Starting phenix.real_space_refine on Fri Jun 6 09:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8x_37360/06_2025/8w8x_37360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8x_37360/06_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_37360/06_2025/8w8x_37360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8x_37360/06_2025/8w8x_37360.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8x_37360/06_2025/8w8x_37360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8x_37360/06_2025/8w8x_37360.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 7} 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: 4.96, per 1000 atoms: 0.65 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: 1.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.77 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: 2.13 Time building geometry restraints manager: 2.08 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.580 Find NCS groups from input model: 0.080 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (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 TRP 0.019 0.002 TRP A 234 HIS 0.006 0.002 HIS A 357 PHE 0.024 0.002 PHE B 151 TYR 0.011 0.002 TYR A 339 ARG 0.003 0.000 ARG A 374 Details of bonding type rmsd hydrogen bonds : bond 0.13083 ( 373) hydrogen bonds : angle 5.27201 ( 1062) SS BOND : bond 0.24036 ( 2) SS BOND : angle 18.16406 ( 4) covalent geometry : bond 0.00572 ( 7760) covalent geometry : angle 0.67802 (10522) *********************** 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 : 0.880 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: 1.2370 time to fit residues: 188.0241 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 : 0.815 ------------------------------------------------------------------------------- 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 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.171848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133098 restraints weight = 8226.622| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.96 r_work: 0.3443 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7762 Z= 0.108 Angle : 0.494 6.839 10526 Z= 0.268 Chirality : 0.041 0.137 1212 Planarity : 0.004 0.052 1332 Dihedral : 5.686 56.406 1083 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.06 % Allowed : 22.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 955 helix: 1.96 (0.27), residues: 365 sheet: 0.14 (0.35), residues: 212 loop : -1.67 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE R 259 TYR 0.010 0.001 TYR R 277 ARG 0.003 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 373) hydrogen bonds : angle 4.06636 ( 1062) SS BOND : bond 0.00801 ( 2) SS BOND : angle 1.66295 ( 4) covalent geometry : bond 0.00234 ( 7760) covalent geometry : angle 0.49325 (10522) *********************** 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 146 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8206 (tptt) cc_final: 0.7848 (tmtm) REVERT: B 96 ARG cc_start: 0.8056 (ttt180) cc_final: 0.7242 (ttt-90) REVERT: B 152 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8108 (mp) REVERT: G 42 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: N 38 ARG cc_start: 0.8266 (ttm170) cc_final: 0.8030 (ttp-170) REVERT: A 38 ARG cc_start: 0.7988 (mmt-90) cc_final: 0.7688 (mtp180) outliers start: 33 outliers final: 13 residues processed: 136 average time/residue: 1.2513 time to fit residues: 179.6942 Evaluate side-chains 124 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR 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 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 42 GLU 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 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 1 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.166429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127194 restraints weight = 8332.848| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.96 r_work: 0.3369 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7762 Z= 0.223 Angle : 0.623 9.464 10526 Z= 0.330 Chirality : 0.046 0.156 1212 Planarity : 0.005 0.057 1332 Dihedral : 4.970 58.023 1057 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.67 % Allowed : 22.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.27), residues: 955 helix: 1.70 (0.26), residues: 365 sheet: -0.09 (0.34), residues: 221 loop : -1.54 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.008 0.002 HIS A 357 PHE 0.024 0.002 PHE B 151 TYR 0.012 0.002 TYR A 339 ARG 0.006 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 373) hydrogen bonds : angle 4.28485 ( 1062) SS BOND : bond 0.00332 ( 2) SS BOND : angle 2.79571 ( 4) covalent geometry : bond 0.00547 ( 7760) covalent geometry : angle 0.62030 (10522) *********************** 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 150 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.6380 (tmt170) REVERT: B 152 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8061 (mp) REVERT: B 234 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8284 (t80) REVERT: G 42 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: N 38 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7932 (ttp-170) outliers start: 46 outliers final: 23 residues processed: 134 average time/residue: 1.2356 time to fit residues: 175.1163 Evaluate side-chains 130 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 59 TYR 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 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 B residue 340 ASN 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 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 217 VAL Chi-restraints excluded: chain A residue 223 ASP 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 73 MET Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.170295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130878 restraints weight = 8219.690| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.98 r_work: 0.3413 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1295 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= 0.122 Angle : 0.509 7.406 10526 Z= 0.274 Chirality : 0.042 0.141 1212 Planarity : 0.004 0.053 1332 Dihedral : 4.644 59.424 1057 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.56 % Allowed : 23.40 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.27), residues: 955 helix: 2.04 (0.26), residues: 365 sheet: 0.12 (0.35), residues: 217 loop : -1.58 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.010 0.001 TYR R 277 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 373) hydrogen bonds : angle 3.98195 ( 1062) SS BOND : bond 0.00275 ( 2) SS BOND : angle 1.96316 ( 4) covalent geometry : bond 0.00276 ( 7760) covalent geometry : angle 0.50734 (10522) *********************** 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 145 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6285 (tmt170) REVERT: B 152 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 234 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8204 (t80) REVERT: G 42 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: N 38 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7949 (ttp-170) REVERT: A 248 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8211 (m) outliers start: 37 outliers final: 20 residues processed: 133 average time/residue: 1.2938 time to fit residues: 181.4965 Evaluate side-chains 133 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 325 MET 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 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 17 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.170178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129763 restraints weight = 8142.152| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.08 r_work: 0.3396 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7762 Z= 0.132 Angle : 0.510 7.563 10526 Z= 0.274 Chirality : 0.042 0.143 1212 Planarity : 0.004 0.052 1332 Dihedral : 4.580 59.530 1057 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.80 % Allowed : 23.15 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.27), residues: 955 helix: 2.16 (0.26), residues: 365 sheet: 0.10 (0.35), residues: 214 loop : -1.56 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE B 151 TYR 0.009 0.001 TYR R 277 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 373) hydrogen bonds : angle 3.94579 ( 1062) SS BOND : bond 0.00360 ( 2) SS BOND : angle 1.16693 ( 4) covalent geometry : bond 0.00309 ( 7760) covalent geometry : angle 0.50965 (10522) *********************** 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 147 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.853 Fit side-chains REVERT: B 13 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7513 (tm-30) REVERT: B 42 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6254 (tmt170) REVERT: B 96 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7293 (ttt-90) REVERT: B 152 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 234 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8194 (t80) REVERT: G 42 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: N 34 MET cc_start: 0.8708 (mmm) cc_final: 0.8380 (mmm) REVERT: N 38 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7940 (ttp-170) REVERT: A 248 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8187 (m) outliers start: 39 outliers final: 22 residues processed: 135 average time/residue: 1.3122 time to fit residues: 186.7390 Evaluate side-chains 135 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 100 VAL 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 66 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.167986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127421 restraints weight = 8224.076| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.07 r_work: 0.3362 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7762 Z= 0.189 Angle : 0.579 8.638 10526 Z= 0.308 Chirality : 0.045 0.153 1212 Planarity : 0.004 0.054 1332 Dihedral : 4.814 59.635 1057 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.17 % Allowed : 22.91 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 955 helix: 1.94 (0.26), residues: 365 sheet: -0.05 (0.34), residues: 222 loop : -1.54 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.002 PHE B 151 TYR 0.011 0.002 TYR A 339 ARG 0.004 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.05435 ( 373) hydrogen bonds : angle 4.11030 ( 1062) SS BOND : bond 0.00395 ( 2) SS BOND : angle 1.09261 ( 4) covalent geometry : bond 0.00460 ( 7760) covalent geometry : angle 0.57876 (10522) *********************** 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 142 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6290 (tmt170) REVERT: B 152 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 217 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7176 (ptt) REVERT: B 234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8263 (t80) REVERT: G 42 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: N 38 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7917 (ttp-170) REVERT: R 70 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5870 (m90) REVERT: R 116 MET cc_start: 0.6103 (ptp) cc_final: 0.5897 (ptp) outliers start: 42 outliers final: 23 residues processed: 129 average time/residue: 1.2732 time to fit residues: 173.3054 Evaluate side-chains 131 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 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 217 MET 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 25 SER 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 99 CYS 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 70 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 5.9990 chunk 24 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.0020 chunk 8 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.172894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132759 restraints weight = 8212.812| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.09 r_work: 0.3397 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1570 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= 0.097 Angle : 0.468 6.642 10526 Z= 0.254 Chirality : 0.041 0.138 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.339 57.846 1057 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.80 % Allowed : 23.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 955 helix: 2.38 (0.27), residues: 366 sheet: 0.21 (0.36), residues: 207 loop : -1.46 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.007 0.001 TYR R 277 ARG 0.001 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 373) hydrogen bonds : angle 3.77489 ( 1062) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.86549 ( 4) covalent geometry : bond 0.00207 ( 7760) covalent geometry : angle 0.46813 (10522) *********************** 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 149 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7492 (tm-30) REVERT: B 96 ARG cc_start: 0.8258 (ttp-170) cc_final: 0.7218 (ttt-90) REVERT: B 152 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8135 (mp) REVERT: B 217 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6956 (ptt) REVERT: B 234 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8244 (t80) REVERT: G 38 MET cc_start: 0.6940 (ttp) cc_final: 0.6658 (ttp) REVERT: G 42 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 27 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7687 (mp0) REVERT: A 38 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7676 (mtp180) REVERT: R 69 LEU cc_start: 0.6203 (tp) cc_final: 0.5995 (mt) REVERT: R 70 HIS cc_start: 0.6043 (OUTLIER) cc_final: 0.5666 (m90) REVERT: R 116 MET cc_start: 0.6018 (ptp) cc_final: 0.5800 (tmm) outliers start: 39 outliers final: 20 residues processed: 138 average time/residue: 1.1574 time to fit residues: 169.0388 Evaluate side-chains 130 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain B residue 217 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.170540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133147 restraints weight = 8252.536| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.88 r_work: 0.3439 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7762 Z= 0.111 Angle : 0.485 6.910 10526 Z= 0.262 Chirality : 0.041 0.149 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.348 57.557 1057 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.19 % Allowed : 24.75 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.27), residues: 955 helix: 2.45 (0.26), residues: 365 sheet: 0.17 (0.35), residues: 214 loop : -1.50 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.008 0.001 TYR R 277 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 373) hydrogen bonds : angle 3.80867 ( 1062) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.86848 ( 4) covalent geometry : bond 0.00249 ( 7760) covalent geometry : angle 0.48448 (10522) *********************** 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 142 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8245 (ttp-170) cc_final: 0.7234 (ttt-90) REVERT: B 152 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 217 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7033 (ptt) REVERT: B 234 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8270 (t80) REVERT: G 42 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: N 108 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: A 38 ARG cc_start: 0.7951 (mmt-90) cc_final: 0.7734 (mtp180) REVERT: R 69 LEU cc_start: 0.6244 (tp) cc_final: 0.5980 (mt) REVERT: R 116 MET cc_start: 0.6138 (ptp) cc_final: 0.5929 (ptp) outliers start: 34 outliers final: 21 residues processed: 133 average time/residue: 1.3027 time to fit residues: 183.0476 Evaluate side-chains 136 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 138 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET 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 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 108 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.169928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132594 restraints weight = 8281.482| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.87 r_work: 0.3431 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1578 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= 0.122 Angle : 0.498 7.106 10526 Z= 0.268 Chirality : 0.042 0.140 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.401 57.710 1057 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.43 % Allowed : 25.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.27), residues: 955 helix: 2.41 (0.26), residues: 366 sheet: 0.16 (0.35), residues: 214 loop : -1.47 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.008 0.001 TYR N 80 ARG 0.001 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 373) hydrogen bonds : angle 3.82829 ( 1062) SS BOND : bond 0.00325 ( 2) SS BOND : angle 0.90836 ( 4) covalent geometry : bond 0.00280 ( 7760) covalent geometry : angle 0.49796 (10522) *********************** 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 144 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7520 (tm-30) REVERT: B 42 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6193 (tmt170) REVERT: B 134 ARG cc_start: 0.7421 (mtm180) cc_final: 0.7075 (mtt-85) REVERT: B 152 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 217 MET cc_start: 0.7481 (OUTLIER) cc_final: 0.7071 (ptt) REVERT: B 234 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8210 (t80) REVERT: G 42 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: N 108 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: A 38 ARG cc_start: 0.7968 (mmt-90) cc_final: 0.7750 (mtp180) REVERT: A 356 ARG cc_start: 0.8494 (mmm160) cc_final: 0.7599 (mpt180) REVERT: R 69 LEU cc_start: 0.6250 (tp) cc_final: 0.5970 (mt) REVERT: R 116 MET cc_start: 0.6114 (ptp) cc_final: 0.5886 (ptp) outliers start: 36 outliers final: 22 residues processed: 136 average time/residue: 1.2395 time to fit residues: 178.3763 Evaluate side-chains 135 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 161 SER Chi-restraints excluded: chain B residue 217 MET 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 N residue 108 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.0000 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.134141 restraints weight = 8272.081| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.11 r_work: 0.3412 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7762 Z= 0.094 Angle : 0.461 6.755 10526 Z= 0.250 Chirality : 0.041 0.144 1212 Planarity : 0.003 0.051 1332 Dihedral : 4.163 56.786 1057 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.33 % Allowed : 26.35 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.27), residues: 955 helix: 2.64 (0.26), residues: 367 sheet: 0.24 (0.35), residues: 214 loop : -1.44 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 261 PHE 0.011 0.001 PHE R 120 TYR 0.008 0.001 TYR N 80 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 373) hydrogen bonds : angle 3.65948 ( 1062) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.81962 ( 4) covalent geometry : bond 0.00202 ( 7760) covalent geometry : angle 0.46106 (10522) ********************** 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 136 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7486 (tm-30) REVERT: B 134 ARG cc_start: 0.7286 (mtm180) cc_final: 0.6921 (mtt-85) REVERT: B 152 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8134 (mp) REVERT: B 234 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8232 (t80) REVERT: G 42 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: A 27 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7672 (mp0) REVERT: A 38 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7672 (mtp180) REVERT: A 356 ARG cc_start: 0.8507 (mmm160) cc_final: 0.7540 (mpt180) REVERT: R 69 LEU cc_start: 0.5963 (tp) cc_final: 0.5212 (mp) outliers start: 27 outliers final: 19 residues processed: 130 average time/residue: 1.1981 time to fit residues: 164.9142 Evaluate side-chains 128 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 82 TRP 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 62 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 R 217 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.173976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133881 restraints weight = 8202.398| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.08 r_work: 0.3444 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7762 Z= 0.098 Angle : 0.470 6.680 10526 Z= 0.254 Chirality : 0.041 0.136 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.170 56.942 1057 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.57 % Allowed : 26.35 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.27), residues: 955 helix: 2.70 (0.26), residues: 367 sheet: 0.25 (0.35), residues: 214 loop : -1.44 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE R 120 TYR 0.008 0.001 TYR N 80 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 373) hydrogen bonds : angle 3.65940 ( 1062) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.78663 ( 4) covalent geometry : bond 0.00213 ( 7760) covalent geometry : angle 0.46937 (10522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6528.06 seconds wall clock time: 112 minutes 45.54 seconds (6765.54 seconds total)