Starting phenix.real_space_refine on Thu Jun 19 15:56:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jcz_6630/06_2025/3jcz_6630.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jcz_6630/06_2025/3jcz_6630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jcz_6630/06_2025/3jcz_6630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jcz_6630/06_2025/3jcz_6630.map" model { file = "/net/cci-nas-00/data/ceres_data/3jcz_6630/06_2025/3jcz_6630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jcz_6630/06_2025/3jcz_6630.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 114 5.16 5 C 14724 2.51 5 N 4074 2.21 5 O 4374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23286 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 8.88, per 1000 atoms: 0.38 Number of scatterers: 23286 At special positions: 0 Unit cell: (112.207, 115.395, 162.573, 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 114 16.00 O 4374 8.00 N 4074 7.00 C 14724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.18 Conformation dependent library (CDL) restraints added in 2.8 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 18 sheets defined 55.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 53 removed outlier: 4.191A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 115 removed outlier: 4.199A pdb=" N ALA A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 removed outlier: 3.830A pdb=" N MET A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR A 190 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 4.285A pdb=" N VAL A 198 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.527A pdb=" N GLY A 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.657A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.517A pdb=" N HIS A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 removed outlier: 3.653A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.796A pdb=" N VAL A 339 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 425 Processing helix chain 'A' and resid 434 through 442 removed outlier: 3.799A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 removed outlier: 4.190A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 115 removed outlier: 4.200A pdb=" N ALA B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS B 143 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.831A pdb=" N MET B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR B 190 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.286A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.526A pdb=" N GLY B 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.657A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.518A pdb=" N HIS B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 removed outlier: 3.652A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.796A pdb=" N VAL B 339 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 425 Processing helix chain 'B' and resid 434 through 442 removed outlier: 3.798A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 466 " --> pdb=" O ARG B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'C' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 53 removed outlier: 4.191A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 115 removed outlier: 4.200A pdb=" N ALA C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 removed outlier: 3.831A pdb=" N MET C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR C 190 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.285A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.527A pdb=" N GLY C 206 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.656A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.518A pdb=" N HIS C 258 " --> pdb=" O ASN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 299 removed outlier: 3.652A pdb=" N LEU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.797A pdb=" N VAL C 339 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP C 357 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 391 removed outlier: 3.687A pdb=" N TRP C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 421 removed outlier: 3.704A pdb=" N LYS C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 Processing helix chain 'C' and resid 434 through 442 removed outlier: 3.798A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 466 " --> pdb=" O ARG C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 497 No H-bonds generated for 'chain 'C' and resid 495 through 497' Processing helix chain 'D' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 53 removed outlier: 4.190A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 115 removed outlier: 4.199A pdb=" N ALA D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.830A pdb=" N MET D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 182 " --> pdb=" O TRP D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR D 190 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.284A pdb=" N VAL D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.527A pdb=" N GLY D 206 " --> pdb=" O ILE D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.656A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.518A pdb=" N HIS D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 299 removed outlier: 3.653A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.797A pdb=" N VAL D 339 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 425 Processing helix chain 'D' and resid 434 through 442 removed outlier: 3.799A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.617A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 466 " --> pdb=" O ARG D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 497 No H-bonds generated for 'chain 'D' and resid 495 through 497' Processing helix chain 'E' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 53 removed outlier: 4.190A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 115 removed outlier: 4.200A pdb=" N ALA E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 139 through 154 removed outlier: 3.663A pdb=" N LYS E 143 " --> pdb=" O ASN E 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 144 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 184 removed outlier: 3.831A pdb=" N MET E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR E 182 " --> pdb=" O TRP E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 4.141A pdb=" N TYR E 190 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.285A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.526A pdb=" N GLY E 206 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.656A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 removed outlier: 3.518A pdb=" N HIS E 258 " --> pdb=" O ASN E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.653A pdb=" N LEU E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.797A pdb=" N VAL E 339 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP E 357 " --> pdb=" O THR E 353 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP E 385 " --> pdb=" O SER E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS E 420 " --> pdb=" O SER E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 425 Processing helix chain 'E' and resid 434 through 442 removed outlier: 3.798A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE E 440 " --> pdb=" O PHE E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN E 463 " --> pdb=" O ARG E 459 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG E 466 " --> pdb=" O ARG E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 497 No H-bonds generated for 'chain 'E' and resid 495 through 497' Processing helix chain 'F' and resid 8 through 29 removed outlier: 3.723A pdb=" N ASP F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 53 removed outlier: 4.190A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG F 50 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 115 removed outlier: 4.200A pdb=" N ALA F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 139 through 154 removed outlier: 3.664A pdb=" N LYS F 143 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 184 removed outlier: 3.831A pdb=" N MET F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F 177 " --> pdb=" O GLU F 173 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR F 182 " --> pdb=" O TRP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 191 removed outlier: 4.142A pdb=" N TYR F 190 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.286A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.527A pdb=" N GLY F 206 " --> pdb=" O ILE F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.657A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.738A pdb=" N SER F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 265 removed outlier: 3.517A pdb=" N HIS F 258 " --> pdb=" O ASN F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.652A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.797A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.777A pdb=" N ASP F 357 " --> pdb=" O THR F 353 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 391 removed outlier: 3.686A pdb=" N TRP F 385 " --> pdb=" O SER F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 421 removed outlier: 3.705A pdb=" N LYS F 420 " --> pdb=" O SER F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 425 Processing helix chain 'F' and resid 434 through 442 removed outlier: 3.798A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 440 " --> pdb=" O PHE F 436 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.618A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN F 463 " --> pdb=" O ARG F 459 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 466 " --> pdb=" O ARG F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 494 removed outlier: 3.793A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 497 No H-bonds generated for 'chain 'F' and resid 495 through 497' Processing sheet with id=A, first strand: chain 'A' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=C, first strand: chain 'A' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 275 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE A 247 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N GLY A 274 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 249 " --> pdb=" O GLY A 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 322 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=F, first strand: chain 'B' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 275 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE B 247 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 9.025A pdb=" N GLY B 274 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 249 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 322 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 63 through 66 Processing sheet with id=I, first strand: chain 'C' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU C 275 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE C 247 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLY C 274 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 249 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C 322 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'D' and resid 63 through 66 Processing sheet with id=L, first strand: chain 'D' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 275 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE D 247 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLY D 274 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL D 249 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU D 322 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'E' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'E' and resid 63 through 66 Processing sheet with id=O, first strand: chain 'E' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 275 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE E 247 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLY E 274 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL E 249 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU E 322 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'F' and resid 57 through 60 removed outlier: 4.343A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=R, first strand: chain 'F' and resid 278 through 281 removed outlier: 4.216A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 275 " --> pdb=" O GLY F 278 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE F 247 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N GLY F 274 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL F 249 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU F 322 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3060 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: 7.52 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7529 1.33 - 1.45: 3147 1.45 - 1.57: 12916 1.57 - 1.69: 0 1.69 - 1.80: 192 Bond restraints: 23784 Sorted by residual: bond pdb=" CB PRO D 88 " pdb=" CG PRO D 88 " ideal model delta sigma weight residual 1.506 1.442 0.064 3.90e-02 6.57e+02 2.66e+00 bond pdb=" CB PRO F 88 " pdb=" CG PRO F 88 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.60e+00 bond pdb=" CB PRO E 88 " pdb=" CG PRO E 88 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.60e+00 bond pdb=" CB PRO B 88 " pdb=" CG PRO B 88 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.60e+00 bond pdb=" CB PRO C 88 " pdb=" CG PRO C 88 " ideal model delta sigma weight residual 1.506 1.443 0.063 3.90e-02 6.57e+02 2.59e+00 ... (remaining 23779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 30014 1.31 - 2.61: 1803 2.61 - 3.92: 223 3.92 - 5.23: 54 5.23 - 6.54: 24 Bond angle restraints: 32118 Sorted by residual: angle pdb=" CA PRO F 64 " pdb=" C PRO F 64 " pdb=" O PRO F 64 " ideal model delta sigma weight residual 123.16 119.66 3.50 1.49e+00 4.50e-01 5.53e+00 angle pdb=" CA PRO C 64 " pdb=" C PRO C 64 " pdb=" O PRO C 64 " ideal model delta sigma weight residual 123.16 119.69 3.47 1.49e+00 4.50e-01 5.44e+00 angle pdb=" CA PRO E 64 " pdb=" C PRO E 64 " pdb=" O PRO E 64 " ideal model delta sigma weight residual 123.16 119.69 3.47 1.49e+00 4.50e-01 5.41e+00 angle pdb=" CA PRO B 64 " pdb=" C PRO B 64 " pdb=" O PRO B 64 " ideal model delta sigma weight residual 123.16 119.69 3.47 1.49e+00 4.50e-01 5.41e+00 angle pdb=" CA PRO D 64 " pdb=" C PRO D 64 " pdb=" O PRO D 64 " ideal model delta sigma weight residual 123.16 119.70 3.46 1.49e+00 4.50e-01 5.38e+00 ... (remaining 32113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.71: 13680 12.71 - 25.42: 488 25.42 - 38.13: 58 38.13 - 50.85: 18 50.85 - 63.56: 6 Dihedral angle restraints: 14250 sinusoidal: 5772 harmonic: 8478 Sorted by residual: dihedral pdb=" CA ALA D 375 " pdb=" C ALA D 375 " pdb=" N GLY D 376 " pdb=" CA GLY D 376 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ALA B 375 " pdb=" C ALA B 375 " pdb=" N GLY B 376 " pdb=" CA GLY B 376 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ALA A 375 " pdb=" C ALA A 375 " pdb=" N GLY A 376 " pdb=" CA GLY A 376 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 14247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1689 0.033 - 0.065: 1231 0.065 - 0.098: 405 0.098 - 0.131: 149 0.131 - 0.164: 18 Chirality restraints: 3492 Sorted by residual: chirality pdb=" CA PRO F 121 " pdb=" N PRO F 121 " pdb=" C PRO F 121 " pdb=" CB PRO F 121 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA PRO A 121 " pdb=" N PRO A 121 " pdb=" C PRO A 121 " pdb=" CB PRO A 121 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CA PRO C 121 " pdb=" N PRO C 121 " pdb=" C PRO C 121 " pdb=" CB PRO C 121 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 3489 not shown) Planarity restraints: 4188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 336 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO E 337 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 336 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO D 337 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 337 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 337 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 336 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.59e+00 pdb=" N PRO A 337 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.030 5.00e-02 4.00e+02 ... (remaining 4185 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 5569 2.78 - 3.31: 22873 3.31 - 3.84: 37423 3.84 - 4.37: 48784 4.37 - 4.90: 80831 Nonbonded interactions: 195480 Sorted by model distance: nonbonded pdb=" OG SER F 83 " pdb=" ND1 HIS F 85 " model vdw 2.244 3.120 nonbonded pdb=" OG SER A 83 " pdb=" ND1 HIS A 85 " model vdw 2.245 3.120 nonbonded pdb=" OG SER D 83 " pdb=" ND1 HIS D 85 " model vdw 2.245 3.120 nonbonded pdb=" OG SER C 83 " pdb=" ND1 HIS C 85 " model vdw 2.245 3.120 nonbonded pdb=" OG SER B 83 " pdb=" ND1 HIS B 85 " model vdw 2.245 3.120 ... (remaining 195475 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.940 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: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 44.830 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.008 0.064 23784 Z= 0.329 Angle : 0.692 6.537 32118 Z= 0.377 Chirality : 0.049 0.164 3492 Planarity : 0.005 0.054 4188 Dihedral : 7.317 63.557 8850 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.13), residues: 2964 helix: -3.40 (0.09), residues: 1374 sheet: -3.08 (0.23), residues: 402 loop : -1.96 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 178 HIS 0.011 0.002 HIS C 450 PHE 0.034 0.003 PHE B 399 TYR 0.020 0.003 TYR F 407 ARG 0.007 0.001 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.27415 ( 1098) hydrogen bonds : angle 10.28568 ( 3060) covalent geometry : bond 0.00766 (23784) covalent geometry : angle 0.69167 (32118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 582 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8401 (tt0) cc_final: 0.8038 (tt0) REVERT: B 25 GLU cc_start: 0.8383 (tt0) cc_final: 0.7439 (tt0) REVERT: C 25 GLU cc_start: 0.8414 (tt0) cc_final: 0.8056 (tt0) REVERT: C 139 ASN cc_start: 0.8730 (m-40) cc_final: 0.8260 (t0) REVERT: D 25 GLU cc_start: 0.8400 (tt0) cc_final: 0.8035 (tt0) REVERT: E 25 GLU cc_start: 0.8383 (tt0) cc_final: 0.8140 (tt0) REVERT: F 25 GLU cc_start: 0.8400 (tt0) cc_final: 0.8134 (tt0) outliers start: 0 outliers final: 0 residues processed: 582 average time/residue: 0.3952 time to fit residues: 349.5546 Evaluate side-chains 324 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 250 GLN B 135 ASN B 463 GLN C 135 ASN C 205 GLN C 414 GLN C 463 GLN D 135 ASN D 250 GLN E 135 ASN E 463 GLN F 135 ASN F 205 GLN F 414 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093482 restraints weight = 38970.259| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.22 r_work: 0.3087 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23784 Z= 0.171 Angle : 0.595 5.431 32118 Z= 0.318 Chirality : 0.044 0.158 3492 Planarity : 0.005 0.040 4188 Dihedral : 5.567 61.284 3258 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.52 % Allowed : 6.33 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.14), residues: 2964 helix: -1.52 (0.12), residues: 1446 sheet: -2.59 (0.23), residues: 384 loop : -1.29 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 281 HIS 0.008 0.002 HIS F 450 PHE 0.021 0.002 PHE D 122 TYR 0.015 0.001 TYR E 382 ARG 0.003 0.000 ARG F 261 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 1098) hydrogen bonds : angle 5.49772 ( 3060) covalent geometry : bond 0.00400 (23784) covalent geometry : angle 0.59533 (32118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 413 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7968 (ttpt) cc_final: 0.7637 (tttm) REVERT: A 163 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: A 264 HIS cc_start: 0.8783 (t-170) cc_final: 0.8582 (t-170) REVERT: A 372 TYR cc_start: 0.8654 (t80) cc_final: 0.8226 (t80) REVERT: A 411 MET cc_start: 0.8783 (tpp) cc_final: 0.8290 (tpt) REVERT: A 484 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8530 (m-40) REVERT: B 372 TYR cc_start: 0.8647 (t80) cc_final: 0.8361 (t80) REVERT: B 411 MET cc_start: 0.8765 (tpp) cc_final: 0.8296 (tpt) REVERT: B 414 GLN cc_start: 0.8655 (tt0) cc_final: 0.8402 (tt0) REVERT: B 419 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7421 (mtm-85) REVERT: C 139 ASN cc_start: 0.8608 (m-40) cc_final: 0.8264 (t0) REVERT: C 233 MET cc_start: 0.6429 (mmm) cc_final: 0.6143 (mmm) REVERT: C 269 LYS cc_start: 0.8394 (ttmm) cc_final: 0.7925 (ptpt) REVERT: C 372 TYR cc_start: 0.8650 (t80) cc_final: 0.8415 (t80) REVERT: C 411 MET cc_start: 0.8807 (tpp) cc_final: 0.8349 (tpt) REVERT: D 27 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7639 (tttm) REVERT: D 163 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: D 372 TYR cc_start: 0.8636 (t80) cc_final: 0.8210 (t80) REVERT: D 484 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8537 (m-40) REVERT: E 372 TYR cc_start: 0.8662 (t80) cc_final: 0.8338 (t80) REVERT: E 411 MET cc_start: 0.8788 (tpp) cc_final: 0.8326 (tpt) REVERT: E 414 GLN cc_start: 0.8670 (tt0) cc_final: 0.8419 (tt0) REVERT: F 81 GLN cc_start: 0.8747 (mt0) cc_final: 0.8493 (mt0) REVERT: F 139 ASN cc_start: 0.8594 (m-40) cc_final: 0.8225 (t0) REVERT: F 163 ASP cc_start: 0.8419 (m-30) cc_final: 0.7865 (m-30) REVERT: F 233 MET cc_start: 0.6440 (mmm) cc_final: 0.6161 (mmm) REVERT: F 269 LYS cc_start: 0.8383 (ttmm) cc_final: 0.7894 (ptpt) REVERT: F 372 TYR cc_start: 0.8655 (t80) cc_final: 0.8429 (t80) REVERT: F 411 MET cc_start: 0.8782 (tpp) cc_final: 0.8312 (tpt) outliers start: 63 outliers final: 43 residues processed: 437 average time/residue: 0.3525 time to fit residues: 239.4539 Evaluate side-chains 347 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 402 GLU Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 402 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 98 optimal weight: 20.0000 chunk 160 optimal weight: 0.5980 chunk 209 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 0.2980 chunk 293 optimal weight: 6.9990 chunk 43 optimal weight: 0.0670 chunk 116 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN F 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.095001 restraints weight = 39417.589| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.20 r_work: 0.3120 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23784 Z= 0.124 Angle : 0.541 5.692 32118 Z= 0.284 Chirality : 0.043 0.148 3492 Planarity : 0.004 0.042 4188 Dihedral : 5.159 58.257 3258 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.52 % Allowed : 8.17 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2964 helix: -0.68 (0.13), residues: 1500 sheet: -2.07 (0.23), residues: 384 loop : -0.83 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 281 HIS 0.010 0.001 HIS E 264 PHE 0.016 0.002 PHE F 10 TYR 0.010 0.001 TYR C 382 ARG 0.003 0.000 ARG C 462 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 1098) hydrogen bonds : angle 4.76048 ( 3060) covalent geometry : bond 0.00281 (23784) covalent geometry : angle 0.54071 (32118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 397 time to evaluate : 2.505 Fit side-chains REVERT: A 27 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7681 (tttm) REVERT: A 139 ASN cc_start: 0.8610 (m-40) cc_final: 0.8277 (t0) REVERT: A 163 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: A 197 CYS cc_start: 0.9155 (p) cc_final: 0.8927 (t) REVERT: A 372 TYR cc_start: 0.8524 (t80) cc_final: 0.8040 (t80) REVERT: A 411 MET cc_start: 0.8748 (tpp) cc_final: 0.8204 (tpt) REVERT: A 419 ARG cc_start: 0.7414 (mtm-85) cc_final: 0.7210 (mtm-85) REVERT: B 63 PHE cc_start: 0.8071 (m-10) cc_final: 0.7783 (m-10) REVERT: B 284 ASP cc_start: 0.8309 (m-30) cc_final: 0.7849 (p0) REVERT: B 411 MET cc_start: 0.8737 (tpp) cc_final: 0.8316 (tpt) REVERT: B 414 GLN cc_start: 0.8678 (tt0) cc_final: 0.8441 (tt0) REVERT: C 139 ASN cc_start: 0.8631 (m-40) cc_final: 0.8332 (t0) REVERT: C 163 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7794 (m-30) REVERT: C 284 ASP cc_start: 0.8332 (m-30) cc_final: 0.8062 (p0) REVERT: C 372 TYR cc_start: 0.8402 (t80) cc_final: 0.8011 (t80) REVERT: C 411 MET cc_start: 0.8725 (tpp) cc_final: 0.8308 (tpt) REVERT: C 469 MET cc_start: 0.7919 (mtm) cc_final: 0.7659 (mmt) REVERT: D 27 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7677 (tttm) REVERT: D 163 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: D 197 CYS cc_start: 0.9156 (p) cc_final: 0.8932 (t) REVERT: D 372 TYR cc_start: 0.8504 (t80) cc_final: 0.8020 (t80) REVERT: D 419 ARG cc_start: 0.7383 (mtm-85) cc_final: 0.7178 (mtm-85) REVERT: E 63 PHE cc_start: 0.8063 (m-10) cc_final: 0.7782 (m-10) REVERT: E 284 ASP cc_start: 0.8293 (m-30) cc_final: 0.7848 (p0) REVERT: E 411 MET cc_start: 0.8704 (tpp) cc_final: 0.8254 (tpt) REVERT: E 414 GLN cc_start: 0.8678 (tt0) cc_final: 0.8415 (tt0) REVERT: F 12 MET cc_start: 0.8612 (mtp) cc_final: 0.8398 (mtp) REVERT: F 81 GLN cc_start: 0.8689 (mt0) cc_final: 0.8451 (mt0) REVERT: F 139 ASN cc_start: 0.8638 (m-40) cc_final: 0.8335 (t0) REVERT: F 163 ASP cc_start: 0.8405 (m-30) cc_final: 0.7783 (m-30) REVERT: F 284 ASP cc_start: 0.8340 (m-30) cc_final: 0.8075 (p0) REVERT: F 372 TYR cc_start: 0.8414 (t80) cc_final: 0.8026 (t80) REVERT: F 411 MET cc_start: 0.8724 (tpp) cc_final: 0.8318 (tpt) outliers start: 63 outliers final: 42 residues processed: 422 average time/residue: 0.3429 time to fit residues: 232.3134 Evaluate side-chains 376 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 331 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 4 optimal weight: 8.9990 chunk 163 optimal weight: 0.1980 chunk 255 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 284 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 181 optimal weight: 0.0270 chunk 259 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 84 GLN B 81 GLN C 81 GLN C 205 GLN D 81 GLN D 84 GLN E 81 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096721 restraints weight = 39731.041| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.20 r_work: 0.3150 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23784 Z= 0.102 Angle : 0.514 6.690 32118 Z= 0.268 Chirality : 0.042 0.142 3492 Planarity : 0.004 0.042 4188 Dihedral : 4.862 56.682 3258 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.00 % Allowed : 10.22 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 2964 helix: -0.21 (0.13), residues: 1500 sheet: -1.68 (0.24), residues: 384 loop : -0.69 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 281 HIS 0.011 0.001 HIS B 264 PHE 0.017 0.001 PHE C 10 TYR 0.010 0.001 TYR F 382 ARG 0.004 0.000 ARG E 419 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 1098) hydrogen bonds : angle 4.35583 ( 3060) covalent geometry : bond 0.00229 (23784) covalent geometry : angle 0.51414 (32118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 387 time to evaluate : 2.890 Fit side-chains REVERT: A 139 ASN cc_start: 0.8552 (m-40) cc_final: 0.8300 (t0) REVERT: A 163 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: A 293 ASP cc_start: 0.7462 (t70) cc_final: 0.7212 (t0) REVERT: A 372 TYR cc_start: 0.8390 (t80) cc_final: 0.7947 (t80) REVERT: A 384 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: A 411 MET cc_start: 0.8715 (tpp) cc_final: 0.8179 (tpt) REVERT: B 63 PHE cc_start: 0.8010 (m-10) cc_final: 0.7797 (m-10) REVERT: B 411 MET cc_start: 0.8698 (tpp) cc_final: 0.8285 (tpt) REVERT: B 414 GLN cc_start: 0.8644 (tt0) cc_final: 0.8398 (tt0) REVERT: C 63 PHE cc_start: 0.8039 (m-10) cc_final: 0.7780 (m-10) REVERT: C 139 ASN cc_start: 0.8618 (m-40) cc_final: 0.8402 (t0) REVERT: C 163 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7846 (m-30) REVERT: C 372 TYR cc_start: 0.8351 (t80) cc_final: 0.7953 (t80) REVERT: C 411 MET cc_start: 0.8644 (tpp) cc_final: 0.8262 (tpt) REVERT: C 465 MET cc_start: 0.8707 (mmm) cc_final: 0.8250 (mtm) REVERT: D 139 ASN cc_start: 0.8586 (m-40) cc_final: 0.8333 (t0) REVERT: D 163 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: D 293 ASP cc_start: 0.7483 (t70) cc_final: 0.7249 (t0) REVERT: D 372 TYR cc_start: 0.8363 (t80) cc_final: 0.7884 (t80) REVERT: D 384 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8760 (tt0) REVERT: D 411 MET cc_start: 0.8816 (tpp) cc_final: 0.8230 (tpt) REVERT: E 63 PHE cc_start: 0.8014 (m-10) cc_final: 0.7798 (m-10) REVERT: F 12 MET cc_start: 0.8527 (mtp) cc_final: 0.8313 (mtp) REVERT: F 63 PHE cc_start: 0.8064 (m-10) cc_final: 0.7816 (m-10) REVERT: F 139 ASN cc_start: 0.8597 (m-40) cc_final: 0.8391 (t0) REVERT: F 372 TYR cc_start: 0.8375 (t80) cc_final: 0.7971 (t80) REVERT: F 411 MET cc_start: 0.8610 (tpp) cc_final: 0.8250 (tpt) REVERT: F 465 MET cc_start: 0.8724 (mmm) cc_final: 0.8339 (mtm) outliers start: 50 outliers final: 31 residues processed: 409 average time/residue: 0.3277 time to fit residues: 216.6967 Evaluate side-chains 379 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 343 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 251 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 51 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 265 optimal weight: 0.0470 chunk 271 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 overall best weight: 2.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN F 81 GLN F 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094813 restraints weight = 39921.109| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.19 r_work: 0.3123 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23784 Z= 0.123 Angle : 0.523 6.919 32118 Z= 0.273 Chirality : 0.043 0.149 3492 Planarity : 0.004 0.047 4188 Dihedral : 4.795 55.775 3258 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.56 % Allowed : 10.74 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.16), residues: 2964 helix: 0.07 (0.13), residues: 1500 sheet: -1.52 (0.25), residues: 384 loop : -0.74 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 281 HIS 0.011 0.001 HIS C 264 PHE 0.017 0.002 PHE D 122 TYR 0.011 0.001 TYR F 382 ARG 0.006 0.000 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 1098) hydrogen bonds : angle 4.28271 ( 3060) covalent geometry : bond 0.00291 (23784) covalent geometry : angle 0.52303 (32118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 2.473 Fit side-chains REVERT: A 139 ASN cc_start: 0.8601 (m-40) cc_final: 0.8332 (t0) REVERT: A 163 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: A 293 ASP cc_start: 0.7406 (t70) cc_final: 0.7149 (t0) REVERT: A 372 TYR cc_start: 0.8477 (t80) cc_final: 0.7992 (t80) REVERT: A 384 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: A 411 MET cc_start: 0.8680 (tpp) cc_final: 0.8180 (tpt) REVERT: A 414 GLN cc_start: 0.8616 (tt0) cc_final: 0.8336 (tt0) REVERT: B 411 MET cc_start: 0.8684 (tpp) cc_final: 0.8222 (tpt) REVERT: B 414 GLN cc_start: 0.8629 (tt0) cc_final: 0.8345 (tt0) REVERT: B 465 MET cc_start: 0.8803 (mmm) cc_final: 0.8513 (mtp) REVERT: C 63 PHE cc_start: 0.8058 (m-10) cc_final: 0.7520 (m-80) REVERT: C 139 ASN cc_start: 0.8643 (m-40) cc_final: 0.8408 (t0) REVERT: C 163 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8022 (m-30) REVERT: C 372 TYR cc_start: 0.8465 (t80) cc_final: 0.8130 (t80) REVERT: C 411 MET cc_start: 0.8643 (tpp) cc_final: 0.8297 (tpt) REVERT: C 465 MET cc_start: 0.8751 (mmm) cc_final: 0.8413 (mtm) REVERT: D 139 ASN cc_start: 0.8606 (m-40) cc_final: 0.8335 (t0) REVERT: D 163 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: D 293 ASP cc_start: 0.7420 (t70) cc_final: 0.7169 (t0) REVERT: D 372 TYR cc_start: 0.8466 (t80) cc_final: 0.8006 (t80) REVERT: D 384 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8771 (tt0) REVERT: E 411 MET cc_start: 0.8838 (tpp) cc_final: 0.8278 (tpt) REVERT: E 414 GLN cc_start: 0.8590 (tt0) cc_final: 0.8354 (tt0) REVERT: E 465 MET cc_start: 0.8812 (mmm) cc_final: 0.8588 (mtp) REVERT: F 12 MET cc_start: 0.8587 (mtp) cc_final: 0.8384 (mtp) REVERT: F 63 PHE cc_start: 0.8073 (m-10) cc_final: 0.7531 (m-80) REVERT: F 139 ASN cc_start: 0.8663 (m-40) cc_final: 0.8412 (t0) REVERT: F 163 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: F 372 TYR cc_start: 0.8493 (t80) cc_final: 0.8157 (t80) REVERT: F 411 MET cc_start: 0.8681 (tpp) cc_final: 0.8324 (tpt) REVERT: F 465 MET cc_start: 0.8767 (mmm) cc_final: 0.8416 (mtm) outliers start: 64 outliers final: 53 residues processed: 378 average time/residue: 0.3112 time to fit residues: 191.1192 Evaluate side-chains 395 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 336 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain E residue 115 CYS Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 271 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 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 = 0.3613 r_free = 0.3613 target = 0.118190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.092308 restraints weight = 39769.163| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.17 r_work: 0.3079 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23784 Z= 0.186 Angle : 0.576 8.484 32118 Z= 0.297 Chirality : 0.045 0.159 3492 Planarity : 0.004 0.052 4188 Dihedral : 4.941 55.582 3258 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.37 % Allowed : 10.26 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.15), residues: 2964 helix: 0.08 (0.13), residues: 1512 sheet: -1.49 (0.25), residues: 384 loop : -0.66 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 281 HIS 0.011 0.001 HIS D 264 PHE 0.025 0.002 PHE D 122 TYR 0.017 0.001 TYR F 382 ARG 0.006 0.000 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 1098) hydrogen bonds : angle 4.41365 ( 3060) covalent geometry : bond 0.00444 (23784) covalent geometry : angle 0.57638 (32118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 324 time to evaluate : 2.478 Fit side-chains REVERT: A 163 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: A 372 TYR cc_start: 0.8602 (t80) cc_final: 0.8139 (t80) REVERT: A 384 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8893 (tt0) REVERT: A 411 MET cc_start: 0.8632 (tpp) cc_final: 0.8204 (tpt) REVERT: B 411 MET cc_start: 0.8625 (tpp) cc_final: 0.8220 (tpt) REVERT: B 414 GLN cc_start: 0.8680 (tt0) cc_final: 0.8351 (tt0) REVERT: B 465 MET cc_start: 0.8849 (mmm) cc_final: 0.8590 (mtp) REVERT: C 63 PHE cc_start: 0.8074 (m-10) cc_final: 0.7601 (m-80) REVERT: C 139 ASN cc_start: 0.8734 (m-40) cc_final: 0.8402 (t0) REVERT: C 163 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8060 (m-30) REVERT: C 372 TYR cc_start: 0.8593 (t80) cc_final: 0.8307 (t80) REVERT: C 411 MET cc_start: 0.8592 (tpp) cc_final: 0.8301 (tpt) REVERT: C 465 MET cc_start: 0.8786 (mmm) cc_final: 0.8488 (mtm) REVERT: D 163 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8075 (m-30) REVERT: D 372 TYR cc_start: 0.8573 (t80) cc_final: 0.8120 (t80) REVERT: D 384 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8889 (tt0) REVERT: D 411 MET cc_start: 0.8776 (tpp) cc_final: 0.8244 (tpt) REVERT: E 411 MET cc_start: 0.8771 (tpp) cc_final: 0.8288 (tpt) REVERT: E 465 MET cc_start: 0.8814 (mmm) cc_final: 0.8468 (mtm) REVERT: F 63 PHE cc_start: 0.8102 (m-10) cc_final: 0.7630 (m-80) REVERT: F 139 ASN cc_start: 0.8731 (m-40) cc_final: 0.8395 (t0) REVERT: F 163 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: F 372 TYR cc_start: 0.8630 (t80) cc_final: 0.8339 (t80) REVERT: F 411 MET cc_start: 0.8620 (tpp) cc_final: 0.8324 (tpt) REVERT: F 465 MET cc_start: 0.8792 (mmm) cc_final: 0.8457 (mtm) outliers start: 84 outliers final: 63 residues processed: 360 average time/residue: 0.3235 time to fit residues: 188.3677 Evaluate side-chains 384 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 384 GLU Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 TRP Chi-restraints excluded: chain F residue 322 LEU Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 130 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 219 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 255 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.118895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093060 restraints weight = 40065.115| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.19 r_work: 0.3095 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23784 Z= 0.142 Angle : 0.546 7.760 32118 Z= 0.282 Chirality : 0.044 0.153 3492 Planarity : 0.004 0.052 4188 Dihedral : 4.844 54.511 3258 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.12 % Allowed : 10.70 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2964 helix: 0.26 (0.13), residues: 1506 sheet: -1.47 (0.26), residues: 396 loop : -0.59 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 281 HIS 0.012 0.002 HIS B 264 PHE 0.019 0.002 PHE D 122 TYR 0.012 0.001 TYR F 382 ARG 0.006 0.000 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 1098) hydrogen bonds : angle 4.31988 ( 3060) covalent geometry : bond 0.00338 (23784) covalent geometry : angle 0.54583 (32118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 338 time to evaluate : 2.701 Fit side-chains REVERT: A 163 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: A 372 TYR cc_start: 0.8563 (t80) cc_final: 0.8090 (t80) REVERT: A 384 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8885 (tt0) REVERT: A 411 MET cc_start: 0.8652 (tpp) cc_final: 0.8200 (tpt) REVERT: B 63 PHE cc_start: 0.8175 (m-10) cc_final: 0.7789 (m-80) REVERT: B 411 MET cc_start: 0.8624 (tpp) cc_final: 0.8263 (tpt) REVERT: B 465 MET cc_start: 0.8797 (mmm) cc_final: 0.8586 (mtp) REVERT: C 40 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8077 (mp10) REVERT: C 63 PHE cc_start: 0.8055 (m-10) cc_final: 0.7623 (m-80) REVERT: C 139 ASN cc_start: 0.8677 (m-40) cc_final: 0.8371 (t0) REVERT: C 163 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: C 372 TYR cc_start: 0.8559 (t80) cc_final: 0.8246 (t80) REVERT: C 411 MET cc_start: 0.8569 (tpp) cc_final: 0.8309 (tpt) REVERT: C 465 MET cc_start: 0.8747 (mmm) cc_final: 0.8495 (mtm) REVERT: D 163 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: D 372 TYR cc_start: 0.8541 (t80) cc_final: 0.8083 (t80) REVERT: E 63 PHE cc_start: 0.8158 (m-10) cc_final: 0.7767 (m-80) REVERT: E 411 MET cc_start: 0.8739 (tpp) cc_final: 0.8197 (tpt) REVERT: F 63 PHE cc_start: 0.8079 (m-10) cc_final: 0.7643 (m-80) REVERT: F 139 ASN cc_start: 0.8682 (m-40) cc_final: 0.8361 (t0) REVERT: F 163 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: F 372 TYR cc_start: 0.8573 (t80) cc_final: 0.8249 (t80) REVERT: F 411 MET cc_start: 0.8611 (tpp) cc_final: 0.8273 (tpt) REVERT: F 465 MET cc_start: 0.8787 (mmm) cc_final: 0.8563 (mtm) outliers start: 78 outliers final: 56 residues processed: 375 average time/residue: 0.3390 time to fit residues: 206.9695 Evaluate side-chains 374 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 313 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 281 TRP Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 186 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 212 optimal weight: 0.0570 chunk 43 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 271 optimal weight: 30.0000 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 84 GLN A 250 GLN A 264 HIS B 81 GLN B 414 GLN C 81 GLN C 84 GLN C 297 GLN D 81 GLN D 84 GLN D 250 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.120967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095361 restraints weight = 39933.474| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.18 r_work: 0.3141 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23784 Z= 0.101 Angle : 0.511 6.268 32118 Z= 0.266 Chirality : 0.042 0.141 3492 Planarity : 0.004 0.049 4188 Dihedral : 4.666 53.114 3258 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.36 % Allowed : 11.50 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2964 helix: 0.53 (0.14), residues: 1494 sheet: -1.29 (0.26), residues: 396 loop : -0.62 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 281 HIS 0.011 0.001 HIS B 264 PHE 0.013 0.001 PHE C 10 TYR 0.008 0.001 TYR C 382 ARG 0.006 0.000 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.02895 ( 1098) hydrogen bonds : angle 4.10390 ( 3060) covalent geometry : bond 0.00234 (23784) covalent geometry : angle 0.51132 (32118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 360 time to evaluate : 2.683 Fit side-chains REVERT: A 19 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7213 (tpt-90) REVERT: A 81 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: A 293 ASP cc_start: 0.7269 (t70) cc_final: 0.7063 (t0) REVERT: A 372 TYR cc_start: 0.8509 (t80) cc_final: 0.8076 (t80) REVERT: A 384 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8818 (tt0) REVERT: A 411 MET cc_start: 0.8629 (tpp) cc_final: 0.8170 (tpt) REVERT: B 63 PHE cc_start: 0.8100 (m-10) cc_final: 0.7743 (m-80) REVERT: B 293 ASP cc_start: 0.7459 (t70) cc_final: 0.7234 (t0) REVERT: B 411 MET cc_start: 0.8599 (tpp) cc_final: 0.8281 (tpt) REVERT: C 63 PHE cc_start: 0.8002 (m-10) cc_final: 0.7615 (m-80) REVERT: C 372 TYR cc_start: 0.8486 (t80) cc_final: 0.8164 (t80) REVERT: C 411 MET cc_start: 0.8619 (tpp) cc_final: 0.8328 (tpt) REVERT: D 19 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7208 (tpt-90) REVERT: D 81 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: D 264 HIS cc_start: 0.8575 (t70) cc_final: 0.8354 (t-170) REVERT: D 293 ASP cc_start: 0.7272 (t70) cc_final: 0.7071 (t0) REVERT: D 372 TYR cc_start: 0.8500 (t80) cc_final: 0.8062 (t80) REVERT: D 411 MET cc_start: 0.8759 (tpp) cc_final: 0.8152 (tpt) REVERT: D 419 ARG cc_start: 0.8363 (ttm-80) cc_final: 0.7880 (ttm-80) REVERT: E 63 PHE cc_start: 0.8091 (m-10) cc_final: 0.7740 (m-80) REVERT: E 293 ASP cc_start: 0.7427 (t70) cc_final: 0.7202 (t0) REVERT: E 411 MET cc_start: 0.8690 (tpp) cc_final: 0.8188 (tpt) REVERT: F 63 PHE cc_start: 0.8026 (m-10) cc_final: 0.7629 (m-80) REVERT: F 139 ASN cc_start: 0.8609 (m-40) cc_final: 0.8380 (t0) REVERT: F 163 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: F 372 TYR cc_start: 0.8496 (t80) cc_final: 0.8174 (t80) REVERT: F 411 MET cc_start: 0.8561 (tpp) cc_final: 0.8289 (tpt) REVERT: F 465 MET cc_start: 0.8701 (mmm) cc_final: 0.8462 (mtm) outliers start: 59 outliers final: 44 residues processed: 394 average time/residue: 0.3300 time to fit residues: 208.3328 Evaluate side-chains 381 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 333 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 378 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 121 optimal weight: 0.8980 chunk 290 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 140 optimal weight: 0.0770 chunk 277 optimal weight: 0.0870 chunk 101 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 184 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 297 GLN ** C 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094355 restraints weight = 39680.270| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.16 r_work: 0.3114 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23784 Z= 0.123 Angle : 0.534 6.754 32118 Z= 0.278 Chirality : 0.043 0.145 3492 Planarity : 0.004 0.049 4188 Dihedral : 4.680 51.872 3258 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.32 % Allowed : 11.38 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2964 helix: 0.59 (0.14), residues: 1494 sheet: -1.24 (0.26), residues: 396 loop : -0.58 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 281 HIS 0.012 0.001 HIS A 264 PHE 0.018 0.001 PHE D 122 TYR 0.009 0.001 TYR A 382 ARG 0.006 0.000 ARG B 419 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 1098) hydrogen bonds : angle 4.11573 ( 3060) covalent geometry : bond 0.00292 (23784) covalent geometry : angle 0.53385 (32118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 329 time to evaluate : 2.504 Fit side-chains REVERT: A 19 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7245 (tpt-90) REVERT: A 81 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: A 293 ASP cc_start: 0.7298 (t70) cc_final: 0.7083 (t0) REVERT: A 372 TYR cc_start: 0.8565 (t80) cc_final: 0.8087 (t80) REVERT: A 384 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8841 (tt0) REVERT: A 411 MET cc_start: 0.8624 (tpp) cc_final: 0.8158 (tpt) REVERT: B 63 PHE cc_start: 0.8111 (m-10) cc_final: 0.7775 (m-80) REVERT: B 411 MET cc_start: 0.8621 (tpp) cc_final: 0.8260 (tpt) REVERT: B 414 GLN cc_start: 0.8642 (tt0) cc_final: 0.8332 (tt0) REVERT: C 63 PHE cc_start: 0.8013 (m-10) cc_final: 0.7657 (m-80) REVERT: C 163 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: C 372 TYR cc_start: 0.8534 (t80) cc_final: 0.8243 (t80) REVERT: C 411 MET cc_start: 0.8592 (tpp) cc_final: 0.8314 (tpt) REVERT: D 27 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7592 (tttm) REVERT: D 81 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: D 293 ASP cc_start: 0.7321 (t70) cc_final: 0.7107 (t0) REVERT: D 372 TYR cc_start: 0.8539 (t80) cc_final: 0.8068 (t80) REVERT: D 411 MET cc_start: 0.8750 (tpp) cc_final: 0.8144 (tpt) REVERT: D 419 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: E 63 PHE cc_start: 0.8101 (m-10) cc_final: 0.7767 (m-80) REVERT: E 411 MET cc_start: 0.8665 (tpp) cc_final: 0.8153 (tpt) REVERT: F 63 PHE cc_start: 0.8034 (m-10) cc_final: 0.7659 (m-80) REVERT: F 139 ASN cc_start: 0.8606 (m-40) cc_final: 0.8378 (t0) REVERT: F 163 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: F 372 TYR cc_start: 0.8555 (t80) cc_final: 0.8249 (t80) REVERT: F 411 MET cc_start: 0.8559 (tpp) cc_final: 0.8280 (tpt) outliers start: 58 outliers final: 49 residues processed: 360 average time/residue: 0.3210 time to fit residues: 187.5724 Evaluate side-chains 376 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 322 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 58 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 226 optimal weight: 40.0000 chunk 187 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 297 GLN D 81 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.092965 restraints weight = 39789.185| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.15 r_work: 0.3085 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23784 Z= 0.159 Angle : 0.565 7.301 32118 Z= 0.294 Chirality : 0.044 0.152 3492 Planarity : 0.004 0.051 4188 Dihedral : 4.776 51.095 3258 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.40 % Allowed : 11.46 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2964 helix: 0.56 (0.14), residues: 1494 sheet: -1.21 (0.27), residues: 396 loop : -0.54 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 281 HIS 0.012 0.001 HIS D 264 PHE 0.021 0.002 PHE D 122 TYR 0.012 0.001 TYR A 382 ARG 0.006 0.000 ARG E 419 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 1098) hydrogen bonds : angle 4.19852 ( 3060) covalent geometry : bond 0.00379 (23784) covalent geometry : angle 0.56472 (32118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 2.529 Fit side-chains REVERT: A 19 ARG cc_start: 0.8129 (mmm160) cc_final: 0.7275 (tpt-90) REVERT: A 81 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: A 163 ASP cc_start: 0.8307 (m-30) cc_final: 0.8085 (m-30) REVERT: A 293 ASP cc_start: 0.7291 (t70) cc_final: 0.7062 (t0) REVERT: A 372 TYR cc_start: 0.8635 (t80) cc_final: 0.8165 (t80) REVERT: A 384 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8883 (tt0) REVERT: A 411 MET cc_start: 0.8631 (tpp) cc_final: 0.8151 (tpt) REVERT: B 63 PHE cc_start: 0.8112 (m-10) cc_final: 0.7778 (m-80) REVERT: B 411 MET cc_start: 0.8585 (tpp) cc_final: 0.8253 (tpt) REVERT: C 63 PHE cc_start: 0.8046 (m-10) cc_final: 0.7683 (m-80) REVERT: C 163 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: C 372 TYR cc_start: 0.8615 (t80) cc_final: 0.8337 (t80) REVERT: C 411 MET cc_start: 0.8609 (tpp) cc_final: 0.8317 (tpt) REVERT: D 81 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: D 163 ASP cc_start: 0.8278 (m-30) cc_final: 0.8048 (m-30) REVERT: D 293 ASP cc_start: 0.7339 (t70) cc_final: 0.7109 (t0) REVERT: D 372 TYR cc_start: 0.8617 (t80) cc_final: 0.8162 (t80) REVERT: D 411 MET cc_start: 0.8749 (tpp) cc_final: 0.8165 (tpt) REVERT: D 419 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.7897 (ttm-80) REVERT: E 63 PHE cc_start: 0.8105 (m-10) cc_final: 0.7776 (m-80) REVERT: E 411 MET cc_start: 0.8647 (tpp) cc_final: 0.8144 (tpt) REVERT: E 414 GLN cc_start: 0.8350 (tt0) cc_final: 0.8039 (tp40) REVERT: F 63 PHE cc_start: 0.8072 (m-10) cc_final: 0.7695 (m-80) REVERT: F 139 ASN cc_start: 0.8672 (m-40) cc_final: 0.8401 (t0) REVERT: F 163 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: F 372 TYR cc_start: 0.8632 (t80) cc_final: 0.8349 (t80) REVERT: F 411 MET cc_start: 0.8583 (tpp) cc_final: 0.8302 (tpt) outliers start: 60 outliers final: 55 residues processed: 351 average time/residue: 0.3246 time to fit residues: 185.0017 Evaluate side-chains 378 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 318 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 238 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 378 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 378 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 285 optimal weight: 5.9990 chunk 275 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 269 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 106 optimal weight: 0.0770 chunk 42 optimal weight: 8.9990 overall best weight: 3.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.092492 restraints weight = 39710.236| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.15 r_work: 0.3081 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23784 Z= 0.159 Angle : 0.565 7.381 32118 Z= 0.294 Chirality : 0.044 0.160 3492 Planarity : 0.004 0.053 4188 Dihedral : 4.772 50.441 3258 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.48 % Allowed : 11.38 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2964 helix: 0.58 (0.13), residues: 1488 sheet: -1.20 (0.27), residues: 396 loop : -0.57 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP E 281 HIS 0.013 0.002 HIS B 264 PHE 0.021 0.002 PHE C 10 TYR 0.012 0.001 TYR A 382 ARG 0.006 0.000 ARG E 419 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 1098) hydrogen bonds : angle 4.21442 ( 3060) covalent geometry : bond 0.00378 (23784) covalent geometry : angle 0.56452 (32118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12615.86 seconds wall clock time: 216 minutes 55.62 seconds (13015.62 seconds total)