Starting phenix.real_space_refine on Fri Oct 10 19:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wwi_37889/10_2025/8wwi_37889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wwi_37889/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wwi_37889/10_2025/8wwi_37889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wwi_37889/10_2025/8wwi_37889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wwi_37889/10_2025/8wwi_37889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wwi_37889/10_2025/8wwi_37889.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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, 'ASN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 2.31, per 1000 atoms: 0.26 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: 0.81 Conformation dependent library (CDL) restraints added in 343.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.26 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: 1.41 Time building geometry restraints manager: 1.07 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.750 ------------------------------------------------------------------------------- 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 : 7.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (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 ARG 0.002 0.000 ARG B 68 TYR 0.010 0.001 TYR A 290 PHE 0.010 0.001 PHE B 151 TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00151 ( 8992) covalent geometry : angle 0.40564 (12214) SS BOND : bond 0.00072 ( 3) SS BOND : angle 0.40284 ( 6) hydrogen bonds : bond 0.25020 ( 453) hydrogen bonds : angle 7.58310 ( 1281) *********************** 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 : 0.342 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: 0.7657 (m) REVERT: E 38 ARG cc_start: 0.7581 (ptt-90) cc_final: 0.7348 (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: 0.6045 (m-80) REVERT: R 272 THR cc_start: 0.7540 (p) cc_final: 0.7287 (p) outliers start: 9 outliers final: 4 residues processed: 299 average time/residue: 0.1025 time to fit residues: 41.7102 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 : 0.418 ------------------------------------------------------------------------------- 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 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 0.4980 overall best weight: 0.8720 ------------------------------------------------------------------------------- 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 A 331 ASN B 91 HIS B 259 GLN E 113 GLN E 167 HIS 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.213406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.169828 restraints weight = 12099.695| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 3.35 r_work: 0.3854 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8995 Z= 0.154 Angle : 0.613 7.092 12220 Z= 0.331 Chirality : 0.045 0.164 1406 Planarity : 0.004 0.037 1546 Dihedral : 4.715 44.918 1237 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.59 % Allowed : 10.76 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1129 helix: 1.18 (0.26), residues: 404 sheet: 0.95 (0.30), residues: 282 loop : 0.06 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 322 TYR 0.016 0.001 TYR R 280 PHE 0.013 0.001 PHE A 189 TRP 0.013 0.002 TRP B 169 HIS 0.007 0.002 HIS R 170 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8992) covalent geometry : angle 0.60962 (12214) SS BOND : bond 0.00400 ( 3) SS BOND : angle 2.79731 ( 6) hydrogen bonds : bond 0.05186 ( 453) hydrogen bonds : angle 5.41887 ( 1281) *********************** 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 254 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.331 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: 0.7827 (ttm-80) cc_final: 0.7488 (mtm-85) REVERT: A 274 PHE cc_start: 0.7681 (t80) cc_final: 0.7262 (t80) REVERT: A 333 GLN cc_start: 0.7779 (tp40) cc_final: 0.7297 (tp-100) REVERT: A 337 ASP cc_start: 0.8253 (m-30) cc_final: 0.7841 (m-30) REVERT: B 220 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6693 (mm-40) REVERT: B 226 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6880 (mt-10) REVERT: B 279 SER cc_start: 0.6758 (p) cc_final: 0.6527 (t) REVERT: E 39 GLN cc_start: 0.7457 (tt0) cc_final: 0.7231 (tt0) REVERT: E 86 LEU cc_start: 0.7816 (mt) cc_final: 0.7559 (tp) REVERT: E 138 ILE cc_start: 0.4702 (mm) cc_final: 0.4452 (mm) REVERT: E 195 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8188 (tp) REVERT: E 203 PHE cc_start: 0.6823 (m-80) cc_final: 0.6506 (m-80) REVERT: E 228 TYR cc_start: 0.5876 (m-80) cc_final: 0.5463 (m-80) REVERT: R 139 LYS cc_start: 0.7048 (ptpt) cc_final: 0.6839 (ptpp) REVERT: R 184 MET cc_start: 0.7931 (mmt) cc_final: 0.7636 (tpp) REVERT: R 218 ILE cc_start: 0.7402 (mm) cc_final: 0.7054 (mm) REVERT: R 275 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6585 (t80) outliers start: 34 outliers final: 20 residues processed: 239 average time/residue: 0.1081 time to fit residues: 34.9100 Evaluate side-chains 216 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 195 LEU 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 221 THR 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 280 TYR Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 32 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.209111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165822 restraints weight = 12104.323| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.41 r_work: 0.3801 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8995 Z= 0.199 Angle : 0.650 8.299 12220 Z= 0.344 Chirality : 0.046 0.159 1406 Planarity : 0.005 0.054 1546 Dihedral : 4.865 40.838 1234 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.32 % Allowed : 13.29 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.25), residues: 1129 helix: 1.30 (0.26), residues: 401 sheet: 0.50 (0.30), residues: 290 loop : 0.18 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 21 TYR 0.022 0.002 TYR B 85 PHE 0.016 0.002 PHE R 387 TRP 0.014 0.002 TRP B 211 HIS 0.005 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8992) covalent geometry : angle 0.64846 (12214) SS BOND : bond 0.00512 ( 3) SS BOND : angle 1.83458 ( 6) hydrogen bonds : bond 0.04906 ( 453) hydrogen bonds : angle 5.27407 ( 1281) *********************** 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: 41 poor density : 212 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7834 (ttm-80) cc_final: 0.7505 (mtm-85) REVERT: A 274 PHE cc_start: 0.7733 (t80) cc_final: 0.7301 (t80) REVERT: A 333 GLN cc_start: 0.7831 (tp40) cc_final: 0.7335 (tp-100) REVERT: A 337 ASP cc_start: 0.8304 (m-30) cc_final: 0.7877 (m-30) REVERT: B 43 ILE cc_start: 0.7728 (mm) cc_final: 0.7465 (mm) REVERT: B 96 ARG cc_start: 0.7686 (mmt90) cc_final: 0.7394 (mmt90) REVERT: B 220 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6790 (mm-40) REVERT: B 260 GLU cc_start: 0.7021 (tt0) cc_final: 0.6779 (mt-10) REVERT: B 279 SER cc_start: 0.6955 (p) cc_final: 0.6719 (t) REVERT: C 38 MET cc_start: 0.8328 (ptm) cc_final: 0.8063 (ptm) REVERT: E 46 GLU cc_start: 0.6285 (tt0) cc_final: 0.5851 (tt0) REVERT: E 138 ILE cc_start: 0.5485 (mm) cc_final: 0.5220 (mm) REVERT: E 176 TRP cc_start: 0.6801 (m100) cc_final: 0.6495 (m100) REVERT: E 194 ASN cc_start: 0.8156 (m-40) cc_final: 0.7725 (m110) REVERT: E 218 ARG cc_start: 0.7473 (tpp-160) cc_final: 0.7241 (tpt170) REVERT: E 228 TYR cc_start: 0.6439 (m-80) cc_final: 0.6090 (m-10) REVERT: E 230 MET cc_start: 0.5484 (ttp) cc_final: 0.5203 (tmm) REVERT: R 184 MET cc_start: 0.7915 (mmt) cc_final: 0.7633 (tpp) REVERT: R 218 ILE cc_start: 0.7543 (mm) cc_final: 0.7272 (mm) REVERT: R 275 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6722 (t80) REVERT: R 299 ARG cc_start: 0.7675 (mmm160) cc_final: 0.7386 (ttm170) outliers start: 41 outliers final: 29 residues processed: 230 average time/residue: 0.1066 time to fit residues: 33.4972 Evaluate side-chains 232 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 255 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 165 MET Chi-restraints excluded: chain R residue 183 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4445 r_free = 0.4445 target = 0.210450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.167078 restraints weight = 12325.428| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.26 r_work: 0.3891 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8995 Z= 0.154 Angle : 0.605 9.457 12220 Z= 0.319 Chirality : 0.044 0.163 1406 Planarity : 0.004 0.054 1546 Dihedral : 4.777 46.169 1234 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.38 % Allowed : 15.82 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1129 helix: 1.46 (0.27), residues: 398 sheet: 0.35 (0.31), residues: 280 loop : 0.11 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.022 0.002 TYR E 190 PHE 0.021 0.002 PHE R 358 TRP 0.016 0.002 TRP B 211 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8992) covalent geometry : angle 0.60416 (12214) SS BOND : bond 0.00612 ( 3) SS BOND : angle 1.54685 ( 6) hydrogen bonds : bond 0.04313 ( 453) hydrogen bonds : angle 5.10776 ( 1281) *********************** 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: 32 poor density : 208 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7454 (mtm-85) REVERT: A 274 PHE cc_start: 0.7760 (t80) cc_final: 0.7284 (t80) REVERT: A 333 GLN cc_start: 0.7733 (tp40) cc_final: 0.7233 (tp-100) REVERT: A 337 ASP cc_start: 0.8220 (m-30) cc_final: 0.7839 (m-30) REVERT: B 45 MET cc_start: 0.5798 (ttm) cc_final: 0.5490 (mtp) REVERT: B 96 ARG cc_start: 0.7630 (mmt90) cc_final: 0.7324 (mmt90) REVERT: B 220 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6565 (mm-40) REVERT: B 234 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: B 279 SER cc_start: 0.6777 (p) cc_final: 0.6531 (t) REVERT: B 325 MET cc_start: 0.7384 (ttt) cc_final: 0.7179 (ttt) REVERT: C 38 MET cc_start: 0.8345 (ptm) cc_final: 0.8055 (ptm) REVERT: E 138 ILE cc_start: 0.5377 (mm) cc_final: 0.5111 (mm) REVERT: E 176 TRP cc_start: 0.6807 (m100) cc_final: 0.6401 (m100) REVERT: E 228 TYR cc_start: 0.6342 (m-80) cc_final: 0.5945 (m-10) REVERT: R 112 MET cc_start: 0.8015 (mtt) cc_final: 0.7459 (mtt) REVERT: R 184 MET cc_start: 0.7879 (mmt) cc_final: 0.7545 (tpp) REVERT: R 218 ILE cc_start: 0.7499 (mm) cc_final: 0.7293 (mm) REVERT: R 275 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6662 (t80) outliers start: 32 outliers final: 25 residues processed: 226 average time/residue: 0.1032 time to fit residues: 31.8331 Evaluate side-chains 225 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 296 TYR 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 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 172 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 165 MET 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 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 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 44 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.210486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.167724 restraints weight = 12380.523| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.21 r_work: 0.3896 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8995 Z= 0.133 Angle : 0.586 8.789 12220 Z= 0.310 Chirality : 0.044 0.161 1406 Planarity : 0.004 0.051 1546 Dihedral : 4.691 48.686 1234 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.11 % Allowed : 15.72 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.26), residues: 1129 helix: 1.67 (0.27), residues: 392 sheet: 0.31 (0.31), residues: 280 loop : 0.05 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.019 0.001 TYR E 103 PHE 0.015 0.001 PHE B 151 TRP 0.015 0.002 TRP B 211 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8992) covalent geometry : angle 0.58502 (12214) SS BOND : bond 0.00354 ( 3) SS BOND : angle 1.30668 ( 6) hydrogen bonds : bond 0.03944 ( 453) hydrogen bonds : angle 4.96769 ( 1281) *********************** 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 243 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6885 (mpp) cc_final: 0.6453 (mtt) REVERT: A 208 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7443 (mtm-85) REVERT: A 274 PHE cc_start: 0.7782 (t80) cc_final: 0.7307 (t80) REVERT: A 304 GLN cc_start: 0.8273 (tt0) cc_final: 0.8026 (tt0) REVERT: A 333 GLN cc_start: 0.7704 (tp40) cc_final: 0.7194 (tp-100) REVERT: A 337 ASP cc_start: 0.8217 (m-30) cc_final: 0.7843 (m-30) REVERT: B 45 MET cc_start: 0.5840 (ttm) cc_final: 0.5468 (mtp) REVERT: B 96 ARG cc_start: 0.7620 (mmt90) cc_final: 0.7297 (mmt90) REVERT: B 220 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6672 (mm-40) REVERT: B 234 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: B 260 GLU cc_start: 0.6968 (tt0) cc_final: 0.6666 (tt0) REVERT: B 279 SER cc_start: 0.6814 (p) cc_final: 0.6539 (t) REVERT: B 297 TRP cc_start: 0.8263 (m100) cc_final: 0.7960 (m100) REVERT: C 38 MET cc_start: 0.8351 (ptm) cc_final: 0.8072 (ptm) REVERT: E 38 ARG cc_start: 0.6846 (ptt90) cc_final: 0.6622 (ptt90) REVERT: E 86 LEU cc_start: 0.7905 (mt) cc_final: 0.7605 (mm) REVERT: E 138 ILE cc_start: 0.5528 (mm) cc_final: 0.5293 (mm) REVERT: E 176 TRP cc_start: 0.6885 (m100) cc_final: 0.6478 (m100) REVERT: E 228 TYR cc_start: 0.6274 (m-80) cc_final: 0.5850 (m-10) REVERT: E 235 TYR cc_start: 0.7713 (m-80) cc_final: 0.7359 (m-80) REVERT: R 112 MET cc_start: 0.8091 (mtt) cc_final: 0.7838 (mtt) REVERT: R 184 MET cc_start: 0.7883 (mmt) cc_final: 0.7549 (tpp) REVERT: R 218 ILE cc_start: 0.7520 (mm) cc_final: 0.7246 (mm) REVERT: R 275 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6525 (t80) REVERT: R 337 CYS cc_start: 0.9113 (m) cc_final: 0.8562 (m) REVERT: R 388 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7578 (ttp-110) outliers start: 39 outliers final: 27 residues processed: 227 average time/residue: 0.1113 time to fit residues: 33.8464 Evaluate side-chains 224 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 255 LEU 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 B residue 334 SER Chi-restraints excluded: chain C residue 62 ARG 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 165 MET 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 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 34 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 95 optimal weight: 0.0010 chunk 99 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.212564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.167971 restraints weight = 12412.136| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.08 r_work: 0.3863 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8995 Z= 0.116 Angle : 0.567 8.689 12220 Z= 0.299 Chirality : 0.043 0.154 1406 Planarity : 0.004 0.056 1546 Dihedral : 4.538 48.895 1234 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.38 % Allowed : 17.19 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.26), residues: 1129 helix: 1.79 (0.26), residues: 394 sheet: 0.35 (0.31), residues: 282 loop : 0.01 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.028 0.001 TYR E 190 PHE 0.022 0.001 PHE R 256 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8992) covalent geometry : angle 0.56666 (12214) SS BOND : bond 0.00350 ( 3) SS BOND : angle 1.13681 ( 6) hydrogen bonds : bond 0.03702 ( 453) hydrogen bonds : angle 4.78895 ( 1281) *********************** 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 236 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7448 (mtm-85) REVERT: A 274 PHE cc_start: 0.7774 (t80) cc_final: 0.7302 (t80) REVERT: A 333 GLN cc_start: 0.7642 (tp40) cc_final: 0.7189 (tp-100) REVERT: A 337 ASP cc_start: 0.8191 (m-30) cc_final: 0.7839 (m-30) REVERT: B 96 ARG cc_start: 0.7544 (mmt90) cc_final: 0.7284 (mmt90) REVERT: B 220 GLN cc_start: 0.7162 (mm-40) cc_final: 0.6610 (mm-40) REVERT: B 234 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: B 260 GLU cc_start: 0.6895 (tt0) cc_final: 0.6600 (tt0) REVERT: B 279 SER cc_start: 0.6587 (p) cc_final: 0.6341 (t) REVERT: B 297 TRP cc_start: 0.8188 (m100) cc_final: 0.7824 (m100) REVERT: C 38 MET cc_start: 0.8314 (ptm) cc_final: 0.8034 (ptm) REVERT: E 38 ARG cc_start: 0.6809 (ptt90) cc_final: 0.6581 (ptt90) REVERT: E 86 LEU cc_start: 0.7884 (mt) cc_final: 0.7542 (mm) REVERT: E 138 ILE cc_start: 0.5553 (mm) cc_final: 0.5335 (mm) REVERT: E 176 TRP cc_start: 0.6795 (m100) cc_final: 0.6482 (m100) REVERT: E 228 TYR cc_start: 0.6412 (m-80) cc_final: 0.5921 (m-10) REVERT: E 235 TYR cc_start: 0.7683 (m-80) cc_final: 0.7343 (m-80) REVERT: R 112 MET cc_start: 0.8098 (mtt) cc_final: 0.7864 (mtt) REVERT: R 165 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7160 (ptp) REVERT: R 184 MET cc_start: 0.7828 (mmt) cc_final: 0.7499 (tpp) REVERT: R 218 ILE cc_start: 0.7468 (mm) cc_final: 0.7136 (mm) REVERT: R 269 ASN cc_start: 0.6865 (OUTLIER) cc_final: 0.6629 (t0) REVERT: R 275 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6480 (t80) REVERT: R 325 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7038 (ttm170) REVERT: R 337 CYS cc_start: 0.9142 (m) cc_final: 0.8639 (m) REVERT: R 388 ARG cc_start: 0.7880 (ttp-170) cc_final: 0.7553 (ttp-110) outliers start: 32 outliers final: 23 residues processed: 224 average time/residue: 0.1078 time to fit residues: 32.6497 Evaluate side-chains 223 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS 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 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 52 SER 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 121 LEU Chi-restraints excluded: chain R residue 165 MET 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 58 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.203721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158676 restraints weight = 12617.748| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.60 r_work: 0.3726 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 8995 Z= 0.305 Angle : 0.751 10.577 12220 Z= 0.400 Chirality : 0.050 0.182 1406 Planarity : 0.005 0.063 1546 Dihedral : 5.298 56.958 1234 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.38 % Allowed : 16.14 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1129 helix: 1.29 (0.26), residues: 394 sheet: -0.18 (0.28), residues: 295 loop : -0.29 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 314 TYR 0.036 0.003 TYR E 103 PHE 0.020 0.003 PHE E 177 TRP 0.020 0.003 TRP B 339 HIS 0.006 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00708 ( 8992) covalent geometry : angle 0.74962 (12214) SS BOND : bond 0.00484 ( 3) SS BOND : angle 1.82760 ( 6) hydrogen bonds : bond 0.05069 ( 453) hydrogen bonds : angle 5.48819 ( 1281) *********************** 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 245 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7506 (mtm-85) REVERT: A 274 PHE cc_start: 0.7903 (t80) cc_final: 0.7307 (t80) REVERT: A 333 GLN cc_start: 0.7738 (tp40) cc_final: 0.7346 (tp-100) REVERT: A 337 ASP cc_start: 0.8238 (m-30) cc_final: 0.7824 (m-30) REVERT: B 96 ARG cc_start: 0.7636 (mmt90) cc_final: 0.7397 (mmt90) REVERT: B 220 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6846 (mm-40) REVERT: B 234 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: B 277 SER cc_start: 0.8597 (t) cc_final: 0.8278 (m) REVERT: B 292 PHE cc_start: 0.8466 (m-10) cc_final: 0.8129 (m-80) REVERT: C 38 MET cc_start: 0.8247 (ptm) cc_final: 0.7996 (ptm) REVERT: E 85 SER cc_start: 0.8755 (m) cc_final: 0.8431 (p) REVERT: E 160 ARG cc_start: 0.6533 (ptm-80) cc_final: 0.5854 (ptm-80) REVERT: R 165 MET cc_start: 0.7522 (OUTLIER) cc_final: 0.7301 (ptm) REVERT: R 184 MET cc_start: 0.8024 (mmt) cc_final: 0.7691 (tpp) REVERT: R 214 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7494 (m) REVERT: R 275 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6729 (t80) REVERT: R 325 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7041 (ttm170) REVERT: R 337 CYS cc_start: 0.9224 (m) cc_final: 0.8660 (m) outliers start: 51 outliers final: 39 residues processed: 225 average time/residue: 0.1055 time to fit residues: 32.0801 Evaluate side-chains 226 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 A residue 318 GLU 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 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 B residue 334 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 52 SER 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 121 LEU Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 214 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 279 LEU Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 336 VAL 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 104 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 76 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 306 GLN ** 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 = 0.4446 r_free = 0.4446 target = 0.210709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165821 restraints weight = 12302.192| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.05 r_work: 0.3843 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8995 Z= 0.130 Angle : 0.644 10.567 12220 Z= 0.335 Chirality : 0.045 0.168 1406 Planarity : 0.004 0.060 1546 Dihedral : 4.907 54.805 1234 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.59 % Allowed : 19.20 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1129 helix: 1.65 (0.27), residues: 391 sheet: -0.16 (0.29), residues: 295 loop : -0.12 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 314 TYR 0.029 0.002 TYR E 190 PHE 0.024 0.001 PHE R 277 TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8992) covalent geometry : angle 0.64340 (12214) SS BOND : bond 0.00452 ( 3) SS BOND : angle 1.22594 ( 6) hydrogen bonds : bond 0.03988 ( 453) hydrogen bonds : angle 5.08931 ( 1281) *********************** 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 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7420 (mtm-85) REVERT: A 274 PHE cc_start: 0.7817 (t80) cc_final: 0.7245 (t80) REVERT: A 304 GLN cc_start: 0.7983 (tt0) cc_final: 0.7717 (tp40) REVERT: A 309 ASP cc_start: 0.8275 (m-30) cc_final: 0.7961 (p0) REVERT: A 333 GLN cc_start: 0.7591 (tp40) cc_final: 0.7137 (tp-100) REVERT: A 337 ASP cc_start: 0.8210 (m-30) cc_final: 0.7867 (m-30) REVERT: B 45 MET cc_start: 0.6246 (ttm) cc_final: 0.5872 (mtp) REVERT: B 220 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6680 (mm-40) REVERT: B 234 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: B 277 SER cc_start: 0.8575 (t) cc_final: 0.8370 (m) REVERT: B 292 PHE cc_start: 0.8315 (m-10) cc_final: 0.8008 (m-80) REVERT: B 297 TRP cc_start: 0.8299 (m100) cc_final: 0.7866 (m100) REVERT: C 38 MET cc_start: 0.8221 (ptm) cc_final: 0.7935 (ptm) REVERT: E 165 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7134 (mm) REVERT: R 184 MET cc_start: 0.7853 (mmt) cc_final: 0.7522 (tpp) REVERT: R 218 ILE cc_start: 0.7473 (mm) cc_final: 0.7146 (mm) REVERT: R 275 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6553 (t80) REVERT: R 325 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.7003 (ttm170) REVERT: R 337 CYS cc_start: 0.9143 (m) cc_final: 0.8674 (m) outliers start: 34 outliers final: 23 residues processed: 220 average time/residue: 0.1030 time to fit residues: 31.1468 Evaluate side-chains 214 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS 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 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 315 SER Chi-restraints excluded: chain R residue 325 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.209719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.166816 restraints weight = 12324.434| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 3.13 r_work: 0.3825 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.4899 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= 0.164 Angle : 0.687 15.504 12220 Z= 0.354 Chirality : 0.045 0.170 1406 Planarity : 0.004 0.063 1546 Dihedral : 4.907 56.494 1234 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.48 % Allowed : 20.25 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1129 helix: 1.62 (0.27), residues: 389 sheet: -0.10 (0.29), residues: 302 loop : -0.18 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 32 TYR 0.026 0.002 TYR E 103 PHE 0.025 0.002 PHE R 256 TRP 0.031 0.002 TRP E 47 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8992) covalent geometry : angle 0.68633 (12214) SS BOND : bond 0.00569 ( 3) SS BOND : angle 1.48581 ( 6) hydrogen bonds : bond 0.04106 ( 453) hydrogen bonds : angle 5.10456 ( 1281) *********************** 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 222 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7479 (mtm-85) REVERT: A 242 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8473 (mtt-85) REVERT: A 274 PHE cc_start: 0.7848 (t80) cc_final: 0.7288 (t80) REVERT: A 304 GLN cc_start: 0.8046 (tt0) cc_final: 0.7823 (tp40) REVERT: A 333 GLN cc_start: 0.7616 (tp40) cc_final: 0.7176 (tp-100) REVERT: A 337 ASP cc_start: 0.8221 (m-30) cc_final: 0.7870 (m-30) REVERT: B 45 MET cc_start: 0.6242 (ttm) cc_final: 0.5848 (mtp) REVERT: B 96 ARG cc_start: 0.7472 (mmt90) cc_final: 0.7079 (mmt90) REVERT: B 220 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6731 (mm-40) REVERT: B 234 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6676 (m-80) REVERT: B 277 SER cc_start: 0.8601 (t) cc_final: 0.8318 (m) REVERT: B 292 PHE cc_start: 0.8326 (m-10) cc_final: 0.8002 (m-80) REVERT: B 297 TRP cc_start: 0.8313 (m100) cc_final: 0.7912 (m100) REVERT: C 38 MET cc_start: 0.8250 (ptm) cc_final: 0.7986 (ptm) REVERT: C 47 GLU cc_start: 0.8015 (tp30) cc_final: 0.7740 (tp30) REVERT: E 165 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7072 (mm) REVERT: E 176 TRP cc_start: 0.6860 (m100) cc_final: 0.5581 (m-10) REVERT: E 218 ARG cc_start: 0.7388 (tpt170) cc_final: 0.7058 (tpm170) REVERT: R 165 MET cc_start: 0.7364 (ptm) cc_final: 0.7092 (ptp) REVERT: R 184 MET cc_start: 0.7915 (mmt) cc_final: 0.7598 (tpp) REVERT: R 218 ILE cc_start: 0.7440 (mm) cc_final: 0.7144 (mm) REVERT: R 275 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6626 (t80) REVERT: R 325 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7020 (ttm170) REVERT: R 337 CYS cc_start: 0.9121 (m) cc_final: 0.8596 (m) outliers start: 33 outliers final: 26 residues processed: 212 average time/residue: 0.1056 time to fit residues: 30.5341 Evaluate side-chains 214 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS 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 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 PHE 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 325 ARG Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 chunk 98 optimal weight: 0.0020 chunk 39 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.213492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.171442 restraints weight = 12359.080| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 3.13 r_work: 0.3881 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8995 Z= 0.126 Angle : 0.666 12.404 12220 Z= 0.341 Chirality : 0.045 0.168 1406 Planarity : 0.004 0.060 1546 Dihedral : 4.761 55.536 1234 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.06 % Allowed : 20.89 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1129 helix: 1.77 (0.27), residues: 387 sheet: 0.10 (0.29), residues: 297 loop : -0.09 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 32 TYR 0.030 0.002 TYR E 190 PHE 0.023 0.001 PHE R 256 TRP 0.033 0.002 TRP E 47 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8992) covalent geometry : angle 0.66591 (12214) SS BOND : bond 0.00518 ( 3) SS BOND : angle 1.24427 ( 6) hydrogen bonds : bond 0.03778 ( 453) hydrogen bonds : angle 4.96050 ( 1281) ********************** 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 222 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7400 (mtm-85) REVERT: A 242 ARG cc_start: 0.8714 (mtt180) cc_final: 0.8407 (mtt-85) REVERT: A 274 PHE cc_start: 0.7805 (t80) cc_final: 0.7239 (t80) REVERT: A 304 GLN cc_start: 0.7979 (tt0) cc_final: 0.7741 (tp40) REVERT: A 333 GLN cc_start: 0.7596 (tp40) cc_final: 0.7138 (tp-100) REVERT: A 337 ASP cc_start: 0.8186 (m-30) cc_final: 0.7847 (m-30) REVERT: B 96 ARG cc_start: 0.7351 (mmt90) cc_final: 0.6989 (mmt90) REVERT: B 214 ARG cc_start: 0.6649 (mmp80) cc_final: 0.6446 (mmp80) REVERT: B 220 GLN cc_start: 0.7118 (mm-40) cc_final: 0.6663 (mm-40) REVERT: B 234 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: B 292 PHE cc_start: 0.8226 (m-10) cc_final: 0.7951 (m-80) REVERT: B 297 TRP cc_start: 0.8253 (m100) cc_final: 0.7820 (m100) REVERT: B 325 MET cc_start: 0.7167 (tpt) cc_final: 0.6938 (tpt) REVERT: E 165 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6955 (mm) REVERT: E 176 TRP cc_start: 0.6774 (m100) cc_final: 0.5469 (m-10) REVERT: E 218 ARG cc_start: 0.7458 (tpt170) cc_final: 0.7240 (tpm170) REVERT: R 184 MET cc_start: 0.7928 (mmt) cc_final: 0.7603 (tpp) REVERT: R 218 ILE cc_start: 0.7370 (mm) cc_final: 0.7067 (mm) REVERT: R 275 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6607 (t80) REVERT: R 325 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7087 (ttm170) REVERT: R 337 CYS cc_start: 0.9129 (m) cc_final: 0.8654 (m) REVERT: R 388 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7632 (ttp-110) outliers start: 29 outliers final: 21 residues processed: 212 average time/residue: 0.1081 time to fit residues: 31.0072 Evaluate side-chains 212 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 254 CYS 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 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 275 TYR Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 325 ARG Chi-restraints excluded: chain R residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.213322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.168936 restraints weight = 12328.375| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 3.04 r_work: 0.3880 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8995 Z= 0.129 Angle : 0.662 12.174 12220 Z= 0.342 Chirality : 0.045 0.320 1406 Planarity : 0.004 0.060 1546 Dihedral : 4.694 55.918 1234 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.06 % Allowed : 20.78 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1129 helix: 1.80 (0.27), residues: 387 sheet: 0.18 (0.29), residues: 297 loop : -0.06 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.027 0.002 TYR E 190 PHE 0.022 0.001 PHE R 256 TRP 0.022 0.002 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8992) covalent geometry : angle 0.66144 (12214) SS BOND : bond 0.00479 ( 3) SS BOND : angle 1.36994 ( 6) hydrogen bonds : bond 0.03788 ( 453) hydrogen bonds : angle 4.92097 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.41 seconds wall clock time: 41 minutes 10.02 seconds (2470.02 seconds total)