Starting phenix.real_space_refine on Wed Mar 4 19:57:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0i_20999/03_2026/6v0i_20999.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0i_20999/03_2026/6v0i_20999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v0i_20999/03_2026/6v0i_20999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0i_20999/03_2026/6v0i_20999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v0i_20999/03_2026/6v0i_20999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0i_20999/03_2026/6v0i_20999.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 24 5.16 5 C 10128 2.51 5 N 2688 2.21 5 O 3102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15942 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2657 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 19, 'TRANS': 331} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 1.78, per 1000 atoms: 0.11 Number of scatterers: 15942 At special positions: 0 Unit cell: (113.97, 103.49, 119.21, 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 24 16.00 O 3102 8.00 N 2688 7.00 C 10128 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: 1.11 Conformation dependent library (CDL) restraints added in 539.0 milliseconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3804 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 30 sheets defined 18.5% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.207A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.674A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.223A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.282A pdb=" N LEU A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU A 443 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.207A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 248' Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.224A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 4.282A pdb=" N LEU B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'C' and resid 211 through 215 Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.206A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'C' and resid 274 through 278 removed outlier: 3.673A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU C 334 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.225A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.281A pdb=" N LEU C 386 " --> pdb=" O GLY C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU C 444 " --> pdb=" O GLN C 440 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 243 through 248 removed outlier: 4.206A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 248' Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.674A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU D 334 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.224A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 386 removed outlier: 4.281A pdb=" N LEU D 386 " --> pdb=" O GLY D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 438 through 446 removed outlier: 4.242A pdb=" N GLU D 443 " --> pdb=" O PRO D 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU D 444 " --> pdb=" O GLN D 440 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 243 through 248 removed outlier: 4.206A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 248' Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.674A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU E 334 " --> pdb=" O SER E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.223A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 4.283A pdb=" N LEU E 386 " --> pdb=" O GLY E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 389 No H-bonds generated for 'chain 'E' and resid 387 through 389' Processing helix chain 'E' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU E 444 " --> pdb=" O GLN E 440 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 243 through 248 removed outlier: 4.205A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 243 through 248' Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.674A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 removed outlier: 3.551A pdb=" N LEU F 334 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.224A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 386 removed outlier: 4.281A pdb=" N LEU F 386 " --> pdb=" O GLY F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 389 No H-bonds generated for 'chain 'F' and resid 387 through 389' Processing helix chain 'F' and resid 438 through 446 removed outlier: 4.241A pdb=" N GLU F 443 " --> pdb=" O PRO F 439 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU F 444 " --> pdb=" O GLN F 440 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 500 through 506 Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.165A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.182A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 449 through 453 removed outlier: 3.609A pdb=" N ILE A 481 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL A 421 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA A 436 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 495 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 458 through 460 Processing sheet with id=AA7, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.166A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 228 through 229 Processing sheet with id=AA9, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.183A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 449 through 453 removed outlier: 3.610A pdb=" N ILE B 481 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL B 421 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA B 436 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 495 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 458 through 460 Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.165A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AB5, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.183A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 449 through 453 removed outlier: 3.609A pdb=" N ILE C 481 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL C 421 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA C 436 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 495 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 458 through 460 Processing sheet with id=AB8, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.165A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 228 through 229 Processing sheet with id=AC1, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.182A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 449 through 453 removed outlier: 3.610A pdb=" N ILE D 481 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL D 421 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA D 436 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 495 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AC4, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.166A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 228 through 229 Processing sheet with id=AC6, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.183A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 449 through 453 removed outlier: 3.610A pdb=" N ILE E 481 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL E 421 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA E 436 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR E 495 " --> pdb=" O THR E 396 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 458 through 460 Processing sheet with id=AC9, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.166A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.183A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 449 through 453 removed outlier: 3.610A pdb=" N ILE F 481 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL F 421 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA F 436 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR F 495 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 458 through 460 564 hydrogen bonds defined for protein. 1386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4969 1.34 - 1.45: 1890 1.45 - 1.57: 9305 1.57 - 1.68: 0 1.68 - 1.80: 48 Bond restraints: 16212 Sorted by residual: bond pdb=" CB VAL C 307 " pdb=" CG1 VAL C 307 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.55e+00 bond pdb=" CB VAL B 307 " pdb=" CG1 VAL B 307 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.54e+00 bond pdb=" CB VAL D 307 " pdb=" CG1 VAL D 307 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.52e+00 bond pdb=" CB VAL F 307 " pdb=" CG1 VAL F 307 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.49e+00 bond pdb=" CB VAL A 307 " pdb=" CG1 VAL A 307 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.45e+00 ... (remaining 16207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 20295 2.01 - 4.01: 1400 4.01 - 6.02: 207 6.02 - 8.03: 64 8.03 - 10.03: 30 Bond angle restraints: 21996 Sorted by residual: angle pdb=" N SER B 472 " pdb=" CA SER B 472 " pdb=" C SER B 472 " ideal model delta sigma weight residual 109.24 103.07 6.17 1.51e+00 4.39e-01 1.67e+01 angle pdb=" N SER D 472 " pdb=" CA SER D 472 " pdb=" C SER D 472 " ideal model delta sigma weight residual 109.24 103.09 6.15 1.51e+00 4.39e-01 1.66e+01 angle pdb=" N SER A 472 " pdb=" CA SER A 472 " pdb=" C SER A 472 " ideal model delta sigma weight residual 109.24 103.09 6.15 1.51e+00 4.39e-01 1.66e+01 angle pdb=" N SER E 472 " pdb=" CA SER E 472 " pdb=" C SER E 472 " ideal model delta sigma weight residual 109.24 103.12 6.12 1.51e+00 4.39e-01 1.64e+01 angle pdb=" N SER F 472 " pdb=" CA SER F 472 " pdb=" C SER F 472 " ideal model delta sigma weight residual 109.24 103.13 6.11 1.51e+00 4.39e-01 1.64e+01 ... (remaining 21991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 9299 15.73 - 31.47: 421 31.47 - 47.20: 96 47.20 - 62.94: 12 62.94 - 78.67: 24 Dihedral angle restraints: 9852 sinusoidal: 3900 harmonic: 5952 Sorted by residual: dihedral pdb=" CA LEU B 411 " pdb=" C LEU B 411 " pdb=" N ILE B 412 " pdb=" CA ILE B 412 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU D 411 " pdb=" C LEU D 411 " pdb=" N ILE D 412 " pdb=" CA ILE D 412 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU C 411 " pdb=" C LEU C 411 " pdb=" N ILE C 412 " pdb=" CA ILE C 412 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1701 0.062 - 0.124: 654 0.124 - 0.186: 185 0.186 - 0.248: 34 0.248 - 0.310: 12 Chirality restraints: 2586 Sorted by residual: chirality pdb=" CA ASN B 338 " pdb=" N ASN B 338 " pdb=" C ASN B 338 " pdb=" CB ASN B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ASN D 338 " pdb=" N ASN D 338 " pdb=" C ASN D 338 " pdb=" CB ASN D 338 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA ASN A 338 " pdb=" N ASN A 338 " pdb=" C ASN A 338 " pdb=" CB ASN A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 2583 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 336 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C ARG F 336 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG F 336 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 337 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 336 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C ARG D 336 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG D 336 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 337 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 336 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C ARG A 336 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 336 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 337 " -0.017 2.00e-02 2.50e+03 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3555 2.80 - 3.32: 13294 3.32 - 3.85: 24404 3.85 - 4.37: 28003 4.37 - 4.90: 50216 Nonbonded interactions: 119472 Sorted by model distance: nonbonded pdb=" O SER B 330 " pdb=" OG1 THR B 333 " model vdw 2.274 3.040 nonbonded pdb=" O SER F 330 " pdb=" OG1 THR F 333 " model vdw 2.274 3.040 nonbonded pdb=" O SER C 330 " pdb=" OG1 THR C 333 " model vdw 2.274 3.040 nonbonded pdb=" O SER A 330 " pdb=" OG1 THR A 333 " model vdw 2.274 3.040 nonbonded pdb=" O SER D 330 " pdb=" OG1 THR D 333 " model vdw 2.274 3.040 ... (remaining 119467 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: 0.05 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.900 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16212 Z= 0.315 Angle : 1.179 10.034 21996 Z= 0.651 Chirality : 0.073 0.310 2586 Planarity : 0.009 0.056 2856 Dihedral : 10.964 78.672 6048 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -2.32 (0.16), residues: 2094 helix: -1.53 (0.33), residues: 234 sheet: -1.17 (0.20), residues: 612 loop : -1.77 (0.14), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 336 TYR 0.012 0.003 TYR C 498 PHE 0.039 0.005 PHE C 221 TRP 0.010 0.004 TRP F 476 HIS 0.008 0.003 HIS A 441 Details of bonding type rmsd covalent geometry : bond 0.00713 (16212) covalent geometry : angle 1.17881 (21996) hydrogen bonds : bond 0.15563 ( 564) hydrogen bonds : angle 8.55324 ( 1386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 TYR cc_start: 0.8690 (t80) cc_final: 0.8476 (t80) REVERT: A 396 THR cc_start: 0.8572 (m) cc_final: 0.8279 (p) REVERT: B 166 GLN cc_start: 0.8061 (mt0) cc_final: 0.7432 (mt0) REVERT: B 240 LEU cc_start: 0.7614 (tt) cc_final: 0.7345 (tp) REVERT: B 267 THR cc_start: 0.8822 (t) cc_final: 0.8297 (t) REVERT: B 453 VAL cc_start: 0.9438 (t) cc_final: 0.9153 (p) REVERT: C 240 LEU cc_start: 0.7727 (tt) cc_final: 0.7518 (tp) REVERT: C 324 GLU cc_start: 0.8122 (pt0) cc_final: 0.7879 (pt0) REVERT: C 482 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7607 (ttt180) REVERT: D 396 THR cc_start: 0.8586 (m) cc_final: 0.8273 (p) REVERT: E 166 GLN cc_start: 0.8063 (mt0) cc_final: 0.7426 (mt0) REVERT: E 240 LEU cc_start: 0.7619 (tt) cc_final: 0.7376 (tp) REVERT: E 267 THR cc_start: 0.8806 (t) cc_final: 0.8232 (t) REVERT: E 453 VAL cc_start: 0.9440 (t) cc_final: 0.9154 (p) REVERT: F 240 LEU cc_start: 0.7746 (tt) cc_final: 0.7544 (tp) REVERT: F 324 GLU cc_start: 0.8101 (pt0) cc_final: 0.7850 (pt0) REVERT: F 363 THR cc_start: 0.7519 (m) cc_final: 0.7250 (m) REVERT: F 401 GLU cc_start: 0.7983 (tt0) cc_final: 0.7633 (tt0) REVERT: F 403 TYR cc_start: 0.9341 (m-80) cc_final: 0.8890 (m-80) REVERT: F 482 ARG cc_start: 0.7864 (ttt-90) cc_final: 0.7615 (ttt180) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.1588 time to fit residues: 100.7708 Evaluate side-chains 236 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN A 409 GLN A 440 GLN B 164 HIS B 316 ASN B 345 ASN B 354 ASN B 454 ASN C 164 HIS C 316 ASN C 345 ASN ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 ASN D 345 ASN D 409 GLN D 440 GLN E 164 HIS E 316 ASN E 345 ASN E 354 ASN E 454 ASN F 164 HIS F 166 GLN F 316 ASN F 345 ASN ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.121849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.094368 restraints weight = 22592.123| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.55 r_work: 0.2859 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16212 Z= 0.149 Angle : 0.667 7.288 21996 Z= 0.347 Chirality : 0.048 0.155 2586 Planarity : 0.005 0.047 2856 Dihedral : 5.269 21.594 2226 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.84 % Allowed : 10.47 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.62 (0.16), residues: 2094 helix: -2.14 (0.27), residues: 204 sheet: -0.31 (0.19), residues: 672 loop : -1.33 (0.15), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 279 TYR 0.011 0.001 TYR C 403 PHE 0.018 0.002 PHE E 364 TRP 0.005 0.001 TRP D 222 HIS 0.010 0.002 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00341 (16212) covalent geometry : angle 0.66733 (21996) hydrogen bonds : bond 0.04846 ( 564) hydrogen bonds : angle 7.16329 ( 1386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ASN cc_start: 0.8529 (m-40) cc_final: 0.8297 (p0) REVERT: A 240 LEU cc_start: 0.7972 (tt) cc_final: 0.7505 (tp) REVERT: A 273 ASP cc_start: 0.8680 (t0) cc_final: 0.8466 (t0) REVERT: A 396 THR cc_start: 0.8648 (m) cc_final: 0.8382 (p) REVERT: A 491 MET cc_start: 0.8296 (tpt) cc_final: 0.7901 (tpt) REVERT: B 224 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8391 (m) REVERT: B 342 GLU cc_start: 0.8473 (pm20) cc_final: 0.8070 (pm20) REVERT: C 444 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8537 (tp) REVERT: C 468 PHE cc_start: 0.7791 (t80) cc_final: 0.7496 (t80) REVERT: C 482 ARG cc_start: 0.8711 (ttt-90) cc_final: 0.8480 (ttt180) REVERT: D 396 THR cc_start: 0.8658 (m) cc_final: 0.8392 (p) REVERT: D 491 MET cc_start: 0.8247 (tpt) cc_final: 0.7833 (tpt) REVERT: E 224 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8416 (m) REVERT: E 267 THR cc_start: 0.9080 (t) cc_final: 0.8863 (m) REVERT: E 342 GLU cc_start: 0.8483 (pm20) cc_final: 0.8084 (pm20) REVERT: F 166 GLN cc_start: 0.8465 (mt0) cc_final: 0.8210 (mt0) REVERT: F 444 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8529 (tp) outliers start: 50 outliers final: 29 residues processed: 296 average time/residue: 0.1186 time to fit residues: 53.1535 Evaluate side-chains 239 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 409 GLN Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 131 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 46 optimal weight: 0.0170 chunk 12 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 chunk 57 optimal weight: 0.0470 chunk 82 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 122 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS B 441 HIS ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.097353 restraints weight = 22788.043| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.57 r_work: 0.2933 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16212 Z= 0.103 Angle : 0.601 8.449 21996 Z= 0.308 Chirality : 0.046 0.144 2586 Planarity : 0.004 0.041 2856 Dihedral : 4.805 18.782 2226 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.59 % Allowed : 12.74 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.52 (0.16), residues: 2094 helix: -1.95 (0.28), residues: 240 sheet: -0.07 (0.20), residues: 672 loop : -1.38 (0.15), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 442 TYR 0.008 0.001 TYR C 403 PHE 0.011 0.001 PHE D 451 TRP 0.005 0.001 TRP E 222 HIS 0.008 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00219 (16212) covalent geometry : angle 0.60102 (21996) hydrogen bonds : bond 0.03836 ( 564) hydrogen bonds : angle 6.77569 ( 1386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.7852 (tt) cc_final: 0.7495 (tp) REVERT: A 273 ASP cc_start: 0.8671 (t0) cc_final: 0.8461 (t0) REVERT: A 396 THR cc_start: 0.8655 (m) cc_final: 0.8397 (p) REVERT: A 491 MET cc_start: 0.8354 (tpt) cc_final: 0.7992 (tpt) REVERT: B 224 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8476 (m) REVERT: C 325 MET cc_start: 0.8773 (mtm) cc_final: 0.8543 (mtm) REVERT: C 444 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8503 (tp) REVERT: D 240 LEU cc_start: 0.7848 (tt) cc_final: 0.7439 (tp) REVERT: D 491 MET cc_start: 0.8341 (tpt) cc_final: 0.7982 (tpt) REVERT: E 224 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8464 (m) REVERT: F 166 GLN cc_start: 0.8534 (mt0) cc_final: 0.8257 (mt0) REVERT: F 426 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9148 (tp) REVERT: F 444 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8407 (tp) outliers start: 28 outliers final: 18 residues processed: 238 average time/residue: 0.1153 time to fit residues: 41.7976 Evaluate side-chains 208 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 110 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 172 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 188 optimal weight: 0.0770 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN B 454 ASN C 454 ASN F 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.090636 restraints weight = 22720.261| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.60 r_work: 0.2834 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16212 Z= 0.156 Angle : 0.626 10.084 21996 Z= 0.322 Chirality : 0.047 0.154 2586 Planarity : 0.004 0.041 2856 Dihedral : 5.028 20.502 2226 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.01 % Allowed : 12.46 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.34 (0.17), residues: 2094 helix: -2.03 (0.28), residues: 240 sheet: 0.07 (0.20), residues: 672 loop : -1.22 (0.15), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 220 TYR 0.011 0.001 TYR C 403 PHE 0.020 0.002 PHE D 451 TRP 0.006 0.001 TRP D 222 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00368 (16212) covalent geometry : angle 0.62616 (21996) hydrogen bonds : bond 0.04072 ( 564) hydrogen bonds : angle 6.97697 ( 1386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.7830 (tt) cc_final: 0.7481 (tp) REVERT: A 273 ASP cc_start: 0.8745 (t0) cc_final: 0.8535 (t0) REVERT: A 396 THR cc_start: 0.8696 (m) cc_final: 0.8423 (p) REVERT: A 446 LYS cc_start: 0.6411 (mtmm) cc_final: 0.6126 (mmmt) REVERT: A 456 ARG cc_start: 0.7284 (mtm110) cc_final: 0.6929 (mmp80) REVERT: A 491 MET cc_start: 0.8386 (tpt) cc_final: 0.8059 (tpt) REVERT: B 166 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8353 (mm-40) REVERT: B 224 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8549 (m) REVERT: C 325 MET cc_start: 0.8893 (mtm) cc_final: 0.8636 (mtm) REVERT: D 240 LEU cc_start: 0.7883 (tt) cc_final: 0.7476 (tp) REVERT: D 482 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8338 (ptt90) REVERT: D 491 MET cc_start: 0.8467 (tpt) cc_final: 0.8143 (tpt) REVERT: E 166 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8362 (mm-40) REVERT: E 224 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8513 (m) REVERT: E 426 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9086 (tp) REVERT: F 166 GLN cc_start: 0.8309 (mt0) cc_final: 0.7869 (mp10) REVERT: F 426 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9044 (tp) outliers start: 53 outliers final: 30 residues processed: 234 average time/residue: 0.1214 time to fit residues: 42.9228 Evaluate side-chains 210 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 482 ARG Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 160 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 174 optimal weight: 0.4980 chunk 195 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 125 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.092028 restraints weight = 22655.767| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.58 r_work: 0.2860 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16212 Z= 0.120 Angle : 0.585 10.441 21996 Z= 0.299 Chirality : 0.046 0.144 2586 Planarity : 0.004 0.039 2856 Dihedral : 4.809 20.081 2226 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.22 % Allowed : 13.88 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.25 (0.17), residues: 2094 helix: -1.87 (0.29), residues: 240 sheet: 0.09 (0.20), residues: 672 loop : -1.14 (0.15), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 279 TYR 0.009 0.001 TYR C 403 PHE 0.017 0.002 PHE D 468 TRP 0.006 0.001 TRP A 222 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00273 (16212) covalent geometry : angle 0.58505 (21996) hydrogen bonds : bond 0.03681 ( 564) hydrogen bonds : angle 6.76576 ( 1386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.551 Fit side-chains REVERT: A 240 LEU cc_start: 0.7736 (tt) cc_final: 0.7419 (tp) REVERT: A 273 ASP cc_start: 0.8686 (t0) cc_final: 0.8478 (t0) REVERT: A 396 THR cc_start: 0.8706 (m) cc_final: 0.8387 (p) REVERT: A 446 LYS cc_start: 0.6373 (mtmm) cc_final: 0.6078 (mmmt) REVERT: A 491 MET cc_start: 0.8510 (tpt) cc_final: 0.8219 (tpt) REVERT: B 224 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8486 (m) REVERT: C 337 GLU cc_start: 0.7918 (tp30) cc_final: 0.7647 (tp30) REVERT: C 444 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8741 (tp) REVERT: D 240 LEU cc_start: 0.7803 (tt) cc_final: 0.7444 (tp) REVERT: D 456 ARG cc_start: 0.7172 (mtm110) cc_final: 0.6876 (mmp80) REVERT: D 491 MET cc_start: 0.8569 (tpt) cc_final: 0.8317 (tpt) REVERT: E 209 ARG cc_start: 0.7127 (mmt180) cc_final: 0.6419 (mmt180) REVERT: E 224 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8509 (m) REVERT: E 411 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8829 (tp) REVERT: E 454 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7501 (m-40) REVERT: F 166 GLN cc_start: 0.8406 (mt0) cc_final: 0.8022 (mp10) REVERT: F 426 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8966 (tp) outliers start: 39 outliers final: 26 residues processed: 231 average time/residue: 0.1266 time to fit residues: 43.6514 Evaluate side-chains 211 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 454 ASN Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 200 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 154 optimal weight: 0.0970 chunk 48 optimal weight: 4.9990 chunk 137 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN E 454 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092484 restraints weight = 22543.711| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.57 r_work: 0.2852 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16212 Z= 0.119 Angle : 0.589 11.462 21996 Z= 0.299 Chirality : 0.046 0.145 2586 Planarity : 0.004 0.046 2856 Dihedral : 4.737 19.797 2226 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.13 % Allowed : 12.86 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.21 (0.17), residues: 2094 helix: -1.82 (0.29), residues: 240 sheet: 0.06 (0.20), residues: 672 loop : -1.08 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 220 TYR 0.009 0.001 TYR C 403 PHE 0.014 0.002 PHE A 451 TRP 0.006 0.001 TRP F 222 HIS 0.007 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00273 (16212) covalent geometry : angle 0.58904 (21996) hydrogen bonds : bond 0.03573 ( 564) hydrogen bonds : angle 6.71579 ( 1386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.379 Fit side-chains REVERT: A 240 LEU cc_start: 0.7724 (tt) cc_final: 0.7428 (tp) REVERT: A 396 THR cc_start: 0.8683 (m) cc_final: 0.8386 (p) REVERT: A 446 LYS cc_start: 0.6445 (mtmm) cc_final: 0.6137 (mmmt) REVERT: A 491 MET cc_start: 0.8572 (tpt) cc_final: 0.8313 (tpt) REVERT: B 224 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8548 (m) REVERT: C 337 GLU cc_start: 0.7923 (tp30) cc_final: 0.7660 (tp30) REVERT: C 350 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5971 (pp) REVERT: D 240 LEU cc_start: 0.7783 (tt) cc_final: 0.7444 (tp) REVERT: D 456 ARG cc_start: 0.7280 (mtm110) cc_final: 0.6888 (mmp80) REVERT: D 491 MET cc_start: 0.8586 (tpt) cc_final: 0.8300 (tpt) REVERT: D 501 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8909 (tp) REVERT: E 166 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8496 (mm-40) REVERT: E 209 ARG cc_start: 0.7076 (mmt180) cc_final: 0.6378 (mmt180) REVERT: E 224 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8519 (m) REVERT: E 365 GLU cc_start: 0.8537 (tp30) cc_final: 0.8085 (tt0) REVERT: E 456 ARG cc_start: 0.5899 (mmt180) cc_final: 0.5527 (mmp-170) REVERT: F 166 GLN cc_start: 0.8407 (mt0) cc_final: 0.8043 (mp10) REVERT: F 325 MET cc_start: 0.8900 (mtm) cc_final: 0.8657 (mtm) REVERT: F 337 GLU cc_start: 0.7958 (tp30) cc_final: 0.7703 (tp30) REVERT: F 350 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5949 (pp) REVERT: F 426 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8867 (tp) REVERT: F 444 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8795 (tp) REVERT: F 506 GLU cc_start: 0.7958 (tp30) cc_final: 0.7567 (tp30) outliers start: 55 outliers final: 39 residues processed: 237 average time/residue: 0.1204 time to fit residues: 43.3021 Evaluate side-chains 222 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 206 optimal weight: 6.9990 chunk 134 optimal weight: 0.0000 chunk 114 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.092255 restraints weight = 22519.732| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.59 r_work: 0.2850 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16212 Z= 0.126 Angle : 0.593 10.863 21996 Z= 0.302 Chirality : 0.046 0.146 2586 Planarity : 0.004 0.041 2856 Dihedral : 4.743 19.809 2226 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.24 % Allowed : 12.86 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.18 (0.17), residues: 2094 helix: -1.82 (0.29), residues: 240 sheet: 0.04 (0.20), residues: 672 loop : -1.03 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 220 TYR 0.008 0.001 TYR C 403 PHE 0.013 0.002 PHE A 451 TRP 0.006 0.001 TRP F 222 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00294 (16212) covalent geometry : angle 0.59288 (21996) hydrogen bonds : bond 0.03606 ( 564) hydrogen bonds : angle 6.75945 ( 1386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.643 Fit side-chains REVERT: A 199 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8396 (mp10) REVERT: A 240 LEU cc_start: 0.7716 (tt) cc_final: 0.7429 (tp) REVERT: A 396 THR cc_start: 0.8704 (m) cc_final: 0.8409 (p) REVERT: A 446 LYS cc_start: 0.6526 (mtmm) cc_final: 0.6204 (mmmt) REVERT: A 491 MET cc_start: 0.8511 (tpt) cc_final: 0.8200 (tpt) REVERT: B 224 VAL cc_start: 0.8737 (OUTLIER) cc_final: 0.8465 (m) REVERT: B 365 GLU cc_start: 0.8503 (tp30) cc_final: 0.8088 (tt0) REVERT: B 446 LYS cc_start: 0.7400 (mmmt) cc_final: 0.6627 (mtmm) REVERT: B 456 ARG cc_start: 0.5964 (mmt180) cc_final: 0.5576 (mmp-170) REVERT: C 337 GLU cc_start: 0.7923 (tp30) cc_final: 0.7666 (tp30) REVERT: C 350 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6011 (pp) REVERT: D 199 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8492 (mp10) REVERT: D 240 LEU cc_start: 0.7822 (tt) cc_final: 0.7492 (tp) REVERT: D 456 ARG cc_start: 0.7316 (mtm110) cc_final: 0.6721 (mmm160) REVERT: D 491 MET cc_start: 0.8533 (tpt) cc_final: 0.8227 (tpt) REVERT: E 209 ARG cc_start: 0.7070 (mmt180) cc_final: 0.6357 (mmt180) REVERT: E 224 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8519 (m) REVERT: E 365 GLU cc_start: 0.8509 (tp30) cc_final: 0.8096 (tt0) REVERT: E 456 ARG cc_start: 0.5965 (mmt180) cc_final: 0.5567 (mmp-170) REVERT: F 166 GLN cc_start: 0.8397 (mt0) cc_final: 0.8031 (mp10) REVERT: F 325 MET cc_start: 0.8934 (mtm) cc_final: 0.8713 (mtm) REVERT: F 337 GLU cc_start: 0.7961 (tp30) cc_final: 0.7701 (tp30) REVERT: F 350 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5975 (pp) REVERT: F 426 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8887 (tp) REVERT: F 444 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8784 (tp) REVERT: F 501 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8867 (mt) outliers start: 57 outliers final: 40 residues processed: 232 average time/residue: 0.1220 time to fit residues: 42.2593 Evaluate side-chains 221 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 501 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 117 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 209 optimal weight: 0.4980 chunk 159 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 182 optimal weight: 0.0770 chunk 147 optimal weight: 10.0000 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.092850 restraints weight = 22671.168| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.58 r_work: 0.2860 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16212 Z= 0.115 Angle : 0.586 9.781 21996 Z= 0.300 Chirality : 0.046 0.141 2586 Planarity : 0.004 0.040 2856 Dihedral : 4.628 19.479 2226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.19 % Allowed : 13.20 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.17 (0.17), residues: 2094 helix: -1.82 (0.29), residues: 240 sheet: 0.04 (0.20), residues: 672 loop : -1.02 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 220 TYR 0.008 0.001 TYR C 403 PHE 0.017 0.001 PHE E 468 TRP 0.006 0.001 TRP A 222 HIS 0.007 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00266 (16212) covalent geometry : angle 0.58621 (21996) hydrogen bonds : bond 0.03440 ( 564) hydrogen bonds : angle 6.72900 ( 1386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 196 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 199 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8544 (mp10) REVERT: A 240 LEU cc_start: 0.7656 (tt) cc_final: 0.7372 (tp) REVERT: A 258 GLU cc_start: 0.7330 (tp30) cc_final: 0.7096 (tp30) REVERT: A 396 THR cc_start: 0.8721 (m) cc_final: 0.8419 (p) REVERT: A 446 LYS cc_start: 0.6516 (mtmm) cc_final: 0.6180 (mmmt) REVERT: A 491 MET cc_start: 0.8505 (tpt) cc_final: 0.8233 (tpt) REVERT: A 501 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8940 (tp) REVERT: B 224 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8523 (m) REVERT: B 365 GLU cc_start: 0.8498 (tp30) cc_final: 0.8077 (tt0) REVERT: B 456 ARG cc_start: 0.5855 (mmt180) cc_final: 0.5483 (mmp-170) REVERT: C 337 GLU cc_start: 0.7943 (tp30) cc_final: 0.7687 (tp30) REVERT: C 350 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6155 (pp) REVERT: D 199 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8489 (mp10) REVERT: D 240 LEU cc_start: 0.7771 (tt) cc_final: 0.7469 (tp) REVERT: D 456 ARG cc_start: 0.7360 (mtm110) cc_final: 0.6710 (mmm160) REVERT: D 491 MET cc_start: 0.8519 (tpt) cc_final: 0.8244 (tpt) REVERT: E 209 ARG cc_start: 0.6870 (mmt180) cc_final: 0.6310 (mmt180) REVERT: E 224 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8460 (m) REVERT: E 365 GLU cc_start: 0.8505 (tp30) cc_final: 0.8083 (tt0) REVERT: F 166 GLN cc_start: 0.8409 (mt0) cc_final: 0.8094 (mp10) REVERT: F 267 THR cc_start: 0.8926 (t) cc_final: 0.8184 (t) REVERT: F 337 GLU cc_start: 0.7959 (tp30) cc_final: 0.7705 (tp30) REVERT: F 350 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6103 (pp) REVERT: F 426 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8939 (tp) outliers start: 56 outliers final: 40 residues processed: 242 average time/residue: 0.1241 time to fit residues: 44.6768 Evaluate side-chains 230 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 426 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 0.2980 chunk 173 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.091833 restraints weight = 22514.371| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.50 r_work: 0.2809 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16212 Z= 0.138 Angle : 0.618 9.691 21996 Z= 0.315 Chirality : 0.046 0.150 2586 Planarity : 0.004 0.041 2856 Dihedral : 4.735 20.710 2226 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.19 % Allowed : 13.88 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.20 (0.17), residues: 2094 helix: -1.90 (0.29), residues: 240 sheet: 0.06 (0.20), residues: 666 loop : -1.04 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 220 TYR 0.007 0.001 TYR C 403 PHE 0.018 0.002 PHE D 468 TRP 0.006 0.001 TRP F 222 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00326 (16212) covalent geometry : angle 0.61840 (21996) hydrogen bonds : bond 0.03616 ( 564) hydrogen bonds : angle 6.86921 ( 1386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 199 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8567 (mp10) REVERT: A 240 LEU cc_start: 0.7655 (tt) cc_final: 0.7350 (tp) REVERT: A 396 THR cc_start: 0.8794 (m) cc_final: 0.8490 (p) REVERT: A 491 MET cc_start: 0.8541 (tpt) cc_final: 0.8211 (tpt) REVERT: B 209 ARG cc_start: 0.7015 (mmt180) cc_final: 0.6776 (mmt180) REVERT: B 456 ARG cc_start: 0.5963 (mmt180) cc_final: 0.5535 (mmp-170) REVERT: C 337 GLU cc_start: 0.7952 (tp30) cc_final: 0.7734 (tp30) REVERT: C 350 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6207 (pp) REVERT: D 199 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8510 (mp10) REVERT: D 240 LEU cc_start: 0.7696 (tt) cc_final: 0.7359 (tp) REVERT: D 456 ARG cc_start: 0.7393 (mtm110) cc_final: 0.6697 (mmm160) REVERT: D 491 MET cc_start: 0.8566 (tpt) cc_final: 0.8253 (tpt) REVERT: E 209 ARG cc_start: 0.6907 (mmt180) cc_final: 0.6293 (mmt180) REVERT: E 224 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8405 (m) REVERT: E 365 GLU cc_start: 0.8516 (tp30) cc_final: 0.8089 (tt0) REVERT: F 166 GLN cc_start: 0.8351 (mt0) cc_final: 0.8045 (mp10) REVERT: F 267 THR cc_start: 0.8931 (t) cc_final: 0.8187 (t) REVERT: F 301 MET cc_start: 0.9245 (mmm) cc_final: 0.9007 (mmm) REVERT: F 337 GLU cc_start: 0.8062 (tp30) cc_final: 0.7828 (tp30) REVERT: F 350 LEU cc_start: 0.6377 (OUTLIER) cc_final: 0.6146 (pp) REVERT: F 426 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8904 (tp) outliers start: 56 outliers final: 44 residues processed: 235 average time/residue: 0.1246 time to fit residues: 43.6013 Evaluate side-chains 223 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 491 MET Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 131 optimal weight: 3.9990 chunk 129 optimal weight: 0.0980 chunk 169 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 183 optimal weight: 0.0980 chunk 142 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 HIS ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.091231 restraints weight = 22590.477| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.52 r_work: 0.2859 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16212 Z= 0.124 Angle : 0.606 8.958 21996 Z= 0.309 Chirality : 0.046 0.145 2586 Planarity : 0.004 0.041 2856 Dihedral : 4.647 20.462 2226 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.84 % Allowed : 14.22 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.18 (0.17), residues: 2094 helix: -1.86 (0.29), residues: 240 sheet: 0.07 (0.20), residues: 666 loop : -1.04 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 456 TYR 0.008 0.001 TYR C 403 PHE 0.020 0.001 PHE B 468 TRP 0.006 0.001 TRP F 222 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00291 (16212) covalent geometry : angle 0.60645 (21996) hydrogen bonds : bond 0.03464 ( 564) hydrogen bonds : angle 6.85739 ( 1386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 180 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 240 LEU cc_start: 0.7663 (tt) cc_final: 0.7393 (tp) REVERT: A 491 MET cc_start: 0.8531 (tpt) cc_final: 0.8248 (tpt) REVERT: B 209 ARG cc_start: 0.7066 (mmt180) cc_final: 0.6673 (mmt180) REVERT: B 365 GLU cc_start: 0.8463 (tp30) cc_final: 0.8094 (tt0) REVERT: C 337 GLU cc_start: 0.8100 (tp30) cc_final: 0.7889 (tp30) REVERT: D 199 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8492 (mp10) REVERT: D 240 LEU cc_start: 0.7696 (tt) cc_final: 0.7388 (tp) REVERT: D 456 ARG cc_start: 0.7471 (mtm110) cc_final: 0.6523 (tpt170) REVERT: D 491 MET cc_start: 0.8550 (tpt) cc_final: 0.8248 (tpt) REVERT: E 209 ARG cc_start: 0.6915 (mmt180) cc_final: 0.6295 (mmt180) REVERT: E 224 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8454 (m) REVERT: E 365 GLU cc_start: 0.8493 (tp30) cc_final: 0.8117 (tt0) REVERT: F 166 GLN cc_start: 0.8326 (mt0) cc_final: 0.8047 (mp10) REVERT: F 267 THR cc_start: 0.8935 (t) cc_final: 0.8219 (t) REVERT: F 337 GLU cc_start: 0.8095 (tp30) cc_final: 0.7886 (tp30) REVERT: F 350 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6193 (pp) REVERT: F 426 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8886 (tp) outliers start: 50 outliers final: 45 residues processed: 224 average time/residue: 0.1286 time to fit residues: 42.9095 Evaluate side-chains 216 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 449 SER Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 350 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 444 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.088682 restraints weight = 22466.857| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.54 r_work: 0.2786 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16212 Z= 0.194 Angle : 0.663 9.270 21996 Z= 0.340 Chirality : 0.048 0.164 2586 Planarity : 0.004 0.042 2856 Dihedral : 5.142 23.972 2226 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.90 % Allowed : 14.28 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.19 (0.17), residues: 2094 helix: -2.00 (0.29), residues: 240 sheet: 0.14 (0.21), residues: 636 loop : -1.04 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 220 TYR 0.008 0.001 TYR D 271 PHE 0.029 0.002 PHE F 468 TRP 0.007 0.002 TRP A 222 HIS 0.006 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00465 (16212) covalent geometry : angle 0.66319 (21996) hydrogen bonds : bond 0.04136 ( 564) hydrogen bonds : angle 7.11314 ( 1386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.58 seconds wall clock time: 59 minutes 4.71 seconds (3544.71 seconds total)