Starting phenix.real_space_refine on Sun May 11 05:33:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w8x_37360/05_2025/8w8x_37360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w8x_37360/05_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_37360/05_2025/8w8x_37360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w8x_37360/05_2025/8w8x_37360.map" model { file = "/net/cci-nas-00/data/ceres_data/8w8x_37360/05_2025/8w8x_37360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w8x_37360/05_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-5687/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: 4.82, per 1000 atoms: 0.63 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: 1.80 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: 0.84 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: 2.09 Time building geometry restraints manager: 2.12 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- 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 (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 : 0.843 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: 1.2162 time to fit residues: 185.0369 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 : 0.864 ------------------------------------------------------------------------------- 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 = 0.171853 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 = 8226.606| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.96 r_work: 0.3442 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 56.409 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 4.06655 ( 1062) SS BOND : bond 0.00812 ( 2) SS BOND : angle 1.66053 ( 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 : 0.855 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8188 (tptt) cc_final: 0.7830 (tmtm) REVERT: B 96 ARG cc_start: 0.8053 (ttt180) cc_final: 0.7238 (ttt-90) REVERT: B 152 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8107 (mp) REVERT: G 42 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: N 38 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8018 (ttp-170) REVERT: A 38 ARG cc_start: 0.7992 (mmt-90) cc_final: 0.7686 (mtp180) outliers start: 33 outliers final: 13 residues processed: 136 average time/residue: 1.2176 time to fit residues: 174.9824 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 : 0.761 ------------------------------------------------------------------------------- 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: 0.9990 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.166891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127683 restraints weight = 8333.405| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.96 r_work: 0.3377 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7762 Z= 0.210 Angle : 0.604 9.094 10526 Z= 0.320 Chirality : 0.045 0.155 1212 Planarity : 0.005 0.056 1332 Dihedral : 4.903 58.039 1057 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.67 % Allowed : 21.92 % Favored : 72.41 % 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: 0.16 (0.27), residues: 955 helix: 1.78 (0.26), residues: 365 sheet: -0.07 (0.34), residues: 221 loop : -1.52 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.002 PHE B 151 TYR 0.012 0.002 TYR R 277 ARG 0.006 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.05762 ( 373) hydrogen bonds : angle 4.23593 ( 1062) SS BOND : bond 0.00521 ( 2) SS BOND : angle 2.54087 ( 4) covalent geometry : bond 0.00515 ( 7760) covalent geometry : angle 0.60201 (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 : 0.917 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6377 (tmt170) REVERT: B 152 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8061 (mp) REVERT: B 234 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.8263 (t80) REVERT: G 38 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6973 (ttp) REVERT: G 42 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: N 38 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.8064 (ttp-170) outliers start: 46 outliers final: 23 residues processed: 134 average time/residue: 1.1723 time to fit residues: 166.1176 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 38 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 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: 0.8980 chunk 90 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 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 = 0.3994 r_free = 0.3994 target = 0.170064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130588 restraints weight = 8214.008| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.97 r_work: 0.3411 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1291 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= 0.128 Angle : 0.515 7.563 10526 Z= 0.277 Chirality : 0.042 0.143 1212 Planarity : 0.004 0.053 1332 Dihedral : 4.650 59.391 1057 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.19 % Allowed : 23.77 % 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: 0.37 (0.27), residues: 955 helix: 2.07 (0.26), residues: 365 sheet: 0.06 (0.35), residues: 219 loop : -1.55 (0.29), residues: 371 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 0.015 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 0.04614 ( 373) hydrogen bonds : angle 3.98496 ( 1062) SS BOND : bond 0.00473 ( 2) SS BOND : angle 2.17601 ( 4) covalent geometry : bond 0.00295 ( 7760) covalent geometry : angle 0.51306 (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 144 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6840 (OUTLIER) cc_final: 0.6294 (tmt170) REVERT: B 152 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8096 (mp) REVERT: B 234 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8209 (t80) REVERT: G 42 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: N 38 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7949 (ttp-170) outliers start: 34 outliers final: 17 residues processed: 134 average time/residue: 1.1822 time to fit residues: 167.4238 Evaluate side-chains 133 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 334 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 86 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: 2.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129524 restraints weight = 8148.785| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.93 r_work: 0.3398 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7762 Z= 0.153 Angle : 0.533 8.002 10526 Z= 0.286 Chirality : 0.043 0.147 1212 Planarity : 0.004 0.053 1332 Dihedral : 4.686 59.741 1057 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.68 % Allowed : 23.40 % 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: 0.35 (0.26), residues: 955 helix: 2.06 (0.26), residues: 365 sheet: 0.02 (0.34), residues: 219 loop : -1.55 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE B 151 TYR 0.010 0.001 TYR R 277 ARG 0.003 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.04946 ( 373) hydrogen bonds : angle 4.01799 ( 1062) SS BOND : bond 0.00398 ( 2) SS BOND : angle 1.19584 ( 4) covalent geometry : bond 0.00366 ( 7760) covalent geometry : angle 0.53294 (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 146 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.827 Fit side-chains REVERT: B 13 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7541 (tm-30) REVERT: B 42 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6251 (tmt170) REVERT: B 152 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 234 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8231 (t80) REVERT: G 42 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6884 (mp0) REVERT: N 38 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7959 (ttp-170) outliers start: 38 outliers final: 21 residues processed: 132 average time/residue: 1.2765 time to fit residues: 177.7551 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 : 0.837 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 20 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129138 restraints weight = 8217.140| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.94 r_work: 0.3394 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7762 Z= 0.161 Angle : 0.549 8.130 10526 Z= 0.293 Chirality : 0.044 0.149 1212 Planarity : 0.004 0.054 1332 Dihedral : 4.721 59.428 1057 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: 0.32 (0.26), residues: 955 helix: 2.03 (0.26), residues: 365 sheet: -0.01 (0.34), residues: 218 loop : -1.55 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE B 151 TYR 0.010 0.001 TYR R 277 ARG 0.003 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.05080 ( 373) hydrogen bonds : angle 4.04044 ( 1062) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.04467 ( 4) covalent geometry : bond 0.00387 ( 7760) covalent geometry : angle 0.54836 (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 145 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6255 (tmt170) REVERT: B 152 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 217 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7131 (ptt) REVERT: B 234 PHE cc_start: 0.8843 (OUTLIER) cc_final: 0.8223 (t80) REVERT: G 42 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: N 38 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7961 (ttp-170) REVERT: R 70 HIS cc_start: 0.6222 (OUTLIER) cc_final: 0.5883 (m90) outliers start: 42 outliers final: 26 residues processed: 132 average time/residue: 1.1966 time to fit residues: 167.1722 Evaluate side-chains 137 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 118 ASP 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 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 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 334 VAL 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 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 70 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.173002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132616 restraints weight = 8225.015| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.11 r_work: 0.3395 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1595 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= 0.098 Angle : 0.464 6.639 10526 Z= 0.251 Chirality : 0.041 0.138 1212 Planarity : 0.003 0.051 1332 Dihedral : 4.327 57.947 1057 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.80 % Allowed : 23.89 % Favored : 71.31 % 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: 0.67 (0.27), residues: 955 helix: 2.40 (0.27), residues: 366 sheet: 0.20 (0.36), residues: 207 loop : -1.43 (0.28), residues: 382 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 0.011 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 0.03859 ( 373) hydrogen bonds : angle 3.77138 ( 1062) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.87762 ( 4) covalent geometry : bond 0.00212 ( 7760) covalent geometry : angle 0.46401 (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 147 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7861 (mm-40) cc_final: 0.7480 (tm-30) REVERT: B 23 LYS cc_start: 0.8123 (tttt) cc_final: 0.7770 (tmtm) REVERT: B 96 ARG cc_start: 0.8232 (ttp-170) cc_final: 0.7207 (ttt-90) REVERT: B 152 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8143 (mp) REVERT: B 234 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8254 (t80) REVERT: G 42 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6896 (mp0) REVERT: A 27 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7664 (mp0) REVERT: A 38 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7667 (mtp180) REVERT: R 69 LEU cc_start: 0.6222 (tp) cc_final: 0.6022 (mt) REVERT: R 70 HIS cc_start: 0.6086 (OUTLIER) cc_final: 0.5703 (m90) outliers start: 39 outliers final: 20 residues processed: 137 average time/residue: 1.1782 time to fit residues: 170.8562 Evaluate side-chains 131 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN 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 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 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: 0.8980 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 15 optimal weight: 0.0170 chunk 71 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.171196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133750 restraints weight = 8240.008| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.89 r_work: 0.3445 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7762 Z= 0.105 Angle : 0.471 6.757 10526 Z= 0.254 Chirality : 0.041 0.139 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.301 57.600 1057 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.43 % Allowed : 24.38 % Favored : 71.18 % 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: 0.74 (0.27), residues: 955 helix: 2.50 (0.26), residues: 366 sheet: 0.24 (0.35), residues: 212 loop : -1.48 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.012 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 0.03973 ( 373) hydrogen bonds : angle 3.74266 ( 1062) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.84792 ( 4) covalent geometry : bond 0.00231 ( 7760) covalent geometry : angle 0.47048 (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 144 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8171 (tttt) cc_final: 0.7813 (tmtm) REVERT: B 96 ARG cc_start: 0.8244 (ttp-170) cc_final: 0.7221 (ttt-90) REVERT: B 152 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8259 (t80) REVERT: G 42 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: N 108 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: A 27 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7686 (mp0) REVERT: R 69 LEU cc_start: 0.6196 (tp) cc_final: 0.5922 (mt) outliers start: 36 outliers final: 23 residues processed: 134 average time/residue: 1.1609 time to fit residues: 164.9681 Evaluate side-chains 134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN 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 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 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 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: 0.2980 chunk 55 optimal weight: 0.0970 chunk 26 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.2274 ------------------------------------------------------------------------------- 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 A 35 GLN A 218 ASN R 217 HIS R 282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.174465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137679 restraints weight = 8267.606| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.88 r_work: 0.3497 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1952 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= 0.084 Angle : 0.442 6.112 10526 Z= 0.241 Chirality : 0.040 0.138 1212 Planarity : 0.003 0.050 1332 Dihedral : 4.071 56.725 1057 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.57 % Allowed : 26.11 % 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: 0.94 (0.27), residues: 955 helix: 2.71 (0.27), residues: 369 sheet: 0.40 (0.36), residues: 201 loop : -1.43 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.000 HIS R 261 PHE 0.009 0.001 PHE B 241 TYR 0.006 0.001 TYR R 277 ARG 0.001 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 373) hydrogen bonds : angle 3.57255 ( 1062) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.74131 ( 4) covalent geometry : bond 0.00168 ( 7760) covalent geometry : angle 0.44141 (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 141 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7478 (tm-30) REVERT: B 16 ASN cc_start: 0.7785 (m110) cc_final: 0.7329 (m-40) REVERT: B 23 LYS cc_start: 0.8119 (tttt) cc_final: 0.7773 (tmtm) REVERT: B 134 ARG cc_start: 0.7393 (mtm180) cc_final: 0.7081 (mtt-85) REVERT: B 152 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8197 (mp) REVERT: B 234 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8187 (t80) REVERT: G 42 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: A 27 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7716 (mp0) REVERT: R 69 LEU cc_start: 0.6000 (tp) cc_final: 0.5266 (mp) outliers start: 29 outliers final: 13 residues processed: 132 average time/residue: 1.1979 time to fit residues: 167.5875 Evaluate side-chains 122 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 59 SER 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 100 ILE 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: 0.9990 chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.169890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132548 restraints weight = 8315.055| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.90 r_work: 0.3430 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7762 Z= 0.126 Angle : 0.506 7.151 10526 Z= 0.272 Chirality : 0.042 0.154 1212 Planarity : 0.004 0.051 1332 Dihedral : 4.357 57.797 1057 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.71 % Allowed : 26.97 % 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: 0.80 (0.27), residues: 955 helix: 2.56 (0.26), residues: 366 sheet: 0.24 (0.35), residues: 214 loop : -1.43 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 151 TYR 0.009 0.001 TYR N 80 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 373) hydrogen bonds : angle 3.79707 ( 1062) SS BOND : bond 0.00374 ( 2) SS BOND : angle 0.89372 ( 4) covalent geometry : bond 0.00292 ( 7760) covalent geometry : angle 0.50580 (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 130 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7486 (tm-30) REVERT: B 16 ASN cc_start: 0.7817 (m-40) cc_final: 0.7407 (m-40) REVERT: B 23 LYS cc_start: 0.8209 (tttt) cc_final: 0.7867 (tmtm) REVERT: B 134 ARG cc_start: 0.7421 (mtm180) cc_final: 0.7084 (mtt-85) REVERT: B 152 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 234 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8291 (t80) REVERT: G 42 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7035 (mp0) REVERT: N 108 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: A 356 ARG cc_start: 0.8505 (mmm160) cc_final: 0.7600 (mpt180) REVERT: R 69 LEU cc_start: 0.6121 (tp) cc_final: 0.5414 (mp) outliers start: 22 outliers final: 13 residues processed: 123 average time/residue: 1.2421 time to fit residues: 161.6992 Evaluate side-chains 123 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 59 SER 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 100 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.168588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.131623 restraints weight = 8240.765| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.85 r_work: 0.3416 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7762 Z= 0.147 Angle : 0.531 7.584 10526 Z= 0.285 Chirality : 0.043 0.145 1212 Planarity : 0.004 0.052 1332 Dihedral : 4.522 57.532 1057 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.83 % Allowed : 26.97 % Favored : 70.20 % 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: 0.64 (0.27), residues: 955 helix: 2.38 (0.26), residues: 366 sheet: 0.16 (0.34), residues: 214 loop : -1.47 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.002 PHE B 151 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 373) hydrogen bonds : angle 3.93380 ( 1062) SS BOND : bond 0.00359 ( 2) SS BOND : angle 0.97306 ( 4) covalent geometry : bond 0.00350 ( 7760) covalent geometry : angle 0.53075 (10522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5896.14 seconds wall clock time: 102 minutes 3.69 seconds (6123.69 seconds total)