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.944A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.745A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.731A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.052A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 209 through 214 removed outlier: 9.392A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2473 1.34 - 1.46: 1459 1.46 - 1.58: 3741 1.58 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 7760 Sorted by residual: bond pdb=" CA CYS N 107 " pdb=" C CYS N 107 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.23e-02 6.61e+03 4.03e+00 bond pdb=" CA TYR N 115 " pdb=" C TYR N 115 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.18e-02 7.18e+03 3.92e+00 bond pdb=" CA SER N 112 " pdb=" C SER N 112 " ideal model delta sigma weight residual 1.528 1.505 0.023 1.37e-02 5.33e+03 2.71e+00 bond pdb=" CG PRO R 272 " pdb=" CD PRO R 272 " ideal model delta sigma weight residual 1.503 1.555 -0.052 3.40e-02 8.65e+02 2.36e+00 bond pdb=" N THR N 114 " pdb=" CA THR N 114 " ideal model delta sigma weight residual 1.462 1.447 0.016 1.20e-02 6.94e+03 1.69e+00 ... (remaining 7755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 10274 1.89 - 3.78: 215 3.78 - 5.67: 28 5.67 - 7.56: 3 7.56 - 9.45: 2 Bond angle restraints: 10522 Sorted by residual: angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 112.24 118.42 -6.18 1.28e+00 6.10e-01 2.33e+01 angle pdb=" CA ASP N 90 " pdb=" C ASP N 90 " pdb=" N THR N 91 " ideal model delta sigma weight residual 118.32 123.28 -4.96 1.35e+00 5.49e-01 1.35e+01 angle pdb=" CA ASP N 90 " pdb=" C ASP N 90 " pdb=" O ASP N 90 " ideal model delta sigma weight residual 119.28 115.83 3.45 1.21e+00 6.83e-01 8.15e+00 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" CB ASP N 109 " ideal model delta sigma weight residual 112.30 108.17 4.13 1.52e+00 4.33e-01 7.38e+00 angle pdb=" CA LEU B 286 " pdb=" CB LEU B 286 " pdb=" CG LEU B 286 " ideal model delta sigma weight residual 116.30 125.75 -9.45 3.50e+00 8.16e-02 7.29e+00 ... (remaining 10517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3991 17.81 - 35.63: 448 35.63 - 53.44: 125 53.44 - 71.26: 19 71.26 - 89.07: 13 Dihedral angle restraints: 4596 sinusoidal: 1751 harmonic: 2845 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 47.93 45.07 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP B 254 " pdb=" CB ASP B 254 " pdb=" CG ASP B 254 " pdb=" OD1 ASP B 254 " ideal model delta sinusoidal sigma weight residual -30.00 -87.66 57.66 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 4593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 673 0.033 - 0.066: 371 0.066 - 0.098: 108 0.098 - 0.131: 50 0.131 - 0.164: 10 Chirality restraints: 1212 Sorted by residual: chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA VAL N 37 " pdb=" N VAL N 37 " pdb=" C VAL N 37 " pdb=" CB VAL N 37 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1209 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO G 60 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO B 236 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 275 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.22e+00 pdb=" C ILE R 275 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE R 275 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS R 276 " 0.011 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 86 2.63 - 3.19: 6325 3.19 - 3.76: 11017 3.76 - 4.33: 15946 4.33 - 4.90: 27622 Nonbonded interactions: 60996 Sorted by model distance: nonbonded pdb=" OD1 ASN N 35 " pdb=" CB ASP N 50 " model vdw 2.057 3.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.159 3.040 nonbonded pdb=" CE LYS N 33 " pdb=" SG CYS N 107 " model vdw 2.200 3.800 nonbonded pdb=" OD2 ASP R 121 " pdb="CA CA R 501 " model vdw 2.245 3.250 nonbonded pdb=" OD2 ASP A 381 " pdb=" NH2 ARG R 220 " model vdw 2.256 3.120 ... (remaining 60991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.520 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.007 0.293 7762 Z= 0.313 Angle : 0.765 24.640 10526 Z= 0.418 Chirality : 0.046 0.164 1212 Planarity : 0.005 0.071 1332 Dihedral : 16.885 89.069 2744 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.71 % Allowed : 22.78 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.26), residues: 955 helix: 1.16 (0.26), residues: 366 sheet: -0.20 (0.33), residues: 229 loop : -1.64 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.011 0.002 TYR A 339 PHE 0.024 0.002 PHE B 151 TRP 0.019 0.002 TRP A 234 HIS 0.006 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 ( 7760) covalent geometry : angle 0.67802 / 0.38 (10522) SS BOND : bond 0.24036 / 12.35 ( 2) SS BOND : angle 18.16406 / 9.77 ( 4) hydrogen bonds : bond 0.13083 / 8.65 ( 373) hydrogen bonds : angle 5.27201 / 3.58 ( 1062) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.7377 (ttt180) cc_final: 0.7141 (ttt-90) REVERT: N 108 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7933 (m-80) outliers start: 22 outliers final: 17 residues processed: 144 average time/residue: 0.4419 time to fit residues: 67.2605 Evaluate side-chains 124 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 276 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 340 ASN L 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130841 restraints weight = 8297.644| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.08 r_work: 0.3409 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7762 Z= 0.125 Angle : 0.519 7.418 10526 Z= 0.281 Chirality : 0.042 0.140 1212 Planarity : 0.004 0.054 1332 Dihedral : 5.877 57.607 1083 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.43 % Allowed : 22.66 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.27), residues: 955 helix: 1.84 (0.27), residues: 365 sheet: 0.10 (0.35), residues: 212 loop : -1.66 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 118 TYR 0.011 0.001 TYR R 277 PHE 0.014 0.001 PHE B 151 TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7760) covalent geometry : angle 0.51765 / 0.28 (10522) SS BOND : bond 0.00999 / 0.50 ( 2) SS BOND : angle 1.73138 / 1.00 ( 4) hydrogen bonds : bond 0.04681 / 3.10 ( 373) hydrogen bonds : angle 4.15839 / 2.85 ( 1062) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8106 (ttt180) cc_final: 0.7305 (ttt-90) REVERT: B 152 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8102 (mp) REVERT: G 38 MET cc_start: 0.7097 (ttp) cc_final: 0.6805 (ttp) REVERT: G 42 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: N 38 ARG cc_start: 0.8266 (ttm170) cc_final: 0.7884 (ttp-170) REVERT: A 38 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7631 (mtp180) outliers start: 36 outliers final: 15 residues processed: 136 average time/residue: 0.4421 time to fit residues: 63.4231 Evaluate side-chains 126 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 0.0870 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.170136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132973 restraints weight = 8197.757| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.87 r_work: 0.3433 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7762 Z= 0.113 Angle : 0.491 7.091 10526 Z= 0.265 Chirality : 0.041 0.141 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.499 58.227 1058 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.43 % Allowed : 23.03 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 955 helix: 2.21 (0.27), residues: 365 sheet: 0.19 (0.36), residues: 210 loop : -1.54 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.009 0.001 TYR R 277 PHE 0.013 0.001 PHE B 151 TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7760) covalent geometry : angle 0.49027 / 0.26 (10522) SS BOND : bond 0.00518 / 0.26 ( 2) SS BOND : angle 1.82437 / 1.00 ( 4) hydrogen bonds : bond 0.04276 / 2.85 ( 373) hydrogen bonds : angle 3.91908 / 2.69 ( 1062) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8174 (tttt) cc_final: 0.7828 (tmtm) REVERT: B 152 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8188 (mp) REVERT: B 234 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8134 (t80) REVERT: G 42 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: N 38 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7965 (ttp-170) REVERT: N 108 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: A 38 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.7773 (mtt180) outliers start: 36 outliers final: 17 residues processed: 136 average time/residue: 0.4660 time to fit residues: 66.7862 Evaluate side-chains 130 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 202 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.169570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130610 restraints weight = 8343.068| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.96 r_work: 0.3411 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7762 Z= 0.136 Angle : 0.515 7.465 10526 Z= 0.276 Chirality : 0.042 0.144 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.577 59.183 1058 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.17 % Allowed : 22.66 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.27), residues: 955 helix: 2.20 (0.26), residues: 365 sheet: 0.14 (0.35), residues: 212 loop : -1.49 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 118 TYR 0.010 0.001 TYR R 277 PHE 0.016 0.001 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7760) covalent geometry : angle 0.51369 / 0.28 (10522) SS BOND : bond 0.00367 / 0.19 ( 2) SS BOND : angle 1.76060 / 0.93 ( 4) hydrogen bonds : bond 0.04634 / 3.09 ( 373) hydrogen bonds : angle 3.95316 / 2.71 ( 1062) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8187 (tttt) cc_final: 0.7819 (tmtm) REVERT: B 152 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8100 (mp) REVERT: B 234 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8276 (t80) REVERT: G 42 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: N 34 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8413 (mmm) REVERT: N 38 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7970 (ttp-170) REVERT: N 108 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 38 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7714 (mtt180) REVERT: A 248 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8232 (m) outliers start: 42 outliers final: 23 residues processed: 136 average time/residue: 0.4786 time to fit residues: 68.8138 Evaluate side-chains 136 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 39 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127439 restraints weight = 8200.840| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.07 r_work: 0.3368 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7762 Z= 0.196 Angle : 0.586 8.739 10526 Z= 0.312 Chirality : 0.045 0.155 1212 Planarity : 0.004 0.054 1332 Dihedral : 4.857 59.528 1058 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.30 % Allowed : 22.54 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 955 helix: 1.94 (0.26), residues: 365 sheet: -0.06 (0.34), residues: 223 loop : -1.50 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 118 TYR 0.011 0.002 TYR A 339 PHE 0.021 0.002 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 ( 7760) covalent geometry : angle 0.58381 / 0.31 (10522) SS BOND : bond 0.00583 / 0.28 ( 2) SS BOND : angle 2.52662 / 1.39 ( 4) hydrogen bonds : bond 0.05534 / 3.69 ( 373) hydrogen bonds : angle 4.12437 / 2.84 ( 1062) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.286 Fit side-chains REVERT: B 13 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7496 (tm-30) REVERT: B 146 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8740 (mp) REVERT: B 152 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8092 (mp) REVERT: B 234 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8256 (t80) REVERT: G 42 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: N 38 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.8000 (ttp-170) REVERT: R 116 MET cc_start: 0.6136 (ptp) cc_final: 0.5887 (ptp) outliers start: 43 outliers final: 22 residues processed: 132 average time/residue: 0.5262 time to fit residues: 73.3942 Evaluate side-chains 127 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.173271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132929 restraints weight = 8252.231| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.10 r_work: 0.3397 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7762 Z= 0.097 Angle : 0.467 6.571 10526 Z= 0.253 Chirality : 0.041 0.137 1212 Planarity : 0.003 0.051 1332 Dihedral : 4.360 58.670 1058 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.43 % Allowed : 23.77 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.27), residues: 955 helix: 2.42 (0.27), residues: 365 sheet: 0.18 (0.36), residues: 207 loop : -1.44 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.008 0.001 TYR R 277 PHE 0.011 0.001 PHE B 199 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 ( 7760) covalent geometry : angle 0.46646 / 0.25 (10522) SS BOND : bond 0.00350 / 0.18 ( 2) SS BOND : angle 1.38780 / 0.77 ( 4) hydrogen bonds : bond 0.03829 / 2.55 ( 373) hydrogen bonds : angle 3.75857 / 2.58 ( 1062) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.229 Fit side-chains REVERT: B 13 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7514 (tm-30) REVERT: B 23 LYS cc_start: 0.8121 (tttt) cc_final: 0.7770 (tmtm) REVERT: B 42 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6357 (tmt170) REVERT: B 152 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8177 (mp) REVERT: B 234 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8235 (t80) REVERT: G 38 MET cc_start: 0.6931 (ttp) cc_final: 0.6644 (ttp) REVERT: G 42 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: A 27 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7696 (mp0) REVERT: A 38 ARG cc_start: 0.7965 (mmt-90) cc_final: 0.7700 (mtt180) REVERT: R 70 HIS cc_start: 0.6002 (OUTLIER) cc_final: 0.5580 (m90) REVERT: R 116 MET cc_start: 0.6061 (ptp) cc_final: 0.5825 (tmm) outliers start: 36 outliers final: 17 residues processed: 135 average time/residue: 0.5306 time to fit residues: 75.7218 Evaluate side-chains 129 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 15 optimal weight: 0.0170 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133824 restraints weight = 8214.962| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.11 r_work: 0.3447 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7762 Z= 0.095 Angle : 0.456 6.557 10526 Z= 0.247 Chirality : 0.041 0.139 1212 Planarity : 0.003 0.050 1332 Dihedral : 4.209 57.977 1057 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.69 % Allowed : 24.75 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.27), residues: 955 helix: 2.60 (0.27), residues: 367 sheet: 0.23 (0.35), residues: 213 loop : -1.49 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 19 TYR 0.007 0.001 TYR R 277 PHE 0.011 0.001 PHE B 151 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 7760) covalent geometry : angle 0.45578 / 0.25 (10522) SS BOND : bond 0.00336 / 0.17 ( 2) SS BOND : angle 1.00813 / 0.58 ( 4) hydrogen bonds : bond 0.03710 / 2.48 ( 373) hydrogen bonds : angle 3.66622 / 2.52 ( 1062) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7466 (tm-30) REVERT: B 23 LYS cc_start: 0.8090 (tttt) cc_final: 0.7725 (tmtm) REVERT: B 42 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6332 (tmt170) REVERT: B 152 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 234 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8227 (t80) REVERT: G 38 MET cc_start: 0.6891 (ttp) cc_final: 0.6593 (ttp) REVERT: G 42 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6869 (mp0) REVERT: A 38 ARG cc_start: 0.7940 (mmt-90) cc_final: 0.7681 (mtp180) outliers start: 30 outliers final: 17 residues processed: 129 average time/residue: 0.5263 time to fit residues: 72.0439 Evaluate side-chains 127 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 0.2980 chunk 39 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.169533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130536 restraints weight = 8281.711| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.95 r_work: 0.3411 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7762 Z= 0.146 Angle : 0.525 7.351 10526 Z= 0.282 Chirality : 0.043 0.144 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.515 58.465 1057 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.06 % Allowed : 25.00 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.27), residues: 955 helix: 2.38 (0.26), residues: 365 sheet: 0.09 (0.35), residues: 209 loop : -1.45 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.010 0.001 TYR R 277 PHE 0.017 0.002 PHE B 151 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7760) covalent geometry : angle 0.52427 / 0.28 (10522) SS BOND : bond 0.00418 / 0.21 ( 2) SS BOND : angle 1.02574 / 0.60 ( 4) hydrogen bonds : bond 0.04716 / 3.14 ( 373) hydrogen bonds : angle 3.90706 / 2.69 ( 1062) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6301 (tmt170) REVERT: B 152 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8111 (mp) REVERT: B 234 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8244 (t80) REVERT: G 42 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: A 356 ARG cc_start: 0.8504 (mmm160) cc_final: 0.7588 (mpt180) REVERT: R 69 LEU cc_start: 0.6528 (mt) cc_final: 0.6037 (tp) REVERT: R 70 HIS cc_start: 0.5908 (OUTLIER) cc_final: 0.5639 (m90) outliers start: 33 outliers final: 20 residues processed: 131 average time/residue: 0.5386 time to fit residues: 74.6070 Evaluate side-chains 132 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 12 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 70 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.171153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.133898 restraints weight = 8277.023| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.89 r_work: 0.3446 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7762 Z= 0.106 Angle : 0.479 7.039 10526 Z= 0.258 Chirality : 0.041 0.137 1212 Planarity : 0.003 0.050 1332 Dihedral : 4.303 57.111 1057 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.19 % Allowed : 25.25 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.27), residues: 955 helix: 2.54 (0.26), residues: 366 sheet: 0.24 (0.35), residues: 212 loop : -1.47 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.008 0.001 TYR R 277 PHE 0.012 0.001 PHE B 151 TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 7760) covalent geometry : angle 0.47830 / 0.26 (10522) SS BOND : bond 0.00331 / 0.17 ( 2) SS BOND : angle 0.87291 / 0.51 ( 4) hydrogen bonds : bond 0.04004 / 2.66 ( 373) hydrogen bonds : angle 3.75264 / 2.57 ( 1062) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7512 (tm-30) REVERT: B 42 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6297 (tmt170) REVERT: B 152 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8163 (mp) REVERT: B 234 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8266 (t80) REVERT: G 42 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: A 38 ARG cc_start: 0.7934 (mmt-90) cc_final: 0.7661 (mtp180) REVERT: R 69 LEU cc_start: 0.6403 (mt) cc_final: 0.5915 (tp) REVERT: R 70 HIS cc_start: 0.5861 (OUTLIER) cc_final: 0.5609 (m90) outliers start: 34 outliers final: 21 residues processed: 131 average time/residue: 0.5070 time to fit residues: 70.2140 Evaluate side-chains 132 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 202 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 20 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 83 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 32 GLN B 340 ASN A 218 ASN R 217 HIS R 282 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.172822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136038 restraints weight = 8188.237| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.86 r_work: 0.3472 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7762 Z= 0.094 Angle : 0.461 7.166 10526 Z= 0.250 Chirality : 0.041 0.136 1212 Planarity : 0.003 0.049 1332 Dihedral : 4.132 56.165 1057 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.20 % Allowed : 26.23 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.27), residues: 955 helix: 2.82 (0.26), residues: 361 sheet: 0.20 (0.35), residues: 208 loop : -1.40 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.008 0.001 TYR N 80 PHE 0.013 0.001 PHE R 120 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 ( 7760) covalent geometry : angle 0.46118 / 0.25 (10522) SS BOND : bond 0.00305 / 0.16 ( 2) SS BOND : angle 0.81889 / 0.48 ( 4) hydrogen bonds : bond 0.03616 / 2.40 ( 373) hydrogen bonds : angle 3.63695 / 2.48 ( 1062) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7519 (tm-30) REVERT: B 42 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6374 (tmt170) REVERT: B 61 MET cc_start: 0.8795 (ppp) cc_final: 0.8292 (ptm) REVERT: B 152 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8194 (mp) REVERT: B 234 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8223 (t80) REVERT: G 42 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: A 27 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7698 (mp0) REVERT: R 69 LEU cc_start: 0.6366 (mt) cc_final: 0.5863 (tp) REVERT: R 70 HIS cc_start: 0.5753 (OUTLIER) cc_final: 0.5469 (m90) outliers start: 26 outliers final: 19 residues processed: 127 average time/residue: 0.4789 time to fit residues: 64.3006 Evaluate side-chains 130 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 70 HIS Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 63 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.167424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128457 restraints weight = 8254.632| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.95 r_work: 0.3384 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7762 Z= 0.202 Angle : 0.595 8.381 10526 Z= 0.317 Chirality : 0.046 0.167 1212 Planarity : 0.004 0.052 1332 Dihedral : 4.739 57.917 1057 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.06 % Allowed : 25.49 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.27), residues: 955 helix: 2.14 (0.26), residues: 366 sheet: 0.04 (0.34), residues: 225 loop : -1.55 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 118 TYR 0.011 0.002 TYR R 277 PHE 0.024 0.002 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 ( 7760) covalent geometry : angle 0.59461 / 0.32 (10522) SS BOND : bond 0.00417 / 0.22 ( 2) SS BOND : angle 1.04582 / 0.61 ( 4) hydrogen bonds : bond 0.05524 / 3.69 ( 373) hydrogen bonds : angle 4.11218 / 2.83 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2569.17 seconds wall clock time: 44 minutes 25.04 seconds (2665.04 seconds total)