Starting phenix.real_space_refine on Sat Jun 7 11:33:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwi_37889/06_2025/8wwi_37889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwi_37889/06_2025/8wwi_37889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wwi_37889/06_2025/8wwi_37889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwi_37889/06_2025/8wwi_37889.map" model { file = "/net/cci-nas-00/data/ceres_data/8wwi_37889/06_2025/8wwi_37889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwi_37889/06_2025/8wwi_37889.cif" } resolution = 3.43 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= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5606 2.51 5 N 1485 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8803 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1741 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" 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: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2225 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 273} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 5.68, per 1000 atoms: 0.65 Number of scatterers: 8803 At special positions: 0 Unit cell: (87.74, 117.7, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1648 8.00 N 1485 7.00 C 5606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 185 " - pdb=" SG CYS R 263 " distance=2.03 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: 3.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.547A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.643A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.176A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.800A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.565A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.517A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.538A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 137 removed outlier: 3.785A pdb=" N MET R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Proline residue: R 113 - end of helix Processing helix chain 'R' and resid 145 through 164 removed outlier: 3.674A pdb=" N SER R 155 " --> pdb=" O ILE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 removed outlier: 3.556A pdb=" N HIS R 170 " --> pdb=" O PRO R 166 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN R 171 " --> pdb=" O PHE R 167 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU R 172 " --> pdb=" O MET R 168 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET R 173 " --> pdb=" O ILE R 169 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY R 174 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 216 removed outlier: 4.155A pdb=" N MET R 184 " --> pdb=" O PHE R 180 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG R 210 " --> pdb=" O MET R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 223 removed outlier: 3.894A pdb=" N LYS R 222 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 244 Processing helix chain 'R' and resid 244 through 250 removed outlier: 3.518A pdb=" N TRP R 248 " --> pdb=" O ILE R 244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR R 250 " --> pdb=" O PRO R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 286 removed outlier: 3.693A pdb=" N LEU R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR R 275 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TRP R 276 " --> pdb=" O THR R 272 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE R 277 " --> pdb=" O ASP R 273 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN R 281 " --> pdb=" O PHE R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 286 through 303 Processing helix chain 'R' and resid 313 through 351 removed outlier: 3.513A pdb=" N ARG R 322 " --> pdb=" O LEU R 318 " (cutoff:3.500A) Proline residue: R 340 - end of helix removed outlier: 4.333A pdb=" N LEU R 349 " --> pdb=" O GLN R 345 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 384 removed outlier: 4.096A pdb=" N SER R 373 " --> pdb=" O GLY R 369 " (cutoff:3.500A) Proline residue: R 377 - end of helix removed outlier: 3.516A pdb=" N TYR R 380 " --> pdb=" O ASN R 376 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS R 384 " --> pdb=" O TYR R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.670A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.936A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.550A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.966A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.843A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.451A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.486A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.780A pdb=" N GLY E 16 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG E 18 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR E 84 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU E 20 " --> pdb=" O GLN E 82 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLN E 82 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS E 22 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA E 24 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR E 78 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.005A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.461A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.630A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 251 through 255 458 hydrogen bonds defined for protein. 1281 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: 3.27 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2841 1.34 - 1.46: 2088 1.46 - 1.58: 3970 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 8992 Sorted by residual: bond pdb=" CB PRO R 217 " pdb=" CG PRO R 217 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.78e-01 bond pdb=" C ASP E 74 " pdb=" N PRO E 75 " ideal model delta sigma weight residual 1.335 1.343 -0.007 1.36e-02 5.41e+03 2.79e-01 bond pdb=" C MET R 165 " pdb=" N PRO R 166 " ideal model delta sigma weight residual 1.335 1.341 -0.006 1.19e-02 7.06e+03 2.68e-01 bond pdb=" N ILE R 110 " pdb=" CA ILE R 110 " ideal model delta sigma weight residual 1.459 1.453 0.006 1.25e-02 6.40e+03 2.31e-01 bond pdb=" CG1 ILE A 19 " pdb=" CD1 ILE A 19 " ideal model delta sigma weight residual 1.513 1.495 0.018 3.90e-02 6.57e+02 2.10e-01 ... (remaining 8987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 12069 1.37 - 2.74: 121 2.74 - 4.11: 13 4.11 - 5.48: 10 5.48 - 6.85: 1 Bond angle restraints: 12214 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.71e+00 angle pdb=" CA LEU B 55 " pdb=" CB LEU B 55 " pdb=" CG LEU B 55 " ideal model delta sigma weight residual 116.30 109.45 6.85 3.50e+00 8.16e-02 3.83e+00 angle pdb=" N LYS R 139 " pdb=" CA LYS R 139 " pdb=" C LYS R 139 " ideal model delta sigma weight residual 112.13 109.92 2.21 1.37e+00 5.33e-01 2.60e+00 angle pdb=" N ALA A 291 " pdb=" CA ALA A 291 " pdb=" C ALA A 291 " ideal model delta sigma weight residual 110.06 112.36 -2.30 1.43e+00 4.89e-01 2.60e+00 angle pdb=" N VAL R 308 " pdb=" CA VAL R 308 " pdb=" CB VAL R 308 " ideal model delta sigma weight residual 111.75 107.41 4.34 2.73e+00 1.34e-01 2.53e+00 ... (remaining 12209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.82: 4992 11.82 - 23.64: 242 23.64 - 35.45: 56 35.45 - 47.27: 17 47.27 - 59.09: 7 Dihedral angle restraints: 5314 sinusoidal: 1997 harmonic: 3317 Sorted by residual: dihedral pdb=" CA ALA A 291 " pdb=" C ALA A 291 " pdb=" N GLY A 292 " pdb=" CA GLY A 292 " ideal model delta harmonic sigma weight residual 180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N ALA A 41 " pdb=" CA ALA A 41 " ideal model delta harmonic sigma weight residual 180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 854 0.027 - 0.053: 346 0.053 - 0.080: 109 0.080 - 0.107: 70 0.107 - 0.134: 27 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA VAL E 199 " pdb=" N VAL E 199 " pdb=" C VAL E 199 " pdb=" CB VAL E 199 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL B 296 " pdb=" N VAL B 296 " pdb=" C VAL B 296 " pdb=" CB VAL B 296 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1403 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO B 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 287 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 288 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 256 " 0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO R 257 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " 0.015 5.00e-02 4.00e+02 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 110 2.65 - 3.21: 7915 3.21 - 3.77: 13781 3.77 - 4.34: 19709 4.34 - 4.90: 32332 Nonbonded interactions: 73847 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.085 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.120 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.235 3.120 nonbonded pdb=" O SER R 243 " pdb=" OH TYR R 280 " model vdw 2.246 3.040 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.263 3.120 ... (remaining 73842 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: 21.200 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8995 Z= 0.073 Angle : 0.406 6.846 12220 Z= 0.218 Chirality : 0.039 0.134 1406 Planarity : 0.003 0.041 1546 Dihedral : 8.184 59.089 3165 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.95 % Allowed : 2.53 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.41 (0.25), residues: 1129 helix: 0.20 (0.26), residues: 404 sheet: 0.79 (0.29), residues: 291 loop : 0.20 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS E 167 PHE 0.010 0.001 PHE B 151 TYR 0.010 0.001 TYR A 290 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.25020 ( 453) hydrogen bonds : angle 7.58310 ( 1281) SS BOND : bond 0.00072 ( 3) SS BOND : angle 0.40284 ( 6) covalent geometry : bond 0.00151 ( 8992) covalent geometry : angle 0.40564 (12214) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 291 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7521 (ttm-80) REVERT: A 230 TYR cc_start: 0.6668 (p90) cc_final: 0.6298 (p90) REVERT: A 274 PHE cc_start: 0.7554 (t80) cc_final: 0.7156 (t80) REVERT: A 328 ASP cc_start: 0.5316 (t0) cc_final: 0.5006 (t70) REVERT: A 333 GLN cc_start: 0.7463 (tp40) cc_final: 0.7066 (tp-100) REVERT: A 337 ASP cc_start: 0.8122 (m-30) cc_final: 0.7715 (m-30) REVERT: B 46 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7782 (mtp85) REVERT: B 226 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6633 (mt-10) REVERT: B 279 SER cc_start: 0.6820 (p) cc_final: 0.6462 (t) REVERT: E 5 VAL cc_start: 0.7920 (t) cc_final: 0.7658 (m) REVERT: E 38 ARG cc_start: 0.7581 (ptt-90) cc_final: 0.7349 (ptt90) REVERT: E 46 GLU cc_start: 0.6942 (tt0) cc_final: 0.6682 (tt0) REVERT: E 108 PHE cc_start: 0.7201 (m-80) cc_final: 0.6991 (m-80) REVERT: E 203 PHE cc_start: 0.7035 (m-80) cc_final: 0.6776 (m-80) REVERT: E 228 TYR cc_start: 0.6264 (m-80) cc_final: 0.6043 (m-80) REVERT: R 272 THR cc_start: 0.7540 (p) cc_final: 0.7286 (p) outliers start: 9 outliers final: 4 residues processed: 299 average time/residue: 0.2651 time to fit residues: 106.8692 Evaluate side-chains 221 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 217 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 91 HIS B 259 GLN E 113 GLN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN E 179 GLN R 170 HIS R 194 ASN R 281 GLN R 313 GLN R 345 GLN R 363 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.207017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.162699 restraints weight = 12201.163| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 3.38 r_work: 0.3770 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8995 Z= 0.258 Angle : 0.710 9.104 12220 Z= 0.384 Chirality : 0.048 0.203 1406 Planarity : 0.005 0.035 1546 Dihedral : 5.251 45.080 1237 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.85 % Allowed : 10.86 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.61 (0.25), residues: 1129 helix: 0.87 (0.25), residues: 402 sheet: 0.45 (0.30), residues: 282 loop : 0.13 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 169 HIS 0.007 0.002 HIS R 170 PHE 0.017 0.002 PHE B 253 TYR 0.019 0.002 TYR E 103 ARG 0.006 0.001 ARG R 322 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 453) hydrogen bonds : angle 5.70121 ( 1281) SS BOND : bond 0.00420 ( 3) SS BOND : angle 2.85824 ( 6) covalent geometry : bond 0.00592 ( 8992) covalent geometry : angle 0.70702 (12214) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7523 (mtm-85) REVERT: A 328 ASP cc_start: 0.6282 (t0) cc_final: 0.5939 (t70) REVERT: A 333 GLN cc_start: 0.7819 (tp40) cc_final: 0.7445 (tp-100) REVERT: A 337 ASP cc_start: 0.8240 (m-30) cc_final: 0.7797 (m-30) REVERT: B 96 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7567 (mmt90) REVERT: B 209 LYS cc_start: 0.7243 (mttm) cc_final: 0.7010 (mttt) REVERT: B 220 GLN cc_start: 0.7338 (mm-40) cc_final: 0.6827 (mm-40) REVERT: B 279 SER cc_start: 0.6783 (p) cc_final: 0.6458 (t) REVERT: E 86 LEU cc_start: 0.8110 (mt) cc_final: 0.7803 (tp) REVERT: E 138 ILE cc_start: 0.5235 (mm) cc_final: 0.4963 (mm) REVERT: E 140 MET cc_start: 0.6272 (mmp) cc_final: 0.6034 (mmp) REVERT: E 228 TYR cc_start: 0.5931 (m-80) cc_final: 0.5424 (m-10) REVERT: E 230 MET cc_start: 0.5494 (ttp) cc_final: 0.5016 (tmm) REVERT: R 139 LYS cc_start: 0.7161 (ptpt) cc_final: 0.6781 (ptpp) REVERT: R 184 MET cc_start: 0.8008 (mmt) cc_final: 0.7687 (tpp) REVERT: R 275 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6643 (t80) REVERT: R 299 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7461 (ttm170) outliers start: 46 outliers final: 31 residues processed: 244 average time/residue: 0.2211 time to fit residues: 72.6323 Evaluate side-chains 238 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 221 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 280 TYR Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.209913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164764 restraints weight = 12406.577| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 3.10 r_work: 0.3809 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8995 Z= 0.139 Angle : 0.592 8.584 12220 Z= 0.314 Chirality : 0.044 0.154 1406 Planarity : 0.004 0.045 1546 Dihedral : 4.830 43.274 1234 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.27 % Allowed : 15.40 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.97 (0.25), residues: 1129 helix: 1.41 (0.26), residues: 397 sheet: 0.47 (0.31), residues: 270 loop : 0.23 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.001 PHE A 189 TYR 0.016 0.002 TYR E 103 ARG 0.009 0.001 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 453) hydrogen bonds : angle 5.24839 ( 1281) SS BOND : bond 0.00597 ( 3) SS BOND : angle 1.78428 ( 6) covalent geometry : bond 0.00312 ( 8992) covalent geometry : angle 0.59058 (12214) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7459 (mtm-85) REVERT: A 274 PHE cc_start: 0.7716 (t80) cc_final: 0.7277 (t80) REVERT: A 333 GLN cc_start: 0.7826 (tp40) cc_final: 0.7371 (tp-100) REVERT: A 337 ASP cc_start: 0.8240 (m-30) cc_final: 0.7890 (m-30) REVERT: B 96 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7482 (mmt90) REVERT: B 220 GLN cc_start: 0.7388 (mm-40) cc_final: 0.6873 (mm-40) REVERT: B 234 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6896 (m-80) REVERT: B 279 SER cc_start: 0.6927 (p) cc_final: 0.6670 (t) REVERT: C 38 MET cc_start: 0.8279 (ptm) cc_final: 0.8037 (ptm) REVERT: E 138 ILE cc_start: 0.5262 (mm) cc_final: 0.5000 (mm) REVERT: E 176 TRP cc_start: 0.6825 (m100) cc_final: 0.6493 (m100) REVERT: E 194 ASN cc_start: 0.8278 (m-40) cc_final: 0.8077 (m110) REVERT: E 228 TYR cc_start: 0.6406 (m-80) cc_final: 0.6034 (m-10) REVERT: E 230 MET cc_start: 0.5192 (ttp) cc_final: 0.4869 (tmm) REVERT: R 184 MET cc_start: 0.7881 (mmt) cc_final: 0.7608 (tpp) REVERT: R 275 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6610 (t80) REVERT: R 376 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7897 (t0) outliers start: 31 outliers final: 19 residues processed: 239 average time/residue: 0.2173 time to fit residues: 70.9306 Evaluate side-chains 227 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 376 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.0770 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.211305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.166498 restraints weight = 12366.495| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 3.06 r_work: 0.3855 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8995 Z= 0.125 Angle : 0.589 8.323 12220 Z= 0.309 Chirality : 0.043 0.154 1406 Planarity : 0.004 0.039 1546 Dihedral : 4.717 43.862 1234 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.16 % Allowed : 16.35 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.01 (0.25), residues: 1129 helix: 1.57 (0.26), residues: 400 sheet: 0.39 (0.30), residues: 281 loop : 0.18 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.027 0.001 PHE B 241 TYR 0.023 0.001 TYR E 190 ARG 0.006 0.000 ARG A 21 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 453) hydrogen bonds : angle 5.01484 ( 1281) SS BOND : bond 0.00508 ( 3) SS BOND : angle 1.45150 ( 6) covalent geometry : bond 0.00268 ( 8992) covalent geometry : angle 0.58818 (12214) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7461 (mtm-85) REVERT: A 274 PHE cc_start: 0.7700 (t80) cc_final: 0.7292 (t80) REVERT: A 333 GLN cc_start: 0.7805 (tp40) cc_final: 0.7337 (tp-100) REVERT: A 337 ASP cc_start: 0.8204 (m-30) cc_final: 0.7854 (m-30) REVERT: B 96 ARG cc_start: 0.7765 (mtt180) cc_final: 0.7528 (mmt90) REVERT: B 234 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.7033 (m-80) REVERT: B 279 SER cc_start: 0.6843 (p) cc_final: 0.6545 (t) REVERT: B 297 TRP cc_start: 0.8366 (m100) cc_final: 0.8072 (m100) REVERT: B 303 ASP cc_start: 0.7194 (t0) cc_final: 0.6378 (m-30) REVERT: C 21 MET cc_start: 0.8144 (mpp) cc_final: 0.7202 (mpp) REVERT: C 38 MET cc_start: 0.8307 (ptm) cc_final: 0.8040 (ptm) REVERT: E 138 ILE cc_start: 0.5463 (mm) cc_final: 0.5223 (mm) REVERT: E 176 TRP cc_start: 0.6802 (m100) cc_final: 0.6371 (m100) REVERT: E 228 TYR cc_start: 0.6312 (m-80) cc_final: 0.5908 (m-10) REVERT: E 230 MET cc_start: 0.5075 (ttp) cc_final: 0.4818 (tmm) REVERT: E 235 TYR cc_start: 0.7620 (m-80) cc_final: 0.7419 (m-80) REVERT: R 112 MET cc_start: 0.7755 (mtt) cc_final: 0.7140 (mtt) REVERT: R 184 MET cc_start: 0.7912 (mmt) cc_final: 0.7579 (tpp) REVERT: R 275 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6474 (t80) REVERT: R 325 ARG cc_start: 0.7420 (ptt-90) cc_final: 0.6832 (ptp90) REVERT: R 337 CYS cc_start: 0.9071 (m) cc_final: 0.8551 (m) REVERT: R 388 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7531 (ttp-110) outliers start: 30 outliers final: 20 residues processed: 228 average time/residue: 0.2077 time to fit residues: 64.6201 Evaluate side-chains 220 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.206969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.166156 restraints weight = 12479.672| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.26 r_work: 0.3793 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8995 Z= 0.190 Angle : 0.639 8.485 12220 Z= 0.338 Chirality : 0.045 0.166 1406 Planarity : 0.004 0.044 1546 Dihedral : 4.945 50.709 1234 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.43 % Allowed : 15.72 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.79 (0.25), residues: 1129 helix: 1.63 (0.26), residues: 394 sheet: 0.05 (0.30), residues: 289 loop : -0.02 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.023 0.002 PHE B 241 TYR 0.025 0.002 TYR B 85 ARG 0.011 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 453) hydrogen bonds : angle 5.15104 ( 1281) SS BOND : bond 0.00430 ( 3) SS BOND : angle 1.69008 ( 6) covalent geometry : bond 0.00440 ( 8992) covalent geometry : angle 0.63819 (12214) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7504 (mtm-85) REVERT: A 242 ARG cc_start: 0.8753 (mtt180) cc_final: 0.8323 (mtt-85) REVERT: A 274 PHE cc_start: 0.7810 (t80) cc_final: 0.7335 (t80) REVERT: A 333 GLN cc_start: 0.7726 (tp40) cc_final: 0.7267 (tp-100) REVERT: A 337 ASP cc_start: 0.8275 (m-30) cc_final: 0.7933 (m-30) REVERT: B 96 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7342 (mmt90) REVERT: B 220 GLN cc_start: 0.7599 (mm-40) cc_final: 0.6882 (mm-40) REVERT: B 234 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: C 38 MET cc_start: 0.8260 (ptm) cc_final: 0.8031 (ptm) REVERT: E 86 LEU cc_start: 0.7943 (mt) cc_final: 0.7378 (mm) REVERT: E 230 MET cc_start: 0.5489 (ttp) cc_final: 0.5144 (tmm) REVERT: R 112 MET cc_start: 0.8078 (mtt) cc_final: 0.7733 (mtt) REVERT: R 184 MET cc_start: 0.7855 (mmt) cc_final: 0.7528 (tpp) REVERT: R 325 ARG cc_start: 0.7467 (ptt-90) cc_final: 0.7135 (ttm170) REVERT: R 337 CYS cc_start: 0.9184 (m) cc_final: 0.8712 (m) REVERT: R 376 ASN cc_start: 0.8119 (t0) cc_final: 0.7887 (t0) outliers start: 42 outliers final: 30 residues processed: 224 average time/residue: 0.2035 time to fit residues: 62.6611 Evaluate side-chains 223 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 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 = 0.4434 r_free = 0.4434 target = 0.209749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166605 restraints weight = 12409.555| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.25 r_work: 0.3817 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8995 Z= 0.138 Angle : 0.607 8.867 12220 Z= 0.318 Chirality : 0.044 0.159 1406 Planarity : 0.004 0.042 1546 Dihedral : 4.789 49.686 1234 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.11 % Allowed : 17.30 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1129 helix: 1.65 (0.27), residues: 396 sheet: -0.01 (0.30), residues: 291 loop : 0.01 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS E 232 PHE 0.027 0.002 PHE B 241 TYR 0.022 0.002 TYR E 190 ARG 0.006 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 453) hydrogen bonds : angle 5.00181 ( 1281) SS BOND : bond 0.00513 ( 3) SS BOND : angle 1.42509 ( 6) covalent geometry : bond 0.00317 ( 8992) covalent geometry : angle 0.60670 (12214) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7843 (ttm-80) cc_final: 0.7483 (mtm-85) REVERT: A 242 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8305 (mtt-85) REVERT: A 274 PHE cc_start: 0.7801 (t80) cc_final: 0.7318 (t80) REVERT: A 304 GLN cc_start: 0.8090 (tt0) cc_final: 0.7743 (tp40) REVERT: A 333 GLN cc_start: 0.7607 (tp40) cc_final: 0.7169 (tp-100) REVERT: A 337 ASP cc_start: 0.8216 (m-30) cc_final: 0.7871 (m-30) REVERT: B 96 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7347 (mmt90) REVERT: B 220 GLN cc_start: 0.7520 (mm-40) cc_final: 0.6772 (mm-40) REVERT: B 234 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.6836 (m-80) REVERT: B 297 TRP cc_start: 0.8289 (m100) cc_final: 0.7992 (m100) REVERT: C 38 MET cc_start: 0.8331 (ptm) cc_final: 0.8056 (ptm) REVERT: E 86 LEU cc_start: 0.8010 (mt) cc_final: 0.7717 (mm) REVERT: E 230 MET cc_start: 0.5326 (ttp) cc_final: 0.4998 (tmm) REVERT: R 184 MET cc_start: 0.7953 (mmt) cc_final: 0.7624 (tpp) REVERT: R 269 ASN cc_start: 0.6799 (OUTLIER) cc_final: 0.6574 (t0) REVERT: R 325 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7156 (ttm170) REVERT: R 337 CYS cc_start: 0.9083 (m) cc_final: 0.8621 (m) outliers start: 39 outliers final: 28 residues processed: 224 average time/residue: 0.2068 time to fit residues: 64.2938 Evaluate side-chains 223 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.208781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165934 restraints weight = 12446.674| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 3.19 r_work: 0.3807 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8995 Z= 0.153 Angle : 0.623 8.949 12220 Z= 0.325 Chirality : 0.044 0.152 1406 Planarity : 0.004 0.043 1546 Dihedral : 4.816 51.603 1234 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.32 % Allowed : 17.62 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.68 (0.25), residues: 1129 helix: 1.64 (0.27), residues: 396 sheet: -0.17 (0.29), residues: 293 loop : -0.07 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.003 0.001 HIS B 142 PHE 0.027 0.002 PHE B 241 TYR 0.019 0.001 TYR E 103 ARG 0.004 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 453) hydrogen bonds : angle 4.97879 ( 1281) SS BOND : bond 0.00502 ( 3) SS BOND : angle 1.40735 ( 6) covalent geometry : bond 0.00350 ( 8992) covalent geometry : angle 0.62258 (12214) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7463 (mtm-85) REVERT: A 242 ARG cc_start: 0.8785 (mtt180) cc_final: 0.8325 (mtt-85) REVERT: A 274 PHE cc_start: 0.7833 (t80) cc_final: 0.7280 (t80) REVERT: A 304 GLN cc_start: 0.8176 (tt0) cc_final: 0.7812 (tp40) REVERT: A 333 GLN cc_start: 0.7601 (tp40) cc_final: 0.7158 (tp-100) REVERT: A 337 ASP cc_start: 0.8204 (m-30) cc_final: 0.7872 (m-30) REVERT: B 96 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7460 (mmt90) REVERT: B 220 GLN cc_start: 0.7552 (mm-40) cc_final: 0.6804 (mm-40) REVERT: B 234 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.6838 (m-80) REVERT: B 297 TRP cc_start: 0.8348 (m100) cc_final: 0.8064 (m100) REVERT: C 38 MET cc_start: 0.8222 (ptm) cc_final: 0.7949 (ptm) REVERT: E 86 LEU cc_start: 0.8070 (mt) cc_final: 0.7784 (mm) REVERT: E 213 THR cc_start: 0.8253 (m) cc_final: 0.8050 (p) REVERT: E 230 MET cc_start: 0.5397 (ttp) cc_final: 0.5060 (tmm) REVERT: R 165 MET cc_start: 0.7480 (ptp) cc_final: 0.7222 (ptm) REVERT: R 184 MET cc_start: 0.7974 (mmt) cc_final: 0.7651 (tpp) REVERT: R 269 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6560 (t0) REVERT: R 337 CYS cc_start: 0.9086 (m) cc_final: 0.8606 (m) outliers start: 41 outliers final: 32 residues processed: 224 average time/residue: 0.2113 time to fit residues: 65.0168 Evaluate side-chains 224 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 372 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.205598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.159761 restraints weight = 12623.648| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.10 r_work: 0.3769 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8995 Z= 0.217 Angle : 0.687 10.066 12220 Z= 0.360 Chirality : 0.046 0.165 1406 Planarity : 0.004 0.046 1546 Dihedral : 5.068 54.538 1234 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.85 % Allowed : 17.41 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1129 helix: 1.35 (0.27), residues: 400 sheet: -0.26 (0.29), residues: 284 loop : -0.18 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.029 0.002 PHE B 241 TYR 0.023 0.002 TYR E 103 ARG 0.007 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 453) hydrogen bonds : angle 5.21300 ( 1281) SS BOND : bond 0.00527 ( 3) SS BOND : angle 1.63452 ( 6) covalent geometry : bond 0.00506 ( 8992) covalent geometry : angle 0.68596 (12214) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7414 (mtm-85) REVERT: A 242 ARG cc_start: 0.8735 (mtt180) cc_final: 0.8335 (mtt-85) REVERT: A 274 PHE cc_start: 0.7872 (t80) cc_final: 0.7279 (t80) REVERT: A 304 GLN cc_start: 0.8103 (tt0) cc_final: 0.7829 (tp40) REVERT: A 309 ASP cc_start: 0.8330 (m-30) cc_final: 0.8101 (p0) REVERT: A 333 GLN cc_start: 0.7620 (tp40) cc_final: 0.7133 (tp-100) REVERT: A 337 ASP cc_start: 0.8188 (m-30) cc_final: 0.7827 (m-30) REVERT: B 96 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7394 (mmt90) REVERT: B 220 GLN cc_start: 0.7554 (mm-40) cc_final: 0.6822 (mm-40) REVERT: B 234 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: B 297 TRP cc_start: 0.8432 (m100) cc_final: 0.8152 (m100) REVERT: C 38 MET cc_start: 0.8196 (ptm) cc_final: 0.7953 (ptm) REVERT: E 218 ARG cc_start: 0.7427 (tpt170) cc_final: 0.7212 (tpm170) REVERT: E 230 MET cc_start: 0.5460 (ttp) cc_final: 0.5091 (tmm) REVERT: R 184 MET cc_start: 0.7939 (mmt) cc_final: 0.7618 (tpp) REVERT: R 269 ASN cc_start: 0.6719 (OUTLIER) cc_final: 0.6498 (t0) REVERT: R 275 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6602 (t80) REVERT: R 337 CYS cc_start: 0.9109 (m) cc_final: 0.8570 (m) outliers start: 46 outliers final: 37 residues processed: 224 average time/residue: 0.2218 time to fit residues: 67.4633 Evaluate side-chains 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 372 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.206929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.163396 restraints weight = 12563.321| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.31 r_work: 0.3782 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8995 Z= 0.184 Angle : 0.690 9.870 12220 Z= 0.355 Chirality : 0.046 0.169 1406 Planarity : 0.004 0.045 1546 Dihedral : 5.047 54.797 1234 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.54 % Allowed : 17.93 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.36 (0.25), residues: 1129 helix: 1.43 (0.27), residues: 395 sheet: -0.43 (0.29), residues: 291 loop : -0.23 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.003 0.001 HIS E 35 PHE 0.034 0.002 PHE B 241 TYR 0.040 0.002 TYR R 201 ARG 0.006 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 453) hydrogen bonds : angle 5.19950 ( 1281) SS BOND : bond 0.00436 ( 3) SS BOND : angle 1.39301 ( 6) covalent geometry : bond 0.00430 ( 8992) covalent geometry : angle 0.68913 (12214) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7754 (ttm-80) cc_final: 0.7417 (mtm-85) REVERT: A 242 ARG cc_start: 0.8761 (mtt180) cc_final: 0.8347 (mtt-85) REVERT: A 274 PHE cc_start: 0.7870 (t80) cc_final: 0.7297 (t80) REVERT: A 304 GLN cc_start: 0.8197 (tt0) cc_final: 0.7939 (tp40) REVERT: A 333 GLN cc_start: 0.7633 (tp40) cc_final: 0.7135 (tp-100) REVERT: A 337 ASP cc_start: 0.8228 (m-30) cc_final: 0.7884 (m-30) REVERT: B 96 ARG cc_start: 0.7786 (mtt180) cc_final: 0.7341 (mmt90) REVERT: B 215 GLU cc_start: 0.7389 (tm-30) cc_final: 0.5743 (tm-30) REVERT: B 217 MET cc_start: 0.7799 (mtp) cc_final: 0.7586 (ptp) REVERT: B 220 GLN cc_start: 0.7524 (mm-40) cc_final: 0.6797 (mm-40) REVERT: B 234 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6754 (m-80) REVERT: B 297 TRP cc_start: 0.8352 (m100) cc_final: 0.8118 (m100) REVERT: C 38 MET cc_start: 0.8185 (ptm) cc_final: 0.7958 (ptm) REVERT: C 47 GLU cc_start: 0.8056 (tp30) cc_final: 0.7832 (tp30) REVERT: E 78 THR cc_start: 0.5456 (m) cc_final: 0.5167 (p) REVERT: E 218 ARG cc_start: 0.7404 (tpt170) cc_final: 0.7186 (tpm170) REVERT: E 230 MET cc_start: 0.5428 (ttp) cc_final: 0.5022 (tmm) REVERT: R 184 MET cc_start: 0.7941 (mmt) cc_final: 0.7633 (tpp) REVERT: R 269 ASN cc_start: 0.6688 (OUTLIER) cc_final: 0.6458 (t0) REVERT: R 275 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.6785 (t80) REVERT: R 337 CYS cc_start: 0.9076 (m) cc_final: 0.8557 (m) outliers start: 43 outliers final: 37 residues processed: 216 average time/residue: 0.2081 time to fit residues: 61.4630 Evaluate side-chains 228 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 372 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.207887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.162769 restraints weight = 12466.794| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.06 r_work: 0.3801 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8995 Z= 0.167 Angle : 0.697 10.512 12220 Z= 0.360 Chirality : 0.046 0.252 1406 Planarity : 0.004 0.045 1546 Dihedral : 5.020 54.469 1234 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.69 % Allowed : 19.73 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1129 helix: 1.48 (0.27), residues: 389 sheet: -0.41 (0.29), residues: 296 loop : -0.14 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.003 0.001 HIS A 188 PHE 0.035 0.002 PHE B 241 TYR 0.049 0.002 TYR R 201 ARG 0.005 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 453) hydrogen bonds : angle 5.16340 ( 1281) SS BOND : bond 0.00447 ( 3) SS BOND : angle 1.33730 ( 6) covalent geometry : bond 0.00389 ( 8992) covalent geometry : angle 0.69688 (12214) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7503 (mtm-85) REVERT: A 242 ARG cc_start: 0.8802 (mtt180) cc_final: 0.8477 (mtt-85) REVERT: A 274 PHE cc_start: 0.7835 (t80) cc_final: 0.7259 (t80) REVERT: A 304 GLN cc_start: 0.8181 (tt0) cc_final: 0.7843 (tp40) REVERT: A 333 GLN cc_start: 0.7615 (tp40) cc_final: 0.7155 (tp-100) REVERT: A 337 ASP cc_start: 0.8214 (m-30) cc_final: 0.7864 (m-30) REVERT: B 96 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7416 (mmt90) REVERT: B 215 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6447 (tm-30) REVERT: B 217 MET cc_start: 0.7806 (mtp) cc_final: 0.7468 (ptp) REVERT: B 220 GLN cc_start: 0.7515 (mm-40) cc_final: 0.6804 (mm-40) REVERT: B 234 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: B 271 CYS cc_start: 0.6525 (m) cc_final: 0.6018 (m) REVERT: B 297 TRP cc_start: 0.8321 (m100) cc_final: 0.8080 (m100) REVERT: C 38 MET cc_start: 0.8335 (ptm) cc_final: 0.8093 (ptm) REVERT: E 218 ARG cc_start: 0.7473 (tpt170) cc_final: 0.7243 (tpm170) REVERT: E 230 MET cc_start: 0.5376 (ttp) cc_final: 0.5007 (tmm) REVERT: R 165 MET cc_start: 0.7601 (ptm) cc_final: 0.7293 (ptm) REVERT: R 184 MET cc_start: 0.7899 (mmt) cc_final: 0.7592 (tpp) REVERT: R 269 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6446 (t0) REVERT: R 275 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6739 (t80) REVERT: R 337 CYS cc_start: 0.9066 (m) cc_final: 0.8546 (m) outliers start: 35 outliers final: 31 residues processed: 215 average time/residue: 0.2171 time to fit residues: 64.1490 Evaluate side-chains 223 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 269 ASN Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 372 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.211385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.166473 restraints weight = 12406.649| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.06 r_work: 0.3848 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8995 Z= 0.132 Angle : 0.665 9.637 12220 Z= 0.343 Chirality : 0.045 0.241 1406 Planarity : 0.004 0.043 1546 Dihedral : 4.821 53.148 1234 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.38 % Allowed : 20.04 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.25), residues: 1129 helix: 1.65 (0.27), residues: 386 sheet: -0.17 (0.29), residues: 302 loop : -0.10 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.031 0.001 PHE B 241 TYR 0.048 0.002 TYR R 201 ARG 0.005 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 453) hydrogen bonds : angle 4.99135 ( 1281) SS BOND : bond 0.00393 ( 3) SS BOND : angle 1.08668 ( 6) covalent geometry : bond 0.00299 ( 8992) covalent geometry : angle 0.66450 (12214) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4524.32 seconds wall clock time: 79 minutes 25.01 seconds (4765.01 seconds total)