Starting phenix.real_space_refine on Fri Aug 22 20:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8x_37360/08_2025/8w8x_37360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8x_37360/08_2025/8w8x_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_37360/08_2025/8w8x_37360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8x_37360/08_2025/8w8x_37360.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8x_37360/08_2025/8w8x_37360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8x_37360/08_2025/8w8x_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-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.25 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: 0.47 Conformation dependent library (CDL) restraints added in 363.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.26 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: 0.98 Time building geometry restraints manager: 0.65 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 2.510 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: 2.380 Set stop_for_unknowns flag: 0.010 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 aren 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 covalent geometry : bond 0.00572 ( 7760) covalent geometry : angle 0.67802 (10522) SS BOND : bond 0.24036 ( 2) SS BOND : angle 18.16406 ( 4) hydrogen bonds : bond 0.13083 ( 373) hydrogen bonds : angle 5.27201 ( 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 : 0.186 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: 0.7932 (m-80) outliers start: 22 outliers final: 17 residues processed: 144 average time/residue: 0.5505 time to fit residues: 83.4005 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 : 0.287 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4005 r_free = 0.4005 target = 0.170877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130839 restraints weight = 8315.134| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.09 r_work: 0.3409 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7762 Z= 0.123 Angle : 0.514 7.398 10526 Z= 0.278 Chirality : 0.042 0.140 1212 Planarity : 0.004 0.054 1332 Dihedral : 5.812 57.409 1083 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.80 % Allowed : 22.17 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.27), residues: 955 helix: 1.86 (0.27), residues: 365 sheet: 0.11 (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 0.013 0.001 PHE B 151 TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7760) covalent geometry : angle 0.51329 (10522) SS BOND : bond 0.00861 ( 2) SS BOND : angle 1.64378 ( 4) hydrogen bonds : bond 0.04556 ( 373) hydrogen bonds : angle 4.12737 ( 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 149 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: B 152 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 234 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8064 (t80) REVERT: G 38 MET cc_start: 0.7160 (ttp) cc_final: 0.6867 (ttp) REVERT: G 42 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: N 38 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7948 (ttp-170) REVERT: A 38 ARG cc_start: 0.7995 (mmt-90) cc_final: 0.7668 (mtp180) outliers start: 39 outliers final: 15 residues processed: 136 average time/residue: 0.5083 time to fit residues: 72.7914 Evaluate side-chains 127 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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 100 ILE 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: 0.0000 chunk 66 optimal weight: 0.0470 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 overall best weight: 0.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4058 r_free = 0.4058 target = 0.176191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.136050 restraints weight = 8191.188| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.09 r_work: 0.3436 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1721 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= 0.088 Angle : 0.443 6.044 10526 Z= 0.242 Chirality : 0.040 0.139 1212 Planarity : 0.003 0.048 1332 Dihedral : 4.498 58.990 1061 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.82 % Allowed : 23.40 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.27), residues: 955 helix: 2.46 (0.27), residues: 369 sheet: 0.32 (0.36), residues: 200 loop : -1.47 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.007 0.001 TYR R 277 PHE 0.009 0.001 PHE B 199 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.000 HIS R 261 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 7760) covalent geometry : angle 0.44268 (10522) SS BOND : bond 0.00591 ( 2) SS BOND : angle 1.23528 ( 4) hydrogen bonds : bond 0.03453 ( 373) hydrogen bonds : angle 3.70059 ( 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 137 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8080 (tttt) cc_final: 0.7727 (tmtm) REVERT: B 96 ARG cc_start: 0.8259 (ttp-170) cc_final: 0.7018 (ttt-90) REVERT: B 152 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8156 (mp) REVERT: G 38 MET cc_start: 0.6776 (ttp) cc_final: 0.6545 (ttp) REVERT: G 42 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: N 38 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7829 (tmm-80) REVERT: N 108 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7202 (m-80) REVERT: A 27 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7810 (mp0) REVERT: A 38 ARG cc_start: 0.7989 (mmt-90) cc_final: 0.7769 (mtp180) REVERT: R 69 LEU cc_start: 0.6396 (tp) cc_final: 0.6102 (mt) outliers start: 31 outliers final: 13 residues processed: 129 average time/residue: 0.5401 time to fit residues: 73.5592 Evaluate side-chains 123 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 279 SER 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 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 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: 0.7980 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3986 r_free = 0.3986 target = 0.169264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130204 restraints weight = 8353.605| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.97 r_work: 0.3406 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7762 Z= 0.152 Angle : 0.533 7.672 10526 Z= 0.284 Chirality : 0.043 0.146 1212 Planarity : 0.004 0.050 1332 Dihedral : 4.543 58.981 1057 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.56 % Allowed : 23.28 % 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 aren not related in a simple way. whole: 0.57 (0.27), residues: 955 helix: 2.28 (0.26), residues: 365 sheet: 0.18 (0.36), residues: 212 loop : -1.48 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 118 TYR 0.010 0.001 TYR A 339 PHE 0.018 0.002 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 7760) covalent geometry : angle 0.53155 (10522) SS BOND : bond 0.00320 ( 2) SS BOND : angle 2.02952 ( 4) hydrogen bonds : bond 0.04791 ( 373) hydrogen bonds : angle 3.93554 ( 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 144 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8215 (tttt) cc_final: 0.7865 (tmtm) REVERT: B 42 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6254 (tmt170) REVERT: B 146 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8708 (mp) REVERT: B 152 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8106 (mp) REVERT: B 234 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8218 (t80) REVERT: B 262 MET cc_start: 0.8993 (tpt) cc_final: 0.8778 (tpt) REVERT: G 42 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: N 108 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: A 38 ARG cc_start: 0.7977 (mmt-90) cc_final: 0.7714 (mtp180) outliers start: 37 outliers final: 19 residues processed: 134 average time/residue: 0.5703 time to fit residues: 80.4936 Evaluate side-chains 129 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 138 GLU Chi-restraints excluded: chain B residue 146 LEU 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 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 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 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: 10.0000 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 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: 0.0050 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4010 r_free = 0.4010 target = 0.171355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132083 restraints weight = 8189.025| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.97 r_work: 0.3434 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7762 Z= 0.119 Angle : 0.494 6.924 10526 Z= 0.266 Chirality : 0.042 0.140 1212 Planarity : 0.004 0.049 1332 Dihedral : 4.452 59.819 1057 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.56 % Allowed : 23.15 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.27), residues: 955 helix: 2.40 (0.26), residues: 365 sheet: 0.21 (0.35), residues: 214 loop : -1.49 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.009 0.001 TYR A 358 PHE 0.014 0.001 PHE B 151 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 7760) covalent geometry : angle 0.49137 (10522) SS BOND : bond 0.00501 ( 2) SS BOND : angle 2.84488 ( 4) hydrogen bonds : bond 0.04336 ( 373) hydrogen bonds : angle 3.83399 ( 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 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8186 (tttt) cc_final: 0.7835 (tmtm) REVERT: B 42 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6170 (tmt170) REVERT: B 152 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8143 (mp) REVERT: B 234 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8244 (t80) REVERT: B 262 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8682 (tpt) REVERT: G 42 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: A 38 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7711 (mtp180) REVERT: A 248 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8250 (m) REVERT: R 69 LEU cc_start: 0.6351 (tp) cc_final: 0.6073 (mt) REVERT: R 156 MET cc_start: 0.8097 (tpp) cc_final: 0.7692 (mmm) outliers start: 37 outliers final: 20 residues processed: 131 average time/residue: 0.5280 time to fit residues: 73.1248 Evaluate side-chains 131 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 262 MET 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 31 GLN Chi-restraints excluded: chain A residue 248 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.169562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132030 restraints weight = 8268.271| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.89 r_work: 0.3423 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7762 Z= 0.127 Angle : 0.497 7.097 10526 Z= 0.267 Chirality : 0.042 0.143 1212 Planarity : 0.004 0.050 1332 Dihedral : 4.454 59.362 1057 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.80 % Allowed : 22.91 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.27), residues: 955 helix: 2.40 (0.26), residues: 365 sheet: 0.18 (0.35), residues: 214 loop : -1.50 (0.28), residues: 376 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 0.015 0.001 PHE B 151 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 7760) covalent geometry : angle 0.49692 (10522) SS BOND : bond 0.00332 ( 2) SS BOND : angle 1.30740 ( 4) hydrogen bonds : bond 0.04430 ( 373) hydrogen bonds : angle 3.84337 ( 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: 39 poor density : 105 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8196 (tttt) cc_final: 0.7846 (tmtm) REVERT: B 42 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6210 (tmt170) REVERT: B 152 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 234 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 262 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8682 (tpt) REVERT: G 42 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 38 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7718 (mtp180) REVERT: A 248 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8222 (m) REVERT: R 69 LEU cc_start: 0.6477 (tp) cc_final: 0.5711 (mp) REVERT: R 156 MET cc_start: 0.8072 (tpp) cc_final: 0.7642 (mmm) outliers start: 39 outliers final: 24 residues processed: 132 average time/residue: 0.5745 time to fit residues: 79.9540 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 42 ARG Chi-restraints excluded: chain B residue 51 LEU 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 262 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 44 optimal weight: 0.0770 chunk 78 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.168879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.131355 restraints weight = 8236.259| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.87 r_work: 0.3415 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7762 Z= 0.143 Angle : 0.518 7.404 10526 Z= 0.279 Chirality : 0.043 0.146 1212 Planarity : 0.004 0.050 1332 Dihedral : 4.542 59.211 1057 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.80 % Allowed : 23.03 % 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 aren not related in a simple way. whole: 0.57 (0.27), residues: 955 helix: 2.33 (0.26), residues: 365 sheet: 0.14 (0.35), residues: 214 loop : -1.52 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 118 TYR 0.010 0.001 TYR A 339 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 covalent geometry : bond 0.00338 ( 7760) covalent geometry : angle 0.51772 (10522) SS BOND : bond 0.00351 ( 2) SS BOND : angle 1.05782 ( 4) hydrogen bonds : bond 0.04708 ( 373) hydrogen bonds : angle 3.90816 ( 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 143 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8215 (tttt) cc_final: 0.7859 (tmtm) REVERT: B 42 ARG cc_start: 0.6765 (OUTLIER) cc_final: 0.6163 (tmt170) REVERT: B 152 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 234 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8272 (t80) REVERT: B 262 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8683 (tpt) REVERT: G 42 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: A 38 ARG cc_start: 0.7986 (mmt-90) cc_final: 0.7752 (mtp180) REVERT: R 69 LEU cc_start: 0.6504 (tp) cc_final: 0.5707 (mp) REVERT: R 70 HIS cc_start: 0.5911 (OUTLIER) cc_final: 0.5495 (m90) outliers start: 39 outliers final: 23 residues processed: 131 average time/residue: 0.5263 time to fit residues: 73.1901 Evaluate side-chains 135 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 42 ARG Chi-restraints excluded: chain B residue 51 LEU 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 262 MET 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 99 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.169455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132109 restraints weight = 8291.783| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.88 r_work: 0.3425 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7762 Z= 0.126 Angle : 0.501 7.039 10526 Z= 0.269 Chirality : 0.042 0.143 1212 Planarity : 0.004 0.050 1332 Dihedral : 4.445 58.026 1057 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.68 % Allowed : 23.52 % 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 aren not related in a simple way. whole: 0.66 (0.27), residues: 955 helix: 2.42 (0.26), residues: 365 sheet: 0.18 (0.35), residues: 214 loop : -1.48 (0.28), residues: 376 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 0.015 0.001 PHE B 151 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7760) covalent geometry : angle 0.50078 (10522) SS BOND : bond 0.00336 ( 2) SS BOND : angle 0.99941 ( 4) hydrogen bonds : bond 0.04418 ( 373) hydrogen bonds : angle 3.84080 ( 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 147 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8206 (tttt) cc_final: 0.7855 (tmtm) REVERT: B 42 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.6194 (tmt170) REVERT: B 152 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 234 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8269 (t80) REVERT: B 262 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8683 (tpt) REVERT: G 42 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 38 ARG cc_start: 0.7946 (mmt-90) cc_final: 0.7691 (mtp180) REVERT: R 69 LEU cc_start: 0.6462 (tp) cc_final: 0.5709 (mp) REVERT: R 70 HIS cc_start: 0.5902 (OUTLIER) cc_final: 0.5488 (m90) REVERT: R 156 MET cc_start: 0.8053 (tpp) cc_final: 0.7630 (tpp) outliers start: 38 outliers final: 23 residues processed: 134 average time/residue: 0.5168 time to fit residues: 73.1620 Evaluate side-chains 137 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 42 ARG Chi-restraints excluded: chain B residue 51 LEU 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 262 MET 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 99 CYS Chi-restraints excluded: chain A residue 31 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132094 restraints weight = 8294.061| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.89 r_work: 0.3424 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7762 Z= 0.125 Angle : 0.502 6.985 10526 Z= 0.270 Chirality : 0.042 0.140 1212 Planarity : 0.004 0.050 1332 Dihedral : 4.422 56.967 1057 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.31 % Allowed : 23.89 % 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 aren not related in a simple way. whole: 0.65 (0.27), residues: 955 helix: 2.43 (0.26), residues: 365 sheet: 0.16 (0.35), residues: 214 loop : -1.48 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.009 0.001 TYR A 358 PHE 0.015 0.001 PHE B 151 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7760) covalent geometry : angle 0.50146 (10522) SS BOND : bond 0.00332 ( 2) SS BOND : angle 1.01615 ( 4) hydrogen bonds : bond 0.04399 ( 373) hydrogen bonds : angle 3.85187 ( 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: 35 poor density : 106 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8226 (tttt) cc_final: 0.7879 (tmtm) REVERT: B 42 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6195 (tmt170) REVERT: B 152 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8147 (mp) REVERT: B 234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8270 (t80) REVERT: B 262 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8681 (tpt) REVERT: G 42 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: A 38 ARG cc_start: 0.7942 (mmt-90) cc_final: 0.7695 (mtp180) REVERT: R 69 LEU cc_start: 0.6489 (tp) cc_final: 0.5736 (mp) REVERT: R 156 MET cc_start: 0.8059 (tpp) cc_final: 0.7625 (tpp) outliers start: 35 outliers final: 25 residues processed: 131 average time/residue: 0.5184 time to fit residues: 71.8003 Evaluate side-chains 135 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 42 ARG Chi-restraints excluded: chain B residue 51 LEU 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 262 MET 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 99 CYS Chi-restraints excluded: chain A residue 31 GLN 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 100 ILE 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: 4.9990 chunk 88 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 3 optimal weight: 0.0570 chunk 92 optimal weight: 0.7980 chunk 10 optimal weight: 0.0470 chunk 12 optimal weight: 0.2980 chunk 33 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 217 HIS R 282 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.136218 restraints weight = 8234.249| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.96 r_work: 0.3482 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7762 Z= 0.085 Angle : 0.446 6.611 10526 Z= 0.242 Chirality : 0.040 0.135 1212 Planarity : 0.003 0.049 1332 Dihedral : 4.074 56.043 1057 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.57 % Allowed : 24.75 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.27), residues: 955 helix: 2.78 (0.27), residues: 363 sheet: 0.34 (0.35), residues: 212 loop : -1.39 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.009 0.001 TYR A 358 PHE 0.012 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 covalent geometry : bond 0.00171 ( 7760) covalent geometry : angle 0.44572 (10522) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.91964 ( 4) hydrogen bonds : bond 0.03370 ( 373) hydrogen bonds : angle 3.57674 ( 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 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8103 (tttt) cc_final: 0.7754 (tmtm) REVERT: B 59 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7705 (t80) REVERT: B 152 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8164 (mp) REVERT: B 234 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8162 (t80) REVERT: G 42 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: A 27 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7701 (mp0) REVERT: R 69 LEU cc_start: 0.6221 (tp) cc_final: 0.5469 (mp) REVERT: R 70 HIS cc_start: 0.5846 (OUTLIER) cc_final: 0.5449 (m90) outliers start: 29 outliers final: 15 residues processed: 128 average time/residue: 0.4880 time to fit residues: 66.3542 Evaluate side-chains 121 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN 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 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 G residue 42 GLU 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 99 CYS 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 70 HIS 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: 0.6980 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.172163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131819 restraints weight = 8237.810| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.11 r_work: 0.3420 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7762 Z= 0.119 Angle : 0.494 6.806 10526 Z= 0.266 Chirality : 0.042 0.144 1212 Planarity : 0.004 0.050 1332 Dihedral : 4.287 56.766 1057 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.96 % Allowed : 26.11 % 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 aren not related in a simple way. whole: 0.82 (0.27), residues: 955 helix: 2.57 (0.26), residues: 366 sheet: 0.29 (0.35), residues: 212 loop : -1.44 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.011 0.001 TYR A 358 PHE 0.016 0.001 PHE R 120 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7760) covalent geometry : angle 0.49361 (10522) SS BOND : bond 0.00348 ( 2) SS BOND : angle 0.93025 ( 4) hydrogen bonds : bond 0.04165 ( 373) hydrogen bonds : angle 3.75033 ( 1062) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2747.96 seconds wall clock time: 47 minutes 34.79 seconds (2854.79 seconds total)