Starting phenix.real_space_refine on Fri Sep 19 03:14:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jcz_6630/09_2025/3jcz_6630.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jcz_6630/09_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_6630/09_2025/3jcz_6630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jcz_6630/09_2025/3jcz_6630.map" model { file = "/net/cci-nas-00/data/ceres_data/3jcz_6630/09_2025/3jcz_6630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jcz_6630/09_2025/3jcz_6630.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 3.13, per 1000 atoms: 0.13 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: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.79 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: 3.84 Time building geometry restraints manager: 2.61 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 1.400 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: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.630 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.370 ------------------------------------------------------------------------------- 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 : 8.73 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.007 0.001 ARG C 396 TYR 0.020 0.003 TYR F 407 PHE 0.034 0.003 PHE B 399 TRP 0.023 0.003 TRP D 178 HIS 0.011 0.002 HIS C 450 Details of bonding type rmsd covalent geometry : bond 0.00766 (23784) covalent geometry : angle 0.69167 (32118) hydrogen bonds : bond 0.27415 ( 1098) hydrogen bonds : angle 10.28568 ( 3060) *********************** 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 : 0.767 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: 0.1610 time to fit residues: 142.6020 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 : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN B 135 ASN B 463 GLN C 135 ASN C 205 GLN C 414 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.093154 restraints weight = 39224.005| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.23 r_work: 0.3083 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23784 Z= 0.176 Angle : 0.599 5.498 32118 Z= 0.319 Chirality : 0.044 0.159 3492 Planarity : 0.005 0.040 4188 Dihedral : 5.601 61.491 3258 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.60 % Allowed : 6.29 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.14), residues: 2964 helix: -1.54 (0.12), residues: 1446 sheet: -2.57 (0.23), residues: 384 loop : -1.30 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 261 TYR 0.017 0.001 TYR E 382 PHE 0.021 0.002 PHE D 122 TRP 0.025 0.002 TRP E 281 HIS 0.008 0.002 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00412 (23784) covalent geometry : angle 0.59892 (32118) hydrogen bonds : bond 0.04804 ( 1098) hydrogen bonds : angle 5.53216 ( 3060) *********************** 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 475 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 410 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7625 (tttm) REVERT: A 163 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: A 264 HIS cc_start: 0.8785 (t-170) cc_final: 0.8579 (t-170) REVERT: A 372 TYR cc_start: 0.8660 (t80) cc_final: 0.8237 (t80) REVERT: A 411 MET cc_start: 0.8782 (tpp) cc_final: 0.8292 (tpt) REVERT: A 484 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8537 (m-40) REVERT: B 73 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: B 372 TYR cc_start: 0.8663 (t80) cc_final: 0.8335 (t80) REVERT: B 411 MET cc_start: 0.8747 (tpp) cc_final: 0.8300 (tpt) REVERT: B 414 GLN cc_start: 0.8657 (tt0) cc_final: 0.8389 (tt0) REVERT: B 419 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: B 469 MET cc_start: 0.8156 (mtm) cc_final: 0.7952 (mmt) REVERT: C 139 ASN cc_start: 0.8605 (m-40) cc_final: 0.8262 (t0) REVERT: C 233 MET cc_start: 0.6403 (mmm) cc_final: 0.6128 (mmm) REVERT: C 269 LYS cc_start: 0.8403 (ttmm) cc_final: 0.7929 (ptpt) REVERT: C 372 TYR cc_start: 0.8663 (t80) cc_final: 0.8426 (t80) REVERT: C 411 MET cc_start: 0.8810 (tpp) cc_final: 0.8351 (tpt) REVERT: D 27 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7627 (tttm) REVERT: D 163 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: D 372 TYR cc_start: 0.8650 (t80) cc_final: 0.8226 (t80) REVERT: D 484 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8537 (m-40) REVERT: E 73 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8308 (pm20) REVERT: E 372 TYR cc_start: 0.8671 (t80) cc_final: 0.8339 (t80) REVERT: E 411 MET cc_start: 0.8783 (tpp) cc_final: 0.8326 (tpt) REVERT: E 414 GLN cc_start: 0.8659 (tt0) cc_final: 0.8394 (tt0) REVERT: E 469 MET cc_start: 0.8141 (mtm) cc_final: 0.7938 (mmt) REVERT: F 81 GLN cc_start: 0.8754 (mt0) cc_final: 0.8500 (mt0) REVERT: F 139 ASN cc_start: 0.8616 (m-40) cc_final: 0.8230 (t0) REVERT: F 163 ASP cc_start: 0.8419 (m-30) cc_final: 0.7868 (m-30) REVERT: F 233 MET cc_start: 0.6419 (mmm) cc_final: 0.6151 (mmm) REVERT: F 269 LYS cc_start: 0.8383 (ttmm) cc_final: 0.7904 (ptpt) REVERT: F 372 TYR cc_start: 0.8671 (t80) cc_final: 0.8441 (t80) REVERT: F 411 MET cc_start: 0.8784 (tpp) cc_final: 0.8316 (tpt) outliers start: 65 outliers final: 43 residues processed: 436 average time/residue: 0.1525 time to fit residues: 103.1972 Evaluate side-chains 341 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 73 GLU 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 73 GLU 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 141 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN C 81 GLN D 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.118904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.093919 restraints weight = 40020.209| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.13 r_work: 0.3093 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 23784 Z= 0.156 Angle : 0.564 5.609 32118 Z= 0.297 Chirality : 0.044 0.153 3492 Planarity : 0.005 0.043 4188 Dihedral : 5.268 58.642 3258 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.88 % Allowed : 8.25 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.15), residues: 2964 helix: -0.70 (0.13), residues: 1482 sheet: -2.14 (0.23), residues: 384 loop : -0.92 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 462 TYR 0.013 0.001 TYR F 382 PHE 0.019 0.002 PHE D 122 TRP 0.030 0.002 TRP B 281 HIS 0.009 0.002 HIS E 264 Details of bonding type rmsd covalent geometry : bond 0.00367 (23784) covalent geometry : angle 0.56392 (32118) hydrogen bonds : bond 0.03923 ( 1098) hydrogen bonds : angle 4.83327 ( 3060) *********************** 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 459 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 387 time to evaluate : 1.022 Fit side-chains REVERT: A 163 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: A 264 HIS cc_start: 0.8745 (t-170) cc_final: 0.8520 (t-170) REVERT: A 372 TYR cc_start: 0.8582 (t80) cc_final: 0.8128 (t80) REVERT: A 411 MET cc_start: 0.8750 (tpp) cc_final: 0.8245 (tpt) REVERT: B 63 PHE cc_start: 0.8112 (m-10) cc_final: 0.7854 (m-10) REVERT: B 411 MET cc_start: 0.8737 (tpp) cc_final: 0.8309 (tpt) REVERT: B 414 GLN cc_start: 0.8708 (tt0) cc_final: 0.8441 (tt0) REVERT: C 139 ASN cc_start: 0.8618 (m-40) cc_final: 0.8334 (t0) REVERT: C 163 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: C 269 LYS cc_start: 0.8395 (ttmm) cc_final: 0.7868 (ptpt) REVERT: C 284 ASP cc_start: 0.8319 (m-30) cc_final: 0.8117 (p0) REVERT: C 372 TYR cc_start: 0.8481 (t80) cc_final: 0.8103 (t80) REVERT: C 411 MET cc_start: 0.8723 (tpp) cc_final: 0.8351 (tpt) REVERT: D 163 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: D 372 TYR cc_start: 0.8575 (t80) cc_final: 0.8113 (t80) REVERT: E 63 PHE cc_start: 0.8103 (m-10) cc_final: 0.7851 (m-10) REVERT: E 411 MET cc_start: 0.8720 (tpp) cc_final: 0.8301 (tpt) REVERT: E 414 GLN cc_start: 0.8690 (tt0) cc_final: 0.8418 (tt0) REVERT: F 81 GLN cc_start: 0.8690 (mt0) cc_final: 0.8454 (mt0) REVERT: F 139 ASN cc_start: 0.8639 (m-40) cc_final: 0.8331 (t0) REVERT: F 269 LYS cc_start: 0.8376 (ttmm) cc_final: 0.7846 (ptpt) REVERT: F 372 TYR cc_start: 0.8482 (t80) cc_final: 0.8105 (t80) REVERT: F 411 MET cc_start: 0.8736 (tpp) cc_final: 0.8359 (tpt) outliers start: 72 outliers final: 58 residues processed: 416 average time/residue: 0.1518 time to fit residues: 102.3849 Evaluate side-chains 385 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 TRP 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 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 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 112 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR 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 D residue 37 THR 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 272 THR 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 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 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 112 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 171 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 91 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 219 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 231 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 116 optimal weight: 0.0470 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 81 GLN C 81 GLN D 81 GLN E 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.119235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.093718 restraints weight = 39847.973| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.17 r_work: 0.3105 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23784 Z= 0.146 Angle : 0.552 6.107 32118 Z= 0.287 Chirality : 0.043 0.151 3492 Planarity : 0.004 0.044 4188 Dihedral : 5.076 56.962 3258 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.21 % Allowed : 8.97 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.15), residues: 2964 helix: -0.34 (0.13), residues: 1506 sheet: -1.98 (0.24), residues: 396 loop : -0.65 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.013 0.001 TYR F 382 PHE 0.019 0.002 PHE A 122 TRP 0.030 0.002 TRP E 281 HIS 0.011 0.002 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00346 (23784) covalent geometry : angle 0.55170 (32118) hydrogen bonds : bond 0.03548 ( 1098) hydrogen bonds : angle 4.54053 ( 3060) *********************** 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 418 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 338 time to evaluate : 0.979 Fit side-chains REVERT: A 163 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: A 372 TYR cc_start: 0.8591 (t80) cc_final: 0.8108 (t80) REVERT: A 402 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7787 (pt0) REVERT: A 411 MET cc_start: 0.8687 (tpp) cc_final: 0.8200 (tpt) REVERT: B 63 PHE cc_start: 0.8082 (m-10) cc_final: 0.7879 (m-10) REVERT: B 411 MET cc_start: 0.8684 (tpp) cc_final: 0.8259 (tpt) REVERT: B 414 GLN cc_start: 0.8677 (tt0) cc_final: 0.8390 (tt0) REVERT: C 12 MET cc_start: 0.8657 (mtp) cc_final: 0.8450 (mtp) REVERT: C 63 PHE cc_start: 0.8139 (m-10) cc_final: 0.7890 (m-10) REVERT: C 139 ASN cc_start: 0.8661 (m-40) cc_final: 0.8358 (t0) REVERT: C 163 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8029 (m-30) REVERT: C 269 LYS cc_start: 0.8394 (ttmm) cc_final: 0.7866 (ptpt) REVERT: C 372 TYR cc_start: 0.8484 (t80) cc_final: 0.8141 (t80) REVERT: C 402 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: C 411 MET cc_start: 0.8674 (tpp) cc_final: 0.8321 (tpt) REVERT: C 465 MET cc_start: 0.8788 (mmm) cc_final: 0.8365 (mtm) REVERT: C 469 MET cc_start: 0.7887 (mtm) cc_final: 0.7670 (mmt) REVERT: D 163 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: D 372 TYR cc_start: 0.8580 (t80) cc_final: 0.8104 (t80) REVERT: D 402 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: E 63 PHE cc_start: 0.8079 (m-10) cc_final: 0.7876 (m-10) REVERT: E 411 MET cc_start: 0.8646 (tpp) cc_final: 0.8235 (tpt) REVERT: E 414 GLN cc_start: 0.8664 (tt0) cc_final: 0.8363 (tt0) REVERT: F 63 PHE cc_start: 0.8130 (m-10) cc_final: 0.7895 (m-10) REVERT: F 81 GLN cc_start: 0.8685 (mt0) cc_final: 0.8347 (mt0) REVERT: F 139 ASN cc_start: 0.8646 (m-40) cc_final: 0.8334 (t0) REVERT: F 163 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: F 372 TYR cc_start: 0.8502 (t80) cc_final: 0.8152 (t80) REVERT: F 402 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: F 411 MET cc_start: 0.8654 (tpp) cc_final: 0.8311 (tpt) REVERT: F 465 MET cc_start: 0.8797 (mmm) cc_final: 0.8411 (mtm) outliers start: 80 outliers final: 61 residues processed: 370 average time/residue: 0.1426 time to fit residues: 86.4008 Evaluate side-chains 389 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 320 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 171 THR 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 393 SER Chi-restraints excluded: chain A residue 402 GLU 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 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 65 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR 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 C residue 402 GLU Chi-restraints excluded: chain D residue 37 THR 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 171 THR 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 393 SER Chi-restraints excluded: chain D residue 402 GLU 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 212 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 65 ILE 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 236 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 252 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 254 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- 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 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092882 restraints weight = 39597.167| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.17 r_work: 0.3075 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23784 Z= 0.162 Angle : 0.554 7.523 32118 Z= 0.289 Chirality : 0.044 0.151 3492 Planarity : 0.004 0.044 4188 Dihedral : 4.986 55.676 3258 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.97 % Allowed : 9.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.16), residues: 2964 helix: -0.14 (0.13), residues: 1506 sheet: -1.79 (0.25), residues: 396 loop : -0.57 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 419 TYR 0.014 0.001 TYR C 382 PHE 0.021 0.002 PHE A 122 TRP 0.030 0.002 TRP B 281 HIS 0.012 0.002 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00386 (23784) covalent geometry : angle 0.55447 (32118) hydrogen bonds : bond 0.03506 ( 1098) hydrogen bonds : angle 4.46054 ( 3060) *********************** 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 429 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 330 time to evaluate : 1.051 Fit side-chains REVERT: A 163 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: A 372 TYR cc_start: 0.8554 (t80) cc_final: 0.8065 (t80) REVERT: A 402 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: A 411 MET cc_start: 0.8668 (tpp) cc_final: 0.8184 (tpt) REVERT: B 411 MET cc_start: 0.8637 (tpp) cc_final: 0.8239 (tpt) REVERT: B 414 GLN cc_start: 0.8699 (tt0) cc_final: 0.8379 (tt0) REVERT: C 63 PHE cc_start: 0.8105 (m-10) cc_final: 0.7631 (m-80) REVERT: C 139 ASN cc_start: 0.8718 (m-40) cc_final: 0.8381 (t0) REVERT: C 163 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: C 269 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7803 (ptpt) REVERT: C 372 TYR cc_start: 0.8544 (t80) cc_final: 0.8228 (t80) REVERT: C 402 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: C 411 MET cc_start: 0.8625 (tpp) cc_final: 0.8315 (tpt) REVERT: C 465 MET cc_start: 0.8818 (mmm) cc_final: 0.8425 (mtm) REVERT: C 472 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.8008 (p0) REVERT: D 163 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: D 372 TYR cc_start: 0.8545 (t80) cc_final: 0.8076 (t80) REVERT: D 402 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: D 411 MET cc_start: 0.8754 (tpp) cc_final: 0.8169 (tpt) REVERT: E 411 MET cc_start: 0.8646 (tpp) cc_final: 0.8241 (tpt) REVERT: E 414 GLN cc_start: 0.8700 (tt0) cc_final: 0.8371 (tt0) REVERT: F 63 PHE cc_start: 0.8105 (m-10) cc_final: 0.7636 (m-80) REVERT: F 81 GLN cc_start: 0.8742 (mt0) cc_final: 0.8382 (mt0) REVERT: F 139 ASN cc_start: 0.8704 (m-40) cc_final: 0.8351 (t0) REVERT: F 163 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: F 372 TYR cc_start: 0.8575 (t80) cc_final: 0.8253 (t80) REVERT: F 402 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7696 (pt0) REVERT: F 411 MET cc_start: 0.8624 (tpp) cc_final: 0.8305 (tpt) REVERT: F 465 MET cc_start: 0.8824 (mmm) cc_final: 0.8465 (mtm) outliers start: 99 outliers final: 69 residues processed: 374 average time/residue: 0.1533 time to fit residues: 94.2160 Evaluate side-chains 392 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 314 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 197 CYS 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 393 SER Chi-restraints excluded: chain A residue 402 GLU 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 197 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 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 B residue 451 SER Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 THR 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 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 171 THR 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 393 SER Chi-restraints excluded: chain D residue 402 GLU 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 197 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 236 LEU 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 E residue 451 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 65 ILE 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 197 CYS 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 Chi-restraints excluded: chain F residue 402 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 192 optimal weight: 1.9990 chunk 280 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 158 optimal weight: 0.0030 chunk 254 optimal weight: 5.9990 chunk 273 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.092858 restraints weight = 40067.745| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.17 r_work: 0.3073 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23784 Z= 0.153 Angle : 0.548 7.847 32118 Z= 0.284 Chirality : 0.044 0.148 3492 Planarity : 0.004 0.044 4188 Dihedral : 4.904 54.744 3258 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.81 % Allowed : 10.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.16), residues: 2964 helix: -0.01 (0.13), residues: 1518 sheet: -1.61 (0.25), residues: 396 loop : -0.50 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 419 TYR 0.012 0.001 TYR F 382 PHE 0.020 0.002 PHE A 122 TRP 0.029 0.002 TRP B 281 HIS 0.010 0.001 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00362 (23784) covalent geometry : angle 0.54801 (32118) hydrogen bonds : bond 0.03391 ( 1098) hydrogen bonds : angle 4.36910 ( 3060) *********************** 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 429 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 334 time to evaluate : 1.011 Fit side-chains REVERT: A 163 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: A 372 TYR cc_start: 0.8578 (t80) cc_final: 0.8113 (t80) REVERT: A 402 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: A 411 MET cc_start: 0.8672 (tpp) cc_final: 0.8187 (tpt) REVERT: A 414 GLN cc_start: 0.8588 (tt0) cc_final: 0.8154 (tt0) REVERT: B 411 MET cc_start: 0.8645 (tpp) cc_final: 0.8254 (tpt) REVERT: B 414 GLN cc_start: 0.8692 (tt0) cc_final: 0.8371 (tt0) REVERT: C 63 PHE cc_start: 0.8072 (m-10) cc_final: 0.7636 (m-80) REVERT: C 139 ASN cc_start: 0.8677 (m-40) cc_final: 0.8352 (t0) REVERT: C 163 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8041 (m-30) REVERT: C 269 LYS cc_start: 0.8411 (ttmm) cc_final: 0.7869 (ptpt) REVERT: C 372 TYR cc_start: 0.8574 (t80) cc_final: 0.8254 (t80) REVERT: C 411 MET cc_start: 0.8635 (tpp) cc_final: 0.8335 (tpt) REVERT: C 465 MET cc_start: 0.8827 (mmm) cc_final: 0.8527 (mtm) REVERT: D 163 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8080 (m-30) REVERT: D 372 TYR cc_start: 0.8556 (t80) cc_final: 0.8093 (t80) REVERT: D 402 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: D 411 MET cc_start: 0.8723 (tpp) cc_final: 0.8158 (tpt) REVERT: E 411 MET cc_start: 0.8645 (tpp) cc_final: 0.8283 (tpt) REVERT: F 63 PHE cc_start: 0.8074 (m-10) cc_final: 0.7642 (m-80) REVERT: F 81 GLN cc_start: 0.8759 (mt0) cc_final: 0.8387 (mt0) REVERT: F 139 ASN cc_start: 0.8673 (m-40) cc_final: 0.8324 (t0) REVERT: F 163 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: F 282 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8020 (m110) REVERT: F 372 TYR cc_start: 0.8576 (t80) cc_final: 0.8254 (t80) REVERT: F 411 MET cc_start: 0.8647 (tpp) cc_final: 0.8328 (tpt) REVERT: F 465 MET cc_start: 0.8820 (mmm) cc_final: 0.8505 (mtm) outliers start: 95 outliers final: 72 residues processed: 382 average time/residue: 0.1478 time to fit residues: 92.5747 Evaluate side-chains 396 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 317 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 CYS 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 393 SER Chi-restraints excluded: chain A residue 402 GLU 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 197 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 VAL 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 65 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 ILE 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 272 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 458 GLU 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 171 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 197 CYS 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 393 SER Chi-restraints excluded: chain D residue 402 GLU 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 197 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 212 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 393 SER Chi-restraints excluded: chain E residue 451 SER Chi-restraints excluded: chain F residue 65 ILE 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 272 THR Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 458 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 42 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 259 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN F 205 GLN F 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.116939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.090972 restraints weight = 40068.279| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.17 r_work: 0.3044 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23784 Z= 0.210 Angle : 0.600 9.017 32118 Z= 0.309 Chirality : 0.046 0.151 3492 Planarity : 0.004 0.045 4188 Dihedral : 5.006 53.200 3258 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.73 % Allowed : 10.30 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.15), residues: 2964 helix: -0.07 (0.13), residues: 1518 sheet: -1.51 (0.25), residues: 396 loop : -0.58 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 419 TYR 0.015 0.001 TYR C 382 PHE 0.025 0.002 PHE C 122 TRP 0.032 0.002 TRP E 281 HIS 0.011 0.002 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00501 (23784) covalent geometry : angle 0.60022 (32118) hydrogen bonds : bond 0.03712 ( 1098) hydrogen bonds : angle 4.46617 ( 3060) *********************** 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 405 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 312 time to evaluate : 1.011 Fit side-chains REVERT: A 40 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8172 (mp10) REVERT: A 163 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: A 372 TYR cc_start: 0.8668 (t80) cc_final: 0.8192 (t80) REVERT: A 411 MET cc_start: 0.8653 (tpp) cc_final: 0.8212 (tpt) REVERT: B 73 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8284 (pm20) REVERT: B 411 MET cc_start: 0.8642 (tpp) cc_final: 0.8306 (tpt) REVERT: C 63 PHE cc_start: 0.8105 (m-10) cc_final: 0.7715 (m-80) REVERT: C 163 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: C 269 LYS cc_start: 0.8454 (ttmm) cc_final: 0.7888 (ptpt) REVERT: C 411 MET cc_start: 0.8642 (tpp) cc_final: 0.8372 (tpt) REVERT: C 465 MET cc_start: 0.8814 (mmm) cc_final: 0.8527 (mtm) REVERT: C 472 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7970 (p0) REVERT: D 40 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8153 (mp10) REVERT: D 163 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: D 372 TYR cc_start: 0.8649 (t80) cc_final: 0.8172 (t80) REVERT: D 411 MET cc_start: 0.8703 (tpp) cc_final: 0.8186 (tpt) REVERT: D 414 GLN cc_start: 0.8607 (tt0) cc_final: 0.8203 (tt0) REVERT: E 73 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: E 411 MET cc_start: 0.8611 (tpp) cc_final: 0.8338 (tpt) REVERT: F 63 PHE cc_start: 0.8119 (m-10) cc_final: 0.7730 (m-80) REVERT: F 81 GLN cc_start: 0.8796 (mt0) cc_final: 0.8406 (mt0) REVERT: F 163 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: F 282 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8067 (m110) REVERT: F 372 TYR cc_start: 0.8686 (t80) cc_final: 0.8483 (t80) REVERT: F 411 MET cc_start: 0.8626 (tpp) cc_final: 0.8323 (tpt) REVERT: F 465 MET cc_start: 0.8834 (mmm) cc_final: 0.8540 (mtm) outliers start: 93 outliers final: 76 residues processed: 361 average time/residue: 0.1497 time to fit residues: 87.4135 Evaluate side-chains 390 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 306 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 CYS 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 393 SER Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 249 VAL 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 65 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 ILE 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 208 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 458 GLU Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 197 CYS 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 281 TRP 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 393 SER Chi-restraints excluded: chain D residue 402 GLU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 458 GLU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 197 CYS Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 249 VAL 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 65 ILE 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 208 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Chi-restraints excluded: chain F residue 458 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 213 optimal weight: 0.9990 chunk 277 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 81 optimal weight: 40.0000 chunk 231 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN C 81 GLN C 297 GLN F 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.093018 restraints weight = 39921.051| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.18 r_work: 0.3094 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3764 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= 0.138 Angle : 0.544 8.118 32118 Z= 0.282 Chirality : 0.043 0.172 3492 Planarity : 0.004 0.044 4188 Dihedral : 4.809 51.966 3258 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.33 % Allowed : 10.78 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.16), residues: 2964 helix: 0.19 (0.13), residues: 1512 sheet: -1.37 (0.26), residues: 396 loop : -0.57 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 419 TYR 0.009 0.001 TYR D 382 PHE 0.017 0.002 PHE A 122 TRP 0.030 0.002 TRP B 281 HIS 0.012 0.002 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00327 (23784) covalent geometry : angle 0.54449 (32118) hydrogen bonds : bond 0.03270 ( 1098) hydrogen bonds : angle 4.27166 ( 3060) *********************** 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 416 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 333 time to evaluate : 1.027 Fit side-chains REVERT: A 163 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: A 372 TYR cc_start: 0.8586 (t80) cc_final: 0.8106 (t80) REVERT: A 402 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: A 411 MET cc_start: 0.8646 (tpp) cc_final: 0.8188 (tpt) REVERT: B 63 PHE cc_start: 0.8142 (m-10) cc_final: 0.7770 (m-80) REVERT: B 411 MET cc_start: 0.8614 (tpp) cc_final: 0.8329 (tpt) REVERT: C 63 PHE cc_start: 0.8050 (m-10) cc_final: 0.7666 (m-80) REVERT: C 139 ASN cc_start: 0.8667 (m-40) cc_final: 0.8308 (t0) REVERT: C 163 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: C 269 LYS cc_start: 0.8428 (ttmm) cc_final: 0.7896 (ptpt) REVERT: C 411 MET cc_start: 0.8570 (tpp) cc_final: 0.8329 (tpt) REVERT: D 163 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: D 372 TYR cc_start: 0.8574 (t80) cc_final: 0.8091 (t80) REVERT: D 402 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7809 (pt0) REVERT: D 411 MET cc_start: 0.8719 (tpp) cc_final: 0.8170 (tpt) REVERT: D 414 GLN cc_start: 0.8607 (tt0) cc_final: 0.8225 (tt0) REVERT: E 63 PHE cc_start: 0.8134 (m-10) cc_final: 0.7776 (m-80) REVERT: E 411 MET cc_start: 0.8622 (tpp) cc_final: 0.8320 (tpt) REVERT: E 414 GLN cc_start: 0.8608 (tt0) cc_final: 0.8356 (tt0) REVERT: F 63 PHE cc_start: 0.8042 (m-10) cc_final: 0.7658 (m-80) REVERT: F 81 GLN cc_start: 0.8743 (mt0) cc_final: 0.8402 (mt0) REVERT: F 163 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7803 (m-30) REVERT: F 282 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8096 (m110) REVERT: F 372 TYR cc_start: 0.8594 (t80) cc_final: 0.8293 (t80) REVERT: F 411 MET cc_start: 0.8605 (tpp) cc_final: 0.8271 (tpt) outliers start: 83 outliers final: 66 residues processed: 376 average time/residue: 0.1393 time to fit residues: 84.6937 Evaluate side-chains 380 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 CYS 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 300 THR Chi-restraints excluded: chain A residue 339 VAL 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 65 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 197 CYS 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 300 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 65 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 158 ILE 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 212 ILE 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 65 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 197 CYS 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 300 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 402 GLU 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 197 CYS 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 300 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 65 ILE Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 177 SER Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 144 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.092350 restraints weight = 40101.157| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.19 r_work: 0.3083 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23784 Z= 0.152 Angle : 0.558 7.793 32118 Z= 0.289 Chirality : 0.044 0.148 3492 Planarity : 0.004 0.045 4188 Dihedral : 4.758 48.969 3258 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.25 % Allowed : 10.74 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.16), residues: 2964 helix: 0.26 (0.13), residues: 1506 sheet: -1.33 (0.26), residues: 396 loop : -0.57 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 419 TYR 0.010 0.001 TYR A 382 PHE 0.019 0.002 PHE A 122 TRP 0.031 0.002 TRP B 281 HIS 0.012 0.002 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00362 (23784) covalent geometry : angle 0.55764 (32118) hydrogen bonds : bond 0.03343 ( 1098) hydrogen bonds : angle 4.25839 ( 3060) *********************** 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 398 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 317 time to evaluate : 0.759 Fit side-chains REVERT: A 163 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: A 372 TYR cc_start: 0.8627 (t80) cc_final: 0.8175 (t80) REVERT: A 402 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7847 (pt0) REVERT: A 411 MET cc_start: 0.8638 (tpp) cc_final: 0.8176 (tpt) REVERT: B 63 PHE cc_start: 0.8141 (m-10) cc_final: 0.7781 (m-80) REVERT: B 411 MET cc_start: 0.8627 (tpp) cc_final: 0.8312 (tpt) REVERT: B 414 GLN cc_start: 0.8612 (tt0) cc_final: 0.8381 (tt0) REVERT: C 63 PHE cc_start: 0.8053 (m-10) cc_final: 0.7691 (m-80) REVERT: C 163 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8095 (m-30) REVERT: C 269 LYS cc_start: 0.8468 (ttmm) cc_final: 0.7932 (ptpt) REVERT: C 411 MET cc_start: 0.8611 (tpp) cc_final: 0.8339 (tpt) REVERT: D 163 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: D 372 TYR cc_start: 0.8613 (t80) cc_final: 0.8163 (t80) REVERT: D 402 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7822 (pt0) REVERT: D 411 MET cc_start: 0.8733 (tpp) cc_final: 0.8190 (tpt) REVERT: D 414 GLN cc_start: 0.8601 (tt0) cc_final: 0.8305 (tt0) REVERT: E 63 PHE cc_start: 0.8120 (m-10) cc_final: 0.7773 (m-80) REVERT: E 411 MET cc_start: 0.8624 (tpp) cc_final: 0.8313 (tpt) REVERT: E 414 GLN cc_start: 0.8617 (tt0) cc_final: 0.8334 (tt0) REVERT: F 63 PHE cc_start: 0.8066 (m-10) cc_final: 0.7702 (m-80) REVERT: F 81 GLN cc_start: 0.8764 (mt0) cc_final: 0.8430 (mt0) REVERT: F 163 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: F 282 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8080 (m110) REVERT: F 372 TYR cc_start: 0.8636 (t80) cc_final: 0.8372 (t80) REVERT: F 411 MET cc_start: 0.8649 (tpp) cc_final: 0.8316 (tpt) outliers start: 81 outliers final: 71 residues processed: 363 average time/residue: 0.1431 time to fit residues: 84.9185 Evaluate side-chains 384 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 CYS 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 281 TRP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 339 VAL 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 65 ILE Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 300 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 65 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 ILE 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 272 THR Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 300 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 158 ILE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 197 CYS 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 300 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 402 GLU 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 197 CYS 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 300 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 65 ILE 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 272 THR Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 48 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 198 optimal weight: 30.0000 chunk 55 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 280 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 161 optimal weight: 0.8980 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 297 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 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 = 0.3603 r_free = 0.3603 target = 0.117517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.091648 restraints weight = 40054.468| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.17 r_work: 0.3057 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3785 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= 0.184 Angle : 0.586 8.477 32118 Z= 0.303 Chirality : 0.045 0.150 3492 Planarity : 0.004 0.046 4188 Dihedral : 4.798 46.415 3258 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.37 % Allowed : 10.82 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.16), residues: 2964 helix: 0.24 (0.13), residues: 1494 sheet: -1.30 (0.26), residues: 396 loop : -0.62 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 419 TYR 0.013 0.001 TYR D 382 PHE 0.022 0.002 PHE A 122 TRP 0.036 0.002 TRP B 281 HIS 0.012 0.002 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00440 (23784) covalent geometry : angle 0.58615 (32118) hydrogen bonds : bond 0.03519 ( 1098) hydrogen bonds : angle 4.31705 ( 3060) ********************** 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 394 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 310 time to evaluate : 0.933 Fit side-chains REVERT: A 163 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: A 372 TYR cc_start: 0.8678 (t80) cc_final: 0.8200 (t80) REVERT: A 402 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: A 411 MET cc_start: 0.8620 (tpp) cc_final: 0.8185 (tpt) REVERT: B 63 PHE cc_start: 0.8161 (m-10) cc_final: 0.7804 (m-80) REVERT: B 411 MET cc_start: 0.8630 (tpp) cc_final: 0.8319 (tpt) REVERT: B 414 GLN cc_start: 0.8607 (tt0) cc_final: 0.8354 (tt0) REVERT: C 63 PHE cc_start: 0.8071 (m-10) cc_final: 0.7709 (m-80) REVERT: C 163 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: C 269 LYS cc_start: 0.8457 (ttmm) cc_final: 0.7926 (ptpt) REVERT: C 411 MET cc_start: 0.8601 (tpp) cc_final: 0.8290 (tpt) REVERT: C 472 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7998 (p0) REVERT: D 163 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: D 372 TYR cc_start: 0.8658 (t80) cc_final: 0.8185 (t80) REVERT: D 402 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7836 (pt0) REVERT: D 411 MET cc_start: 0.8748 (tpp) cc_final: 0.8209 (tpt) REVERT: E 63 PHE cc_start: 0.8141 (m-10) cc_final: 0.7793 (m-80) REVERT: E 411 MET cc_start: 0.8627 (tpp) cc_final: 0.8329 (tpt) REVERT: E 414 GLN cc_start: 0.8619 (tt0) cc_final: 0.8318 (tt0) REVERT: F 63 PHE cc_start: 0.8078 (m-10) cc_final: 0.7712 (m-80) REVERT: F 81 GLN cc_start: 0.8767 (mt0) cc_final: 0.8398 (mt0) REVERT: F 163 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: F 282 ASN cc_start: 0.8346 (OUTLIER) cc_final: 0.8097 (m110) REVERT: F 372 TYR cc_start: 0.8674 (t80) cc_final: 0.8389 (t80) REVERT: F 411 MET cc_start: 0.8647 (tpp) cc_final: 0.8335 (tpt) outliers start: 84 outliers final: 72 residues processed: 360 average time/residue: 0.1436 time to fit residues: 84.2274 Evaluate side-chains 381 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 301 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 339 VAL 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 A residue 458 GLU 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 177 SER Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 300 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 65 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 472 ASN 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 171 THR Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 300 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 402 GLU 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 177 SER Chi-restraints excluded: chain E residue 197 CYS 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 300 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 65 ILE 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 177 SER Chi-restraints excluded: chain F residue 197 CYS Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 282 ASN Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 378 VAL Chi-restraints excluded: chain F residue 393 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 31 optimal weight: 0.0270 chunk 223 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 270 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 overall best weight: 3.5844 ------------------------------------------------------------------------------- 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 297 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 GLN 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 = 0.118147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.092255 restraints weight = 39788.365| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.17 r_work: 0.3072 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23784 Z= 0.154 Angle : 0.564 7.719 32118 Z= 0.292 Chirality : 0.044 0.148 3492 Planarity : 0.004 0.045 4188 Dihedral : 4.689 44.465 3258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.25 % Allowed : 11.06 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2964 helix: 0.42 (0.13), residues: 1476 sheet: -1.24 (0.26), residues: 396 loop : -0.52 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 419 TYR 0.010 0.001 TYR D 382 PHE 0.019 0.002 PHE A 122 TRP 0.037 0.002 TRP B 281 HIS 0.012 0.002 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00367 (23784) covalent geometry : angle 0.56424 (32118) hydrogen bonds : bond 0.03355 ( 1098) hydrogen bonds : angle 4.24784 ( 3060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5964.74 seconds wall clock time: 103 minutes 7.95 seconds (6187.95 seconds total)