Starting phenix.real_space_refine on Thu Dec 26 03:58:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ey6_31321/12_2024/7ey6_31321.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ey6_31321/12_2024/7ey6_31321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ey6_31321/12_2024/7ey6_31321.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ey6_31321/12_2024/7ey6_31321.map" model { file = "/net/cci-nas-00/data/ceres_data/7ey6_31321/12_2024/7ey6_31321.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ey6_31321/12_2024/7ey6_31321.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.013 sd= 2.048 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 204 5.16 5 C 27756 2.51 5 N 7428 2.21 5 O 8640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 44028 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3669 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 11.82, per 1000 atoms: 0.27 Number of scatterers: 44028 At special positions: 0 Unit cell: (189.23, 189.23, 118.11, 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 204 16.00 O 8640 8.00 N 7428 7.00 C 27756 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: 10.80 Conformation dependent library (CDL) restraints added in 6.5 seconds 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10512 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 60 sheets defined 51.8% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA A 9 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 10 " --> pdb=" O GLY A 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6 through 10' Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Proline residue: A 26 - end of helix Processing helix chain 'A' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE A 43 " --> pdb=" O PRO A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 43' Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 272' Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.599A pdb=" N LYS A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE A 474 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA B 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 10 " --> pdb=" O GLY B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 6 through 10' Processing helix chain 'B' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 26 - end of helix Processing helix chain 'B' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE B 43 " --> pdb=" O PRO B 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 43' Processing helix chain 'B' and resid 60 through 78 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.520A pdb=" N GLN B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 4.018A pdb=" N GLU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 267 through 272' Processing helix chain 'B' and resid 272 through 295 removed outlier: 3.599A pdb=" N LYS B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Processing helix chain 'B' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 462 through 474 removed outlier: 4.161A pdb=" N ILE B 474 " --> pdb=" O ILE B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 10 " --> pdb=" O GLY C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 6 through 10' Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 26 - end of helix Processing helix chain 'C' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE C 43 " --> pdb=" O PRO C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 43' Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 removed outlier: 4.015A pdb=" N GLU C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 267 through 272' Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 Processing helix chain 'C' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 379 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'C' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE C 474 " --> pdb=" O ILE C 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA D 9 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU D 10 " --> pdb=" O GLY D 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 6 through 10' Processing helix chain 'D' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 26 - end of helix Processing helix chain 'D' and resid 40 through 43 removed outlier: 3.697A pdb=" N PHE D 43 " --> pdb=" O PRO D 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 43' Processing helix chain 'D' and resid 60 through 78 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.522A pdb=" N GLN D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 267 through 272' Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 357 Processing helix chain 'D' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 379 " --> pdb=" O ARG D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 396 removed outlier: 3.610A pdb=" N ILE D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 410 " --> pdb=" O LYS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'D' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE D 474 " --> pdb=" O ILE D 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA E 9 " --> pdb=" O THR E 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 10 " --> pdb=" O GLY E 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 6 through 10' Processing helix chain 'E' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 26 - end of helix Processing helix chain 'E' and resid 40 through 43 removed outlier: 3.695A pdb=" N PHE E 43 " --> pdb=" O PRO E 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 43' Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 140 Processing helix chain 'E' and resid 191 through 202 removed outlier: 3.520A pdb=" N GLN E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 272 removed outlier: 4.015A pdb=" N GLU E 271 " --> pdb=" O SER E 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 267 through 272' Processing helix chain 'E' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 357 Processing helix chain 'E' and resid 372 through 385 removed outlier: 4.085A pdb=" N TYR E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER E 379 " --> pdb=" O ARG E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE E 391 " --> pdb=" O GLY E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 412 removed outlier: 3.524A pdb=" N GLN E 409 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA E 410 " --> pdb=" O LYS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 451 Processing helix chain 'E' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE E 474 " --> pdb=" O ILE E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA F 9 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 10 " --> pdb=" O GLY F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 6 through 10' Processing helix chain 'F' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 26 - end of helix Processing helix chain 'F' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE F 43 " --> pdb=" O PRO F 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 43' Processing helix chain 'F' and resid 60 through 78 Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'F' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 4.017A pdb=" N GLU F 271 " --> pdb=" O SER F 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 267 through 272' Processing helix chain 'F' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS F 295 " --> pdb=" O MET F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU F 311 " --> pdb=" O GLN F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 357 Processing helix chain 'F' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER F 379 " --> pdb=" O ARG F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 396 removed outlier: 3.608A pdb=" N ILE F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN F 409 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA F 410 " --> pdb=" O LYS F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 451 Processing helix chain 'F' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE F 474 " --> pdb=" O ILE F 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA G 9 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU G 10 " --> pdb=" O GLY G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP G 23 " --> pdb=" O ARG G 19 " (cutoff:3.500A) Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 40 through 43 removed outlier: 3.695A pdb=" N PHE G 43 " --> pdb=" O PRO G 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 43' Processing helix chain 'G' and resid 60 through 78 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 140 Processing helix chain 'G' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU G 271 " --> pdb=" O SER G 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 267 through 272' Processing helix chain 'G' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS G 295 " --> pdb=" O MET G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU G 311 " --> pdb=" O GLN G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 357 Processing helix chain 'G' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR G 376 " --> pdb=" O GLU G 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER G 379 " --> pdb=" O ARG G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE G 391 " --> pdb=" O GLY G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN G 409 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA G 410 " --> pdb=" O LYS G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 451 Processing helix chain 'G' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE G 474 " --> pdb=" O ILE G 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA H 9 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU H 10 " --> pdb=" O GLY H 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 6 through 10' Processing helix chain 'H' and resid 12 through 39 removed outlier: 3.648A pdb=" N ASP H 23 " --> pdb=" O ARG H 19 " (cutoff:3.500A) Proline residue: H 26 - end of helix Processing helix chain 'H' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE H 43 " --> pdb=" O PRO H 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 43' Processing helix chain 'H' and resid 60 through 78 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 140 Processing helix chain 'H' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 267 through 272' Processing helix chain 'H' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS H 295 " --> pdb=" O MET H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU H 311 " --> pdb=" O GLN H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 357 Processing helix chain 'H' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR H 376 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER H 379 " --> pdb=" O ARG H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 removed outlier: 3.610A pdb=" N ILE H 391 " --> pdb=" O GLY H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN H 409 " --> pdb=" O LEU H 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA H 410 " --> pdb=" O LYS H 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 451 Processing helix chain 'H' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE H 474 " --> pdb=" O ILE H 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 10 removed outlier: 3.852A pdb=" N ALA I 9 " --> pdb=" O THR I 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU I 10 " --> pdb=" O GLY I 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 6 through 10' Processing helix chain 'I' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) Proline residue: I 26 - end of helix Processing helix chain 'I' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE I 43 " --> pdb=" O PRO I 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 43' Processing helix chain 'I' and resid 60 through 78 Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 125 through 140 Processing helix chain 'I' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN I 201 " --> pdb=" O ALA I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU I 271 " --> pdb=" O SER I 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 267 through 272' Processing helix chain 'I' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS I 295 " --> pdb=" O MET I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU I 311 " --> pdb=" O GLN I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 357 Processing helix chain 'I' and resid 372 through 385 removed outlier: 4.085A pdb=" N TYR I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER I 379 " --> pdb=" O ARG I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE I 391 " --> pdb=" O GLY I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN I 409 " --> pdb=" O LEU I 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA I 410 " --> pdb=" O LYS I 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 440 through 451 Processing helix chain 'I' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE I 474 " --> pdb=" O ILE I 470 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA J 9 " --> pdb=" O THR J 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU J 10 " --> pdb=" O GLY J 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 6 through 10' Processing helix chain 'J' and resid 12 through 39 removed outlier: 3.646A pdb=" N ASP J 23 " --> pdb=" O ARG J 19 " (cutoff:3.500A) Proline residue: J 26 - end of helix Processing helix chain 'J' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE J 43 " --> pdb=" O PRO J 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 43' Processing helix chain 'J' and resid 60 through 78 Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU J 103 " --> pdb=" O ASP J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 140 Processing helix chain 'J' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN J 201 " --> pdb=" O ALA J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU J 271 " --> pdb=" O SER J 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 267 through 272' Processing helix chain 'J' and resid 272 through 295 removed outlier: 3.601A pdb=" N LYS J 295 " --> pdb=" O MET J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU J 311 " --> pdb=" O GLN J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 357 Processing helix chain 'J' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR J 376 " --> pdb=" O GLU J 372 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER J 379 " --> pdb=" O ARG J 375 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE J 391 " --> pdb=" O GLY J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 396 through 412 removed outlier: 3.523A pdb=" N GLN J 409 " --> pdb=" O LEU J 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA J 410 " --> pdb=" O LYS J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 440 through 451 Processing helix chain 'J' and resid 462 through 474 removed outlier: 4.163A pdb=" N ILE J 474 " --> pdb=" O ILE J 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA K 9 " --> pdb=" O THR K 6 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU K 10 " --> pdb=" O GLY K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 10' Processing helix chain 'K' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP K 23 " --> pdb=" O ARG K 19 " (cutoff:3.500A) Proline residue: K 26 - end of helix Processing helix chain 'K' and resid 40 through 43 removed outlier: 3.696A pdb=" N PHE K 43 " --> pdb=" O PRO K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 43' Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'K' and resid 91 through 96 Processing helix chain 'K' and resid 99 through 124 removed outlier: 3.717A pdb=" N LEU K 103 " --> pdb=" O ASP K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 140 Processing helix chain 'K' and resid 191 through 202 removed outlier: 3.521A pdb=" N GLN K 201 " --> pdb=" O ALA K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 272 removed outlier: 4.016A pdb=" N GLU K 271 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 267 through 272' Processing helix chain 'K' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS K 295 " --> pdb=" O MET K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 314 removed outlier: 4.269A pdb=" N LEU K 311 " --> pdb=" O GLN K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 357 Processing helix chain 'K' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER K 379 " --> pdb=" O ARG K 375 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE K 391 " --> pdb=" O GLY K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 396 through 412 removed outlier: 3.522A pdb=" N GLN K 409 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA K 410 " --> pdb=" O LYS K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 451 Processing helix chain 'K' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE K 474 " --> pdb=" O ILE K 470 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 10 removed outlier: 3.851A pdb=" N ALA L 9 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU L 10 " --> pdb=" O GLY L 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 6 through 10' Processing helix chain 'L' and resid 12 through 39 removed outlier: 3.647A pdb=" N ASP L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) Proline residue: L 26 - end of helix Processing helix chain 'L' and resid 40 through 43 removed outlier: 3.697A pdb=" N PHE L 43 " --> pdb=" O PRO L 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 43' Processing helix chain 'L' and resid 60 through 78 Processing helix chain 'L' and resid 91 through 96 Processing helix chain 'L' and resid 99 through 124 removed outlier: 3.716A pdb=" N LEU L 103 " --> pdb=" O ASP L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 140 Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.519A pdb=" N GLN L 201 " --> pdb=" O ALA L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 272 removed outlier: 4.017A pdb=" N GLU L 271 " --> pdb=" O SER L 267 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 267 through 272' Processing helix chain 'L' and resid 272 through 295 removed outlier: 3.600A pdb=" N LYS L 295 " --> pdb=" O MET L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 314 removed outlier: 4.268A pdb=" N LEU L 311 " --> pdb=" O GLN L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 357 Processing helix chain 'L' and resid 372 through 385 removed outlier: 4.086A pdb=" N TYR L 376 " --> pdb=" O GLU L 372 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER L 379 " --> pdb=" O ARG L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 396 removed outlier: 3.609A pdb=" N ILE L 391 " --> pdb=" O GLY L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 412 removed outlier: 3.524A pdb=" N GLN L 409 " --> pdb=" O LEU L 405 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA L 410 " --> pdb=" O LYS L 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 440 through 451 Processing helix chain 'L' and resid 462 through 474 removed outlier: 4.162A pdb=" N ILE L 474 " --> pdb=" O ILE L 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS A 159 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A 146 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 143 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 145 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN A 178 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 300 Processing sheet with id=AA6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS B 159 " --> pdb=" O TYR B 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 146 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 143 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 145 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.759A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 169 removed outlier: 3.759A pdb=" N GLN B 178 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 298 through 300 Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB3, first strand: chain 'C' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS C 159 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 146 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 143 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 145 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN C 178 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 298 through 300 Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 86 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 162 removed outlier: 3.719A pdb=" N LYS D 159 " --> pdb=" O TYR D 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR D 146 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 143 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 145 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN D 178 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 298 through 300 Processing sheet with id=AC3, first strand: chain 'E' and resid 85 through 86 Processing sheet with id=AC4, first strand: chain 'E' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS E 159 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR E 146 " --> pdb=" O LYS E 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 143 " --> pdb=" O ILE E 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU E 145 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 166 through 169 removed outlier: 3.762A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR E 215 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 166 through 169 removed outlier: 3.762A pdb=" N GLN E 178 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR E 215 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 298 through 300 Processing sheet with id=AC8, first strand: chain 'F' and resid 85 through 86 Processing sheet with id=AC9, first strand: chain 'F' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS F 159 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR F 146 " --> pdb=" O LYS F 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL F 143 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 145 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 215 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN F 178 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR F 215 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 298 through 300 Processing sheet with id=AD4, first strand: chain 'G' and resid 85 through 86 Processing sheet with id=AD5, first strand: chain 'G' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS G 159 " --> pdb=" O TYR G 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR G 146 " --> pdb=" O LYS G 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL G 143 " --> pdb=" O ILE G 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 145 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 215 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN G 178 " --> pdb=" O GLN G 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 215 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 298 through 300 Processing sheet with id=AD9, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AE1, first strand: chain 'H' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS H 159 " --> pdb=" O TYR H 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR H 146 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL H 143 " --> pdb=" O ILE H 254 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 145 " --> pdb=" O ILE H 252 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 215 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN H 178 " --> pdb=" O GLN H 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR H 215 " --> pdb=" O THR H 181 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 298 through 300 Processing sheet with id=AE5, first strand: chain 'I' and resid 85 through 86 Processing sheet with id=AE6, first strand: chain 'I' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS I 159 " --> pdb=" O TYR I 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR I 146 " --> pdb=" O LYS I 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL I 143 " --> pdb=" O ILE I 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU I 145 " --> pdb=" O ILE I 252 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR I 215 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 166 through 169 removed outlier: 3.761A pdb=" N GLN I 178 " --> pdb=" O GLN I 169 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR I 215 " --> pdb=" O THR I 181 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 298 through 300 Processing sheet with id=AF1, first strand: chain 'J' and resid 85 through 86 Processing sheet with id=AF2, first strand: chain 'J' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS J 159 " --> pdb=" O TYR J 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR J 146 " --> pdb=" O LYS J 159 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL J 143 " --> pdb=" O ILE J 254 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU J 145 " --> pdb=" O ILE J 252 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR J 215 " --> pdb=" O THR J 181 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN J 178 " --> pdb=" O GLN J 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR J 215 " --> pdb=" O THR J 181 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 298 through 300 Processing sheet with id=AF6, first strand: chain 'K' and resid 85 through 86 Processing sheet with id=AF7, first strand: chain 'K' and resid 159 through 162 removed outlier: 3.721A pdb=" N LYS K 159 " --> pdb=" O TYR K 146 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR K 146 " --> pdb=" O LYS K 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL K 143 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU K 145 " --> pdb=" O ILE K 252 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR K 215 " --> pdb=" O THR K 181 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN K 178 " --> pdb=" O GLN K 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR K 215 " --> pdb=" O THR K 181 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 298 through 300 Processing sheet with id=AG2, first strand: chain 'L' and resid 85 through 86 Processing sheet with id=AG3, first strand: chain 'L' and resid 159 through 162 removed outlier: 3.720A pdb=" N LYS L 159 " --> pdb=" O TYR L 146 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR L 146 " --> pdb=" O LYS L 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL L 143 " --> pdb=" O ILE L 254 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU L 145 " --> pdb=" O ILE L 252 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR L 215 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 166 through 169 removed outlier: 3.760A pdb=" N GLN L 178 " --> pdb=" O GLN L 169 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR L 215 " --> pdb=" O THR L 181 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 298 through 300 2232 hydrogen bonds defined for protein. 6588 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: 19.53 Time building geometry restraints manager: 12.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 13494 1.33 - 1.46: 8674 1.46 - 1.58: 22196 1.58 - 1.71: 0 1.71 - 1.84: 372 Bond restraints: 44736 Sorted by residual: bond pdb=" CA THR I 56 " pdb=" C THR I 56 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.08e-02 8.57e+03 1.94e+01 bond pdb=" CA THR B 56 " pdb=" C THR B 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.93e+01 bond pdb=" CA THR H 56 " pdb=" C THR H 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.93e+01 bond pdb=" CA THR J 56 " pdb=" C THR J 56 " ideal model delta sigma weight residual 1.528 1.480 0.047 1.08e-02 8.57e+03 1.90e+01 bond pdb=" CA THR C 56 " pdb=" C THR C 56 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.08e-02 8.57e+03 1.89e+01 ... (remaining 44731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 56296 2.68 - 5.36: 3293 5.36 - 8.04: 735 8.04 - 10.73: 192 10.73 - 13.41: 72 Bond angle restraints: 60588 Sorted by residual: angle pdb=" N ASP D 208 " pdb=" CA ASP D 208 " pdb=" C ASP D 208 " ideal model delta sigma weight residual 111.36 124.14 -12.78 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 111.36 124.13 -12.77 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP B 208 " pdb=" CA ASP B 208 " pdb=" C ASP B 208 " ideal model delta sigma weight residual 111.36 124.13 -12.77 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP E 208 " pdb=" CA ASP E 208 " pdb=" C ASP E 208 " ideal model delta sigma weight residual 111.36 124.11 -12.75 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N ASP J 208 " pdb=" CA ASP J 208 " pdb=" C ASP J 208 " ideal model delta sigma weight residual 111.36 124.10 -12.74 1.09e+00 8.42e-01 1.37e+02 ... (remaining 60583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 23928 17.81 - 35.62: 2364 35.62 - 53.42: 829 53.42 - 71.23: 359 71.23 - 89.04: 84 Dihedral angle restraints: 27564 sinusoidal: 11184 harmonic: 16380 Sorted by residual: dihedral pdb=" C TYR K 37 " pdb=" N TYR K 37 " pdb=" CA TYR K 37 " pdb=" CB TYR K 37 " ideal model delta harmonic sigma weight residual -122.60 -137.73 15.13 0 2.50e+00 1.60e-01 3.66e+01 dihedral pdb=" C TYR I 37 " pdb=" N TYR I 37 " pdb=" CA TYR I 37 " pdb=" CB TYR I 37 " ideal model delta harmonic sigma weight residual -122.60 -137.70 15.10 0 2.50e+00 1.60e-01 3.65e+01 dihedral pdb=" C TYR F 37 " pdb=" N TYR F 37 " pdb=" CA TYR F 37 " pdb=" CB TYR F 37 " ideal model delta harmonic sigma weight residual -122.60 -137.70 15.10 0 2.50e+00 1.60e-01 3.65e+01 ... (remaining 27561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 5578 0.126 - 0.252: 1130 0.252 - 0.378: 96 0.378 - 0.504: 44 0.504 - 0.630: 28 Chirality restraints: 6876 Sorted by residual: chirality pdb=" CA TYR F 37 " pdb=" N TYR F 37 " pdb=" C TYR F 37 " pdb=" CB TYR F 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.91e+00 chirality pdb=" CA TYR K 37 " pdb=" N TYR K 37 " pdb=" C TYR K 37 " pdb=" CB TYR K 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.87e+00 chirality pdb=" CA TYR I 37 " pdb=" N TYR I 37 " pdb=" C TYR I 37 " pdb=" CB TYR I 37 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.83e+00 ... (remaining 6873 not shown) Planarity restraints: 7932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 398 " -0.056 5.00e-02 4.00e+02 8.46e-02 1.14e+01 pdb=" N PRO G 399 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO G 399 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 399 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 398 " -0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO J 399 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO J 399 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO J 399 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 398 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO D 399 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 399 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 399 " 0.047 5.00e-02 4.00e+02 ... (remaining 7929 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1395 2.65 - 3.21: 44769 3.21 - 3.78: 70733 3.78 - 4.34: 93193 4.34 - 4.90: 143138 Nonbonded interactions: 353228 Sorted by model distance: nonbonded pdb=" O THR I 6 " pdb=" OG1 THR I 6 " model vdw 2.089 3.040 nonbonded pdb=" O THR H 6 " pdb=" OG1 THR H 6 " model vdw 2.089 3.040 nonbonded pdb=" O THR K 6 " pdb=" OG1 THR K 6 " model vdw 2.089 3.040 nonbonded pdb=" O THR F 6 " pdb=" OG1 THR F 6 " model vdw 2.089 3.040 nonbonded pdb=" O THR G 6 " pdb=" OG1 THR G 6 " model vdw 2.090 3.040 ... (remaining 353223 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.10 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.610 Check model and map are aligned: 0.300 Set scattering table: 0.350 Process input model: 83.340 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 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 : 0.009 0.051 44736 Z= 0.616 Angle : 1.559 13.408 60588 Z= 1.053 Chirality : 0.108 0.630 6876 Planarity : 0.007 0.085 7932 Dihedral : 18.035 89.041 17052 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.02 % Favored : 93.76 % Rotamer: Outliers : 16.41 % Allowed : 11.87 % Favored : 71.72 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.11), residues: 5580 helix: 1.35 (0.10), residues: 2472 sheet: -0.88 (0.19), residues: 648 loop : -2.37 (0.11), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 83 HIS 0.001 0.001 HIS I 216 PHE 0.012 0.002 PHE H 319 TYR 0.018 0.002 TYR L 37 ARG 0.006 0.001 ARG J 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2305 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 780 poor density : 1525 time to evaluate : 4.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8854 (tp) cc_final: 0.8571 (pt) REVERT: A 58 TRP cc_start: 0.7793 (m100) cc_final: 0.7249 (m100) REVERT: A 91 TYR cc_start: 0.6758 (t80) cc_final: 0.6489 (t80) REVERT: A 137 LEU cc_start: 0.7764 (tp) cc_final: 0.7460 (tp) REVERT: A 151 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8372 (tt0) REVERT: A 263 SER cc_start: 0.7481 (OUTLIER) cc_final: 0.7242 (m) REVERT: A 268 TYR cc_start: 0.7656 (t80) cc_final: 0.6668 (t80) REVERT: A 273 LEU cc_start: 0.7824 (tp) cc_final: 0.7437 (tt) REVERT: A 284 GLU cc_start: 0.8749 (tt0) cc_final: 0.8442 (tt0) REVERT: A 470 ILE cc_start: 0.6655 (mm) cc_final: 0.5915 (pt) REVERT: A 474 ILE cc_start: 0.4977 (OUTLIER) cc_final: 0.4553 (tp) REVERT: B 52 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7873 (p) REVERT: B 54 TYR cc_start: 0.6795 (m-10) cc_final: 0.6087 (m-10) REVERT: B 58 TRP cc_start: 0.8203 (m100) cc_final: 0.7833 (m100) REVERT: B 114 GLU cc_start: 0.7049 (tp30) cc_final: 0.6706 (tp30) REVERT: B 124 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.4893 (m-40) REVERT: B 132 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8233 (tp30) REVERT: B 193 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7037 (p0) REVERT: B 222 ASP cc_start: 0.6236 (m-30) cc_final: 0.5918 (m-30) REVERT: B 352 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 353 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8801 (m) REVERT: B 368 ARG cc_start: 0.0842 (OUTLIER) cc_final: 0.0459 (mmm160) REVERT: B 389 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 412 GLN cc_start: 0.0445 (OUTLIER) cc_final: -0.0570 (pt0) REVERT: B 465 MET cc_start: 0.4105 (mtm) cc_final: 0.2788 (ttt) REVERT: C 91 TYR cc_start: 0.7001 (t80) cc_final: 0.6654 (t80) REVERT: C 235 MET cc_start: 0.7523 (mmm) cc_final: 0.6876 (ptt) REVERT: C 388 VAL cc_start: 0.7633 (m) cc_final: 0.7409 (p) REVERT: C 470 ILE cc_start: 0.6437 (mm) cc_final: 0.5661 (pt) REVERT: C 474 ILE cc_start: 0.4317 (OUTLIER) cc_final: 0.3866 (tp) REVERT: D 58 TRP cc_start: 0.8078 (m100) cc_final: 0.7860 (m100) REVERT: D 59 GLN cc_start: 0.8635 (pp30) cc_final: 0.8407 (pp30) REVERT: D 114 GLU cc_start: 0.7203 (tp30) cc_final: 0.6731 (tp30) REVERT: D 132 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8329 (tp30) REVERT: D 156 ASN cc_start: 0.8393 (t0) cc_final: 0.8118 (m-40) REVERT: D 340 VAL cc_start: 0.8932 (m) cc_final: 0.8624 (t) REVERT: D 446 VAL cc_start: 0.4531 (OUTLIER) cc_final: 0.4303 (p) REVERT: D 465 MET cc_start: 0.3332 (mtm) cc_final: 0.2071 (ttt) REVERT: E 54 TYR cc_start: 0.6579 (m-10) cc_final: 0.6345 (m-10) REVERT: E 58 TRP cc_start: 0.7743 (m100) cc_final: 0.7179 (m100) REVERT: E 88 ILE cc_start: 0.5323 (OUTLIER) cc_final: 0.5003 (tp) REVERT: E 91 TYR cc_start: 0.6674 (t80) cc_final: 0.6469 (t80) REVERT: E 235 MET cc_start: 0.7739 (mmm) cc_final: 0.6941 (ptt) REVERT: E 263 SER cc_start: 0.7290 (OUTLIER) cc_final: 0.7047 (m) REVERT: E 268 TYR cc_start: 0.7685 (t80) cc_final: 0.6634 (t80) REVERT: E 273 LEU cc_start: 0.8195 (tp) cc_final: 0.7671 (tt) REVERT: E 470 ILE cc_start: 0.6932 (mm) cc_final: 0.6218 (pt) REVERT: E 474 ILE cc_start: 0.4801 (OUTLIER) cc_final: 0.4595 (tp) REVERT: F 58 TRP cc_start: 0.8290 (m100) cc_final: 0.7871 (m100) REVERT: F 84 MET cc_start: 0.5740 (ptt) cc_final: 0.5535 (ptt) REVERT: F 114 GLU cc_start: 0.7262 (tp30) cc_final: 0.6580 (tp30) REVERT: F 118 MET cc_start: 0.8275 (mtp) cc_final: 0.7704 (mtp) REVERT: F 124 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.5745 (m-40) REVERT: F 156 ASN cc_start: 0.8598 (t0) cc_final: 0.8075 (m110) REVERT: F 222 ASP cc_start: 0.6250 (m-30) cc_final: 0.6045 (m-30) REVERT: F 268 TYR cc_start: 0.8306 (t80) cc_final: 0.7947 (t80) REVERT: F 340 VAL cc_start: 0.8867 (m) cc_final: 0.8578 (t) REVERT: F 381 LEU cc_start: 0.7674 (mt) cc_final: 0.7438 (tp) REVERT: F 389 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6356 (t80) REVERT: F 392 LEU cc_start: 0.8746 (tp) cc_final: 0.8413 (mm) REVERT: F 412 GLN cc_start: 0.0231 (OUTLIER) cc_final: -0.0354 (mm-40) REVERT: F 446 VAL cc_start: 0.4250 (OUTLIER) cc_final: 0.3984 (p) REVERT: F 465 MET cc_start: 0.3738 (mtm) cc_final: 0.2170 (ttt) REVERT: G 39 ILE cc_start: 0.8859 (tp) cc_final: 0.8540 (pt) REVERT: G 58 TRP cc_start: 0.7790 (m100) cc_final: 0.7211 (m100) REVERT: G 91 TYR cc_start: 0.6661 (t80) cc_final: 0.6452 (t80) REVERT: G 137 LEU cc_start: 0.7717 (tp) cc_final: 0.7348 (tp) REVERT: G 151 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8372 (tt0) REVERT: G 263 SER cc_start: 0.7465 (OUTLIER) cc_final: 0.7264 (m) REVERT: G 268 TYR cc_start: 0.7772 (t80) cc_final: 0.6742 (t80) REVERT: G 273 LEU cc_start: 0.7834 (tp) cc_final: 0.7434 (tt) REVERT: G 284 GLU cc_start: 0.8774 (tt0) cc_final: 0.8449 (tt0) REVERT: G 470 ILE cc_start: 0.6633 (mm) cc_final: 0.5908 (pt) REVERT: G 474 ILE cc_start: 0.4536 (OUTLIER) cc_final: 0.4287 (tp) REVERT: H 54 TYR cc_start: 0.6818 (m-10) cc_final: 0.6117 (m-10) REVERT: H 58 TRP cc_start: 0.8178 (m100) cc_final: 0.7795 (m100) REVERT: H 101 ASP cc_start: 0.6154 (t0) cc_final: 0.5792 (t70) REVERT: H 114 GLU cc_start: 0.7056 (tp30) cc_final: 0.6697 (tp30) REVERT: H 124 ASN cc_start: 0.7500 (OUTLIER) cc_final: 0.4902 (m-40) REVERT: H 132 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8224 (tp30) REVERT: H 193 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7033 (p0) REVERT: H 222 ASP cc_start: 0.6292 (m-30) cc_final: 0.6026 (m-30) REVERT: H 352 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9008 (mm) REVERT: H 353 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8673 (m) REVERT: H 368 ARG cc_start: 0.0880 (OUTLIER) cc_final: 0.0496 (mmm160) REVERT: H 389 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6245 (t80) REVERT: H 412 GLN cc_start: 0.0334 (OUTLIER) cc_final: -0.0635 (pt0) REVERT: H 449 TRP cc_start: 0.2726 (m-10) cc_final: 0.2498 (m-10) REVERT: H 465 MET cc_start: 0.4102 (mtm) cc_final: 0.2779 (ttt) REVERT: I 91 TYR cc_start: 0.6987 (t80) cc_final: 0.6607 (t80) REVERT: I 388 VAL cc_start: 0.7629 (m) cc_final: 0.7401 (p) REVERT: I 470 ILE cc_start: 0.6391 (mm) cc_final: 0.5625 (pt) REVERT: I 474 ILE cc_start: 0.4317 (OUTLIER) cc_final: 0.3844 (tp) REVERT: J 58 TRP cc_start: 0.8141 (m100) cc_final: 0.7903 (m100) REVERT: J 59 GLN cc_start: 0.8566 (pp30) cc_final: 0.8319 (pp30) REVERT: J 114 GLU cc_start: 0.7123 (tp30) cc_final: 0.6669 (tp30) REVERT: J 132 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8344 (tp30) REVERT: J 340 VAL cc_start: 0.8921 (m) cc_final: 0.8622 (t) REVERT: J 446 VAL cc_start: 0.3796 (OUTLIER) cc_final: 0.3519 (p) REVERT: J 465 MET cc_start: 0.3374 (mtm) cc_final: 0.2125 (ttt) REVERT: K 54 TYR cc_start: 0.6581 (m-10) cc_final: 0.6350 (m-10) REVERT: K 58 TRP cc_start: 0.7742 (m100) cc_final: 0.7190 (m100) REVERT: K 88 ILE cc_start: 0.5329 (OUTLIER) cc_final: 0.5028 (tp) REVERT: K 91 TYR cc_start: 0.6667 (t80) cc_final: 0.6447 (t80) REVERT: K 235 MET cc_start: 0.7734 (mmm) cc_final: 0.6941 (ptt) REVERT: K 263 SER cc_start: 0.7273 (OUTLIER) cc_final: 0.7031 (m) REVERT: K 268 TYR cc_start: 0.7691 (t80) cc_final: 0.6658 (t80) REVERT: K 273 LEU cc_start: 0.8177 (tp) cc_final: 0.7673 (tt) REVERT: K 470 ILE cc_start: 0.6920 (mm) cc_final: 0.6220 (pt) REVERT: K 474 ILE cc_start: 0.4809 (OUTLIER) cc_final: 0.4594 (tp) REVERT: L 58 TRP cc_start: 0.8286 (m100) cc_final: 0.7868 (m100) REVERT: L 84 MET cc_start: 0.5698 (ptt) cc_final: 0.5215 (ptt) REVERT: L 114 GLU cc_start: 0.7237 (tp30) cc_final: 0.6595 (tp30) REVERT: L 118 MET cc_start: 0.8313 (mtp) cc_final: 0.7419 (mtp) REVERT: L 124 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.5551 (m-40) REVERT: L 156 ASN cc_start: 0.8599 (t0) cc_final: 0.8074 (m110) REVERT: L 222 ASP cc_start: 0.6052 (m-30) cc_final: 0.5795 (m-30) REVERT: L 268 TYR cc_start: 0.8367 (t80) cc_final: 0.7983 (t80) REVERT: L 340 VAL cc_start: 0.8868 (m) cc_final: 0.8531 (t) REVERT: L 381 LEU cc_start: 0.7700 (mt) cc_final: 0.7471 (tp) REVERT: L 389 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6317 (t80) REVERT: L 392 LEU cc_start: 0.8754 (tp) cc_final: 0.8445 (mm) REVERT: L 412 GLN cc_start: 0.0469 (OUTLIER) cc_final: -0.0290 (pt0) REVERT: L 428 THR cc_start: 0.8555 (t) cc_final: 0.8321 (t) REVERT: L 446 VAL cc_start: 0.4305 (OUTLIER) cc_final: 0.4031 (p) REVERT: L 465 MET cc_start: 0.3659 (mtm) cc_final: 0.2131 (ttt) outliers start: 780 outliers final: 155 residues processed: 1990 average time/residue: 0.5697 time to fit residues: 1843.6233 Evaluate side-chains 1005 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 813 time to evaluate : 4.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 2.9990 chunk 418 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 282 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 432 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 322 optimal weight: 9.9990 chunk 501 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 124 ASN B 55 GLN B 68 ASN B 169 GLN C 55 GLN C 124 ASN C 397 GLN D 55 GLN D 169 GLN E 55 GLN E 68 ASN E 124 ASN E 407 GLN F 55 GLN ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 GLN G 124 ASN H 55 GLN H 68 ASN H 169 GLN I 55 GLN I 124 ASN I 397 GLN J 55 GLN J 169 GLN K 55 GLN K 68 ASN K 124 ASN K 407 GLN L 55 GLN ** L 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 44736 Z= 0.253 Angle : 0.738 11.285 60588 Z= 0.381 Chirality : 0.046 0.147 6876 Planarity : 0.005 0.051 7932 Dihedral : 5.050 23.431 6204 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.11), residues: 5580 helix: 1.10 (0.10), residues: 2508 sheet: -0.95 (0.19), residues: 576 loop : -1.62 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 83 HIS 0.004 0.001 HIS J 216 PHE 0.030 0.002 PHE F 131 TYR 0.036 0.002 TYR I 91 ARG 0.006 0.001 ARG F 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1033 time to evaluate : 5.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8939 (tp) cc_final: 0.8437 (pt) REVERT: A 137 LEU cc_start: 0.7403 (tp) cc_final: 0.7133 (tp) REVERT: A 151 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8425 (tm-30) REVERT: A 158 MET cc_start: 0.7692 (tpp) cc_final: 0.7249 (mmm) REVERT: A 268 TYR cc_start: 0.7721 (t80) cc_final: 0.6565 (t80) REVERT: A 329 PHE cc_start: 0.8499 (m-80) cc_final: 0.8260 (m-80) REVERT: A 392 LEU cc_start: 0.9008 (tp) cc_final: 0.8799 (tp) REVERT: A 465 MET cc_start: 0.4385 (mpp) cc_final: 0.3341 (mpp) REVERT: B 54 TYR cc_start: 0.6246 (m-10) cc_final: 0.5811 (m-10) REVERT: B 132 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8199 (tp30) REVERT: B 222 ASP cc_start: 0.6052 (m-30) cc_final: 0.5717 (m-30) REVERT: B 289 MET cc_start: 0.8199 (ttm) cc_final: 0.7910 (ttm) REVERT: B 353 SER cc_start: 0.8730 (p) cc_final: 0.8451 (m) REVERT: C 108 GLU cc_start: 0.7251 (pt0) cc_final: 0.7026 (tp30) REVERT: C 130 LEU cc_start: 0.8702 (mm) cc_final: 0.8432 (mm) REVERT: C 158 MET cc_start: 0.7462 (tpp) cc_final: 0.7211 (tpp) REVERT: C 396 LEU cc_start: 0.8536 (mt) cc_final: 0.8322 (tp) REVERT: C 465 MET cc_start: 0.3990 (mpp) cc_final: 0.3470 (mmt) REVERT: D 132 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8332 (tp30) REVERT: D 268 TYR cc_start: 0.8131 (t80) cc_final: 0.7794 (t80) REVERT: D 301 ASN cc_start: 0.8952 (t0) cc_final: 0.8744 (t0) REVERT: D 392 LEU cc_start: 0.8156 (tp) cc_final: 0.7892 (tp) REVERT: E 112 MET cc_start: 0.8390 (mtt) cc_final: 0.8136 (mtm) REVERT: E 130 LEU cc_start: 0.8771 (mm) cc_final: 0.8445 (mm) REVERT: E 268 TYR cc_start: 0.7275 (t80) cc_final: 0.6496 (t80) REVERT: E 381 LEU cc_start: 0.8043 (tp) cc_final: 0.7560 (tp) REVERT: E 396 LEU cc_start: 0.9079 (tp) cc_final: 0.8834 (tp) REVERT: E 469 ARG cc_start: 0.4673 (mtt180) cc_final: 0.4412 (mpt-90) REVERT: E 472 ASN cc_start: 0.5910 (m-40) cc_final: 0.5612 (m-40) REVERT: F 118 MET cc_start: 0.7492 (mtp) cc_final: 0.6500 (mtp) REVERT: F 268 TYR cc_start: 0.8208 (t80) cc_final: 0.7721 (t80) REVERT: F 301 ASN cc_start: 0.8836 (t0) cc_final: 0.8545 (t0) REVERT: G 39 ILE cc_start: 0.8961 (tp) cc_final: 0.8469 (pt) REVERT: G 112 MET cc_start: 0.8025 (mtt) cc_final: 0.7781 (mtm) REVERT: G 137 LEU cc_start: 0.7415 (tp) cc_final: 0.7214 (tp) REVERT: G 151 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8404 (tm-30) REVERT: G 158 MET cc_start: 0.7647 (tpp) cc_final: 0.7245 (mmm) REVERT: G 268 TYR cc_start: 0.7745 (t80) cc_final: 0.6582 (t80) REVERT: G 392 LEU cc_start: 0.9035 (tp) cc_final: 0.8784 (tp) REVERT: G 465 MET cc_start: 0.4409 (mpp) cc_final: 0.3461 (mpp) REVERT: H 132 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8190 (tp30) REVERT: H 163 LEU cc_start: 0.8823 (tp) cc_final: 0.8601 (tp) REVERT: H 222 ASP cc_start: 0.6067 (m-30) cc_final: 0.5736 (m-30) REVERT: H 353 SER cc_start: 0.8685 (p) cc_final: 0.8423 (m) REVERT: I 130 LEU cc_start: 0.8684 (mm) cc_final: 0.8418 (mm) REVERT: I 158 MET cc_start: 0.7473 (tpp) cc_final: 0.7252 (tpp) REVERT: I 396 LEU cc_start: 0.8524 (mt) cc_final: 0.8317 (tp) REVERT: I 465 MET cc_start: 0.3875 (mpp) cc_final: 0.3424 (mmt) REVERT: J 132 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8337 (tp30) REVERT: J 268 TYR cc_start: 0.8166 (t80) cc_final: 0.7789 (t80) REVERT: J 301 ASN cc_start: 0.8935 (t0) cc_final: 0.8696 (t0) REVERT: J 392 LEU cc_start: 0.8199 (tp) cc_final: 0.7963 (tp) REVERT: K 54 TYR cc_start: 0.7359 (m-10) cc_final: 0.7100 (m-10) REVERT: K 84 MET cc_start: 0.7676 (ptt) cc_final: 0.7469 (ptp) REVERT: K 112 MET cc_start: 0.8372 (mtt) cc_final: 0.8101 (mtm) REVERT: K 268 TYR cc_start: 0.7280 (t80) cc_final: 0.6528 (t80) REVERT: K 381 LEU cc_start: 0.8036 (tp) cc_final: 0.7543 (tp) REVERT: K 469 ARG cc_start: 0.4675 (mtt180) cc_final: 0.4394 (mpt-90) REVERT: K 472 ASN cc_start: 0.5890 (m-40) cc_final: 0.5631 (m-40) REVERT: L 80 MET cc_start: 0.7260 (tpp) cc_final: 0.7032 (tpp) REVERT: L 83 TRP cc_start: 0.5766 (p90) cc_final: 0.5563 (p90) REVERT: L 118 MET cc_start: 0.7396 (mtp) cc_final: 0.6726 (mtp) REVERT: L 301 ASN cc_start: 0.8840 (t0) cc_final: 0.8503 (t0) outliers start: 4 outliers final: 0 residues processed: 1037 average time/residue: 0.6160 time to fit residues: 1057.9784 Evaluate side-chains 651 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 651 time to evaluate : 5.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 278 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 417 optimal weight: 1.9990 chunk 341 optimal weight: 7.9990 chunk 138 optimal weight: 0.6980 chunk 502 optimal weight: 8.9990 chunk 542 optimal weight: 4.9990 chunk 447 optimal weight: 0.8980 chunk 497 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 402 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 124 ASN D 169 GLN E 49 ASN E 68 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN F 335 GLN G 49 ASN G 124 ASN I 49 ASN J 169 GLN K 49 ASN K 68 ASN L 169 GLN L 335 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44736 Z= 0.193 Angle : 0.644 9.321 60588 Z= 0.329 Chirality : 0.043 0.163 6876 Planarity : 0.004 0.048 7932 Dihedral : 4.599 23.736 6204 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.04 % Allowed : 4.61 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.11), residues: 5580 helix: 1.31 (0.10), residues: 2568 sheet: -1.01 (0.18), residues: 696 loop : -1.59 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 449 HIS 0.004 0.001 HIS D 216 PHE 0.018 0.002 PHE E 354 TYR 0.043 0.002 TYR I 91 ARG 0.005 0.000 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 947 time to evaluate : 4.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8889 (tp) cc_final: 0.8628 (tt) REVERT: A 151 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8420 (tm-30) REVERT: A 268 TYR cc_start: 0.7452 (t80) cc_final: 0.6622 (t80) REVERT: A 329 PHE cc_start: 0.8205 (m-80) cc_final: 0.7727 (m-80) REVERT: B 41 SER cc_start: 0.8041 (p) cc_final: 0.7743 (p) REVERT: B 54 TYR cc_start: 0.5999 (m-10) cc_final: 0.5769 (m-10) REVERT: B 132 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8330 (tp30) REVERT: B 289 MET cc_start: 0.8255 (ttm) cc_final: 0.8010 (ttm) REVERT: C 58 TRP cc_start: 0.7808 (m100) cc_final: 0.7488 (m100) REVERT: C 130 LEU cc_start: 0.8897 (mm) cc_final: 0.8610 (mm) REVERT: C 134 LEU cc_start: 0.8338 (tt) cc_final: 0.8026 (tp) REVERT: C 284 GLU cc_start: 0.8526 (tt0) cc_final: 0.8253 (tp30) REVERT: C 329 PHE cc_start: 0.8299 (m-80) cc_final: 0.8089 (m-80) REVERT: C 465 MET cc_start: 0.3985 (mpp) cc_final: 0.3353 (mmt) REVERT: C 470 ILE cc_start: 0.6190 (mm) cc_final: 0.5601 (mm) REVERT: D 37 TYR cc_start: 0.7517 (m-80) cc_final: 0.7317 (m-10) REVERT: D 78 PHE cc_start: 0.8055 (m-80) cc_final: 0.7845 (m-80) REVERT: D 216 HIS cc_start: 0.7316 (t-90) cc_final: 0.7033 (t-170) REVERT: D 268 TYR cc_start: 0.8013 (t80) cc_final: 0.7723 (t80) REVERT: D 301 ASN cc_start: 0.8694 (t0) cc_final: 0.8493 (t0) REVERT: D 472 ASN cc_start: 0.7283 (t0) cc_final: 0.7077 (p0) REVERT: E 112 MET cc_start: 0.8418 (mtt) cc_final: 0.8200 (mtm) REVERT: E 130 LEU cc_start: 0.8713 (mm) cc_final: 0.8489 (mm) REVERT: E 268 TYR cc_start: 0.7067 (t80) cc_final: 0.6639 (t80) REVERT: E 357 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6807 (tpt) REVERT: E 381 LEU cc_start: 0.7793 (tp) cc_final: 0.7310 (tp) REVERT: E 469 ARG cc_start: 0.5093 (mtt180) cc_final: 0.4739 (mpt-90) REVERT: F 47 SER cc_start: 0.7649 (m) cc_final: 0.7090 (p) REVERT: F 114 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7423 (tp30) REVERT: F 121 ILE cc_start: 0.8217 (mm) cc_final: 0.7990 (mm) REVERT: F 268 TYR cc_start: 0.8171 (t80) cc_final: 0.7758 (t80) REVERT: F 301 ASN cc_start: 0.8844 (t0) cc_final: 0.8546 (t0) REVERT: G 39 ILE cc_start: 0.8932 (tp) cc_final: 0.8653 (tt) REVERT: G 151 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8416 (tm-30) REVERT: G 268 TYR cc_start: 0.7425 (t80) cc_final: 0.6694 (t80) REVERT: H 41 SER cc_start: 0.7946 (p) cc_final: 0.7681 (p) REVERT: H 52 THR cc_start: 0.6419 (p) cc_final: 0.5954 (t) REVERT: H 132 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8411 (tp30) REVERT: I 58 TRP cc_start: 0.7803 (m100) cc_final: 0.7485 (m100) REVERT: I 130 LEU cc_start: 0.8877 (mm) cc_final: 0.8586 (mm) REVERT: I 134 LEU cc_start: 0.8324 (tt) cc_final: 0.8004 (tp) REVERT: I 284 GLU cc_start: 0.8494 (tt0) cc_final: 0.8255 (tp30) REVERT: I 329 PHE cc_start: 0.8291 (m-80) cc_final: 0.8066 (m-80) REVERT: I 465 MET cc_start: 0.3950 (mpp) cc_final: 0.3382 (mmt) REVERT: I 470 ILE cc_start: 0.5969 (mm) cc_final: 0.5285 (mm) REVERT: J 301 ASN cc_start: 0.8761 (t0) cc_final: 0.8531 (t0) REVERT: K 54 TYR cc_start: 0.7378 (m-10) cc_final: 0.7121 (m-10) REVERT: K 112 MET cc_start: 0.8366 (mtt) cc_final: 0.8114 (mtm) REVERT: K 130 LEU cc_start: 0.8653 (mm) cc_final: 0.8361 (mm) REVERT: K 268 TYR cc_start: 0.7108 (t80) cc_final: 0.6578 (t80) REVERT: K 357 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6766 (tpt) REVERT: K 381 LEU cc_start: 0.7688 (tp) cc_final: 0.7284 (tp) REVERT: K 469 ARG cc_start: 0.5008 (mtt180) cc_final: 0.4610 (mpt-90) REVERT: L 47 SER cc_start: 0.7661 (m) cc_final: 0.7112 (p) REVERT: L 114 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7490 (tp30) REVERT: L 271 GLU cc_start: 0.8028 (mp0) cc_final: 0.7776 (mp0) REVERT: L 301 ASN cc_start: 0.8809 (t0) cc_final: 0.8551 (t0) outliers start: 2 outliers final: 0 residues processed: 947 average time/residue: 0.5970 time to fit residues: 938.5343 Evaluate side-chains 619 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 617 time to evaluate : 5.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 20.0000 chunk 377 optimal weight: 0.6980 chunk 260 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 337 optimal weight: 6.9990 chunk 503 optimal weight: 9.9990 chunk 533 optimal weight: 0.9980 chunk 263 optimal weight: 0.3980 chunk 477 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 216 HIS ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN B 283 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN D 169 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 216 HIS G 335 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN H 283 GLN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 407 GLN ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 44736 Z= 0.202 Angle : 0.631 7.942 60588 Z= 0.323 Chirality : 0.042 0.187 6876 Planarity : 0.004 0.046 7932 Dihedral : 4.477 23.670 6204 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 5580 helix: 1.30 (0.10), residues: 2580 sheet: -0.80 (0.19), residues: 636 loop : -1.58 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 58 HIS 0.005 0.001 HIS D 216 PHE 0.027 0.002 PHE D 354 TYR 0.027 0.002 TYR B 126 ARG 0.007 0.000 ARG B 444 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 893 time to evaluate : 4.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8895 (tp) cc_final: 0.8629 (tt) REVERT: A 124 ASN cc_start: 0.8456 (m-40) cc_final: 0.8241 (m110) REVERT: A 151 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8412 (tm-30) REVERT: A 251 TYR cc_start: 0.7554 (m-10) cc_final: 0.7354 (m-10) REVERT: A 268 TYR cc_start: 0.7497 (t80) cc_final: 0.6907 (t80) REVERT: A 351 ARG cc_start: 0.6759 (ttm170) cc_final: 0.6451 (ttm170) REVERT: B 41 SER cc_start: 0.7638 (p) cc_final: 0.7377 (p) REVERT: B 106 VAL cc_start: 0.7399 (t) cc_final: 0.7192 (t) REVERT: B 114 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7692 (tp30) REVERT: B 132 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8213 (tp30) REVERT: B 289 MET cc_start: 0.8299 (ttm) cc_final: 0.8026 (ttm) REVERT: B 291 MET cc_start: 0.8119 (mmp) cc_final: 0.7521 (mmm) REVERT: B 353 SER cc_start: 0.8489 (m) cc_final: 0.8114 (t) REVERT: B 374 ILE cc_start: 0.7964 (mt) cc_final: 0.7689 (mm) REVERT: C 58 TRP cc_start: 0.7820 (m100) cc_final: 0.7397 (m100) REVERT: C 80 MET cc_start: 0.7564 (mpp) cc_final: 0.7326 (mpp) REVERT: C 158 MET cc_start: 0.6923 (mmm) cc_final: 0.6543 (tpp) REVERT: C 465 MET cc_start: 0.4062 (mpp) cc_final: 0.3479 (mmm) REVERT: D 37 TYR cc_start: 0.7548 (m-80) cc_final: 0.7299 (m-10) REVERT: D 83 TRP cc_start: 0.4895 (p90) cc_final: 0.4352 (p90) REVERT: D 121 ILE cc_start: 0.8365 (mm) cc_final: 0.8163 (mm) REVERT: D 216 HIS cc_start: 0.7301 (t-90) cc_final: 0.6739 (t-170) REVERT: D 291 MET cc_start: 0.7888 (mmp) cc_final: 0.6663 (ttt) REVERT: D 301 ASN cc_start: 0.8740 (t0) cc_final: 0.8526 (t0) REVERT: E 54 TYR cc_start: 0.7118 (m-10) cc_final: 0.6897 (m-10) REVERT: E 268 TYR cc_start: 0.7362 (t80) cc_final: 0.6870 (t80) REVERT: E 279 LEU cc_start: 0.9036 (tp) cc_final: 0.8768 (tt) REVERT: E 381 LEU cc_start: 0.7591 (tp) cc_final: 0.7370 (tp) REVERT: F 37 TYR cc_start: 0.7372 (m-80) cc_final: 0.7084 (m-10) REVERT: F 47 SER cc_start: 0.7673 (m) cc_final: 0.7066 (p) REVERT: F 235 MET cc_start: 0.7404 (ptp) cc_final: 0.7090 (ptt) REVERT: F 268 TYR cc_start: 0.8167 (t80) cc_final: 0.7754 (t80) REVERT: F 301 ASN cc_start: 0.8898 (t0) cc_final: 0.8581 (t0) REVERT: G 39 ILE cc_start: 0.8964 (tp) cc_final: 0.8676 (tt) REVERT: G 151 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8418 (tm-30) REVERT: G 268 TYR cc_start: 0.7530 (t80) cc_final: 0.6876 (t80) REVERT: G 470 ILE cc_start: 0.5895 (mm) cc_final: 0.5624 (mm) REVERT: H 114 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7724 (tp30) REVERT: H 132 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8239 (tp30) REVERT: H 353 SER cc_start: 0.8550 (m) cc_final: 0.8115 (m) REVERT: H 374 ILE cc_start: 0.7930 (mt) cc_final: 0.7699 (mm) REVERT: I 58 TRP cc_start: 0.7829 (m100) cc_final: 0.7500 (m100) REVERT: I 158 MET cc_start: 0.6970 (mmm) cc_final: 0.6614 (tpp) REVERT: I 465 MET cc_start: 0.3457 (mpp) cc_final: 0.2802 (mmm) REVERT: I 470 ILE cc_start: 0.6045 (mm) cc_final: 0.5610 (mm) REVERT: J 37 TYR cc_start: 0.7548 (m-80) cc_final: 0.7329 (m-10) REVERT: J 291 MET cc_start: 0.7991 (mmp) cc_final: 0.6631 (ttt) REVERT: K 268 TYR cc_start: 0.7178 (t80) cc_final: 0.6971 (t80) REVERT: K 381 LEU cc_start: 0.7488 (tp) cc_final: 0.7209 (tp) REVERT: K 465 MET cc_start: 0.4367 (mpp) cc_final: 0.4139 (mmt) REVERT: K 469 ARG cc_start: 0.4790 (mtt180) cc_final: 0.4539 (mpt-90) REVERT: L 37 TYR cc_start: 0.7368 (m-80) cc_final: 0.7069 (m-10) REVERT: L 47 SER cc_start: 0.7690 (m) cc_final: 0.7128 (p) REVERT: L 114 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7571 (tm-30) REVERT: L 121 ILE cc_start: 0.8096 (mm) cc_final: 0.7546 (mm) REVERT: L 235 MET cc_start: 0.7478 (ptp) cc_final: 0.6971 (ptt) REVERT: L 301 ASN cc_start: 0.8875 (t0) cc_final: 0.8605 (t0) REVERT: L 353 SER cc_start: 0.8398 (m) cc_final: 0.8151 (m) outliers start: 4 outliers final: 0 residues processed: 897 average time/residue: 0.5607 time to fit residues: 832.1678 Evaluate side-chains 613 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 4.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 397 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 455 optimal weight: 8.9990 chunk 368 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 478 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 136 GLN C 409 GLN D 68 ASN ** D 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN D 363 GLN D 472 ASN E 32 GLN E 216 HIS E 409 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 216 HIS ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 335 GLN G 409 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 136 GLN I 409 GLN J 68 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN K 216 HIS K 409 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 44736 Z= 0.400 Angle : 0.802 8.571 60588 Z= 0.419 Chirality : 0.047 0.172 6876 Planarity : 0.006 0.055 7932 Dihedral : 5.321 25.631 6204 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.11), residues: 5580 helix: 0.38 (0.09), residues: 2568 sheet: -1.27 (0.19), residues: 672 loop : -1.67 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 58 HIS 0.011 0.002 HIS G 216 PHE 0.033 0.003 PHE F 354 TYR 0.022 0.003 TYR J 268 ARG 0.011 0.001 ARG J 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 749 time to evaluate : 4.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9231 (tp) cc_final: 0.8873 (tt) REVERT: A 112 MET cc_start: 0.8505 (mtm) cc_final: 0.8289 (mtm) REVERT: A 151 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8447 (tm-30) REVERT: A 268 TYR cc_start: 0.7750 (t80) cc_final: 0.7526 (t80) REVERT: B 114 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 132 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8314 (tp30) REVERT: B 289 MET cc_start: 0.8241 (ttm) cc_final: 0.8008 (ttm) REVERT: B 291 MET cc_start: 0.8558 (mmp) cc_final: 0.7785 (mmm) REVERT: B 301 ASN cc_start: 0.8885 (t0) cc_final: 0.8265 (p0) REVERT: B 326 ASP cc_start: 0.8474 (m-30) cc_final: 0.8248 (m-30) REVERT: B 340 VAL cc_start: 0.9126 (m) cc_final: 0.8788 (t) REVERT: C 381 LEU cc_start: 0.7972 (tp) cc_final: 0.7765 (tp) REVERT: D 37 TYR cc_start: 0.7680 (m-80) cc_final: 0.7424 (m-10) REVERT: D 42 LEU cc_start: 0.8451 (tp) cc_final: 0.8139 (tt) REVERT: D 78 PHE cc_start: 0.8398 (m-80) cc_final: 0.8079 (m-10) REVERT: D 108 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6566 (pm20) REVERT: D 179 MET cc_start: 0.7774 (ptt) cc_final: 0.7306 (ptt) REVERT: D 301 ASN cc_start: 0.8936 (t0) cc_final: 0.8702 (t0) REVERT: D 340 VAL cc_start: 0.9319 (m) cc_final: 0.8922 (t) REVERT: D 472 ASN cc_start: 0.7569 (t0) cc_final: 0.6959 (m110) REVERT: F 37 TYR cc_start: 0.7857 (m-80) cc_final: 0.7534 (m-10) REVERT: F 301 ASN cc_start: 0.9014 (t0) cc_final: 0.8618 (t0) REVERT: F 340 VAL cc_start: 0.9201 (m) cc_final: 0.8830 (t) REVERT: F 465 MET cc_start: 0.3065 (mtt) cc_final: 0.2330 (mtm) REVERT: G 39 ILE cc_start: 0.9242 (tp) cc_final: 0.8868 (tt) REVERT: G 124 ASN cc_start: 0.8931 (m-40) cc_final: 0.8659 (m110) REVERT: G 273 LEU cc_start: 0.8043 (tp) cc_final: 0.7635 (tp) REVERT: H 132 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8371 (tp30) REVERT: H 301 ASN cc_start: 0.8863 (t0) cc_final: 0.8253 (p0) REVERT: H 326 ASP cc_start: 0.8497 (m-30) cc_final: 0.8273 (m-30) REVERT: I 467 LYS cc_start: 0.7230 (mmmt) cc_final: 0.7014 (mmmt) REVERT: J 108 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6531 (pm20) REVERT: J 256 MET cc_start: 0.6682 (tmm) cc_final: 0.6449 (tpp) REVERT: J 301 ASN cc_start: 0.8737 (t0) cc_final: 0.8510 (t0) REVERT: K 305 ILE cc_start: 0.8699 (pt) cc_final: 0.8406 (tt) REVERT: L 37 TYR cc_start: 0.7825 (m-80) cc_final: 0.7576 (m-10) REVERT: L 291 MET cc_start: 0.8159 (mmp) cc_final: 0.7578 (mmm) REVERT: L 301 ASN cc_start: 0.8995 (t0) cc_final: 0.8747 (t0) REVERT: L 340 VAL cc_start: 0.9260 (m) cc_final: 0.8855 (t) REVERT: L 384 THR cc_start: 0.6795 (p) cc_final: 0.6527 (p) REVERT: L 465 MET cc_start: 0.2476 (mtt) cc_final: 0.1780 (mtm) outliers start: 4 outliers final: 0 residues processed: 753 average time/residue: 0.5625 time to fit residues: 705.7175 Evaluate side-chains 536 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 534 time to evaluate : 4.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 179 optimal weight: 4.9990 chunk 480 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 313 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 534 optimal weight: 3.9990 chunk 443 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 136 GLN A 175 ASN ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN F 283 GLN G 175 ASN G 409 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 GLN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 GLN J 363 GLN ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 283 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44736 Z= 0.241 Angle : 0.672 10.919 60588 Z= 0.345 Chirality : 0.044 0.188 6876 Planarity : 0.004 0.045 7932 Dihedral : 4.764 23.998 6204 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 5580 helix: 0.62 (0.10), residues: 2640 sheet: -1.15 (0.18), residues: 792 loop : -1.69 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP J 449 HIS 0.009 0.003 HIS F 216 PHE 0.027 0.002 PHE J 131 TYR 0.020 0.002 TYR L 268 ARG 0.008 0.001 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 777 time to evaluate : 5.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9034 (tp) cc_final: 0.8685 (tt) REVERT: A 465 MET cc_start: 0.3974 (mmt) cc_final: 0.3134 (mmm) REVERT: A 470 ILE cc_start: 0.5988 (mm) cc_final: 0.5726 (mm) REVERT: B 112 MET cc_start: 0.6026 (mtm) cc_final: 0.5643 (tpp) REVERT: B 137 LEU cc_start: 0.7875 (tp) cc_final: 0.7426 (tp) REVERT: B 289 MET cc_start: 0.8193 (ttm) cc_final: 0.7883 (ttm) REVERT: B 291 MET cc_start: 0.8474 (mmp) cc_final: 0.7928 (mmm) REVERT: B 301 ASN cc_start: 0.8860 (t0) cc_final: 0.8274 (p0) REVERT: B 326 ASP cc_start: 0.8406 (m-30) cc_final: 0.8142 (m-30) REVERT: B 408 LEU cc_start: 0.8042 (mp) cc_final: 0.6735 (tp) REVERT: C 58 TRP cc_start: 0.7917 (m100) cc_final: 0.6937 (m100) REVERT: C 112 MET cc_start: 0.8345 (mtt) cc_final: 0.8068 (mtm) REVERT: C 208 ASP cc_start: 0.7843 (m-30) cc_final: 0.7614 (p0) REVERT: C 259 LEU cc_start: 0.8088 (mt) cc_final: 0.7878 (mp) REVERT: C 351 ARG cc_start: 0.6091 (ttp80) cc_final: 0.5855 (ttp-110) REVERT: C 470 ILE cc_start: 0.5569 (mm) cc_final: 0.5142 (mm) REVERT: D 37 TYR cc_start: 0.7590 (m-80) cc_final: 0.7357 (m-10) REVERT: D 42 LEU cc_start: 0.8168 (tp) cc_final: 0.7904 (tt) REVERT: D 114 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7612 (tp30) REVERT: D 179 MET cc_start: 0.7569 (ptt) cc_final: 0.7235 (ptt) REVERT: D 291 MET cc_start: 0.7987 (mmp) cc_final: 0.6941 (ttt) REVERT: D 301 ASN cc_start: 0.8822 (t0) cc_final: 0.8571 (t0) REVERT: D 376 TYR cc_start: 0.7248 (t80) cc_final: 0.6501 (t80) REVERT: D 449 TRP cc_start: 0.2893 (m-10) cc_final: 0.2639 (m-10) REVERT: E 61 VAL cc_start: 0.8944 (t) cc_final: 0.8714 (t) REVERT: E 108 GLU cc_start: 0.7175 (pt0) cc_final: 0.6962 (tp30) REVERT: E 357 MET cc_start: 0.6870 (tpt) cc_final: 0.6643 (tpt) REVERT: E 470 ILE cc_start: 0.5774 (mm) cc_final: 0.5386 (mm) REVERT: F 112 MET cc_start: 0.5833 (mtm) cc_final: 0.5278 (tpp) REVERT: F 216 HIS cc_start: 0.7595 (t-90) cc_final: 0.7256 (t-170) REVERT: F 235 MET cc_start: 0.7561 (ptp) cc_final: 0.7115 (ptt) REVERT: F 291 MET cc_start: 0.8066 (mmp) cc_final: 0.7593 (mmm) REVERT: F 301 ASN cc_start: 0.9020 (t0) cc_final: 0.8681 (t0) REVERT: G 39 ILE cc_start: 0.9066 (tp) cc_final: 0.8733 (tt) REVERT: G 273 LEU cc_start: 0.8122 (tp) cc_final: 0.7742 (tp) REVERT: G 357 MET cc_start: 0.6798 (tpt) cc_final: 0.6397 (tpt) REVERT: G 465 MET cc_start: 0.4657 (mmt) cc_final: 0.4197 (mmt) REVERT: H 54 TYR cc_start: 0.5984 (m-10) cc_final: 0.5751 (m-10) REVERT: H 106 VAL cc_start: 0.7485 (t) cc_final: 0.7268 (t) REVERT: H 112 MET cc_start: 0.6053 (mtm) cc_final: 0.5665 (tpp) REVERT: H 132 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8294 (tp30) REVERT: H 137 LEU cc_start: 0.7769 (tp) cc_final: 0.7345 (tp) REVERT: H 301 ASN cc_start: 0.8823 (t0) cc_final: 0.8250 (p0) REVERT: H 408 LEU cc_start: 0.8055 (mp) cc_final: 0.6698 (tp) REVERT: I 208 ASP cc_start: 0.7835 (m-30) cc_final: 0.7602 (p0) REVERT: J 256 MET cc_start: 0.7063 (tmm) cc_final: 0.6806 (tpp) REVERT: J 291 MET cc_start: 0.7959 (mmp) cc_final: 0.6885 (ttt) REVERT: J 376 TYR cc_start: 0.7114 (t80) cc_final: 0.6464 (t80) REVERT: K 108 GLU cc_start: 0.7182 (pt0) cc_final: 0.6966 (tp30) REVERT: K 138 VAL cc_start: 0.8195 (p) cc_final: 0.7961 (p) REVERT: K 279 LEU cc_start: 0.9285 (tp) cc_final: 0.9055 (tt) REVERT: K 381 LEU cc_start: 0.7941 (tp) cc_final: 0.7707 (pp) REVERT: L 235 MET cc_start: 0.7543 (ptp) cc_final: 0.7076 (ptt) REVERT: L 291 MET cc_start: 0.8242 (mmp) cc_final: 0.7606 (mmm) REVERT: L 301 ASN cc_start: 0.8927 (t0) cc_final: 0.8633 (t0) REVERT: L 381 LEU cc_start: 0.7674 (pp) cc_final: 0.6992 (pp) outliers start: 2 outliers final: 1 residues processed: 779 average time/residue: 0.5783 time to fit residues: 753.1838 Evaluate side-chains 557 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 556 time to evaluate : 4.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 514 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 304 optimal weight: 5.9990 chunk 390 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 449 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 chunk 532 optimal weight: 7.9990 chunk 332 optimal weight: 8.9990 chunk 324 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN E 335 GLN E 409 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 GLN G 68 ASN G 124 ASN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 409 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.6877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 44736 Z= 0.202 Angle : 0.642 11.140 60588 Z= 0.327 Chirality : 0.043 0.186 6876 Planarity : 0.004 0.043 7932 Dihedral : 4.509 22.647 6204 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.02 % Allowed : 1.77 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 5580 helix: 0.83 (0.10), residues: 2604 sheet: -1.04 (0.18), residues: 792 loop : -1.70 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP J 449 HIS 0.007 0.002 HIS E 216 PHE 0.021 0.002 PHE B 131 TYR 0.026 0.001 TYR I 91 ARG 0.009 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 746 time to evaluate : 5.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9071 (tp) cc_final: 0.8658 (tt) REVERT: A 273 LEU cc_start: 0.8019 (tp) cc_final: 0.7701 (tp) REVERT: A 465 MET cc_start: 0.4363 (mmt) cc_final: 0.3453 (mmm) REVERT: B 54 TYR cc_start: 0.5968 (m-10) cc_final: 0.5743 (m-10) REVERT: B 289 MET cc_start: 0.8238 (ttm) cc_final: 0.7951 (ttm) REVERT: B 291 MET cc_start: 0.8290 (mmp) cc_final: 0.7709 (mmm) REVERT: B 301 ASN cc_start: 0.8854 (t0) cc_final: 0.8622 (t0) REVERT: B 376 TYR cc_start: 0.6125 (t80) cc_final: 0.5688 (t80) REVERT: B 408 LEU cc_start: 0.8071 (mp) cc_final: 0.6878 (tp) REVERT: C 58 TRP cc_start: 0.7339 (m100) cc_final: 0.6803 (m100) REVERT: C 112 MET cc_start: 0.8251 (mtt) cc_final: 0.7870 (mtm) REVERT: C 208 ASP cc_start: 0.7933 (m-30) cc_final: 0.7642 (p0) REVERT: C 470 ILE cc_start: 0.5620 (mm) cc_final: 0.5225 (mm) REVERT: D 37 TYR cc_start: 0.7442 (m-80) cc_final: 0.7225 (m-10) REVERT: D 78 PHE cc_start: 0.8419 (m-10) cc_final: 0.8126 (m-10) REVERT: D 114 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7804 (tp30) REVERT: D 179 MET cc_start: 0.7458 (ptt) cc_final: 0.7164 (ptt) REVERT: D 291 MET cc_start: 0.7912 (mmp) cc_final: 0.6874 (ttt) REVERT: D 301 ASN cc_start: 0.8788 (t0) cc_final: 0.8474 (t0) REVERT: D 376 TYR cc_start: 0.7076 (t80) cc_final: 0.6460 (t80) REVERT: D 449 TRP cc_start: 0.2857 (m-10) cc_final: 0.2562 (m-10) REVERT: D 472 ASN cc_start: 0.7457 (t0) cc_final: 0.6858 (m-40) REVERT: E 74 MET cc_start: 0.8279 (tpp) cc_final: 0.7341 (tpp) REVERT: E 108 GLU cc_start: 0.7254 (pt0) cc_final: 0.6820 (tp30) REVERT: E 279 LEU cc_start: 0.9150 (tp) cc_final: 0.8818 (tt) REVERT: E 470 ILE cc_start: 0.5494 (mm) cc_final: 0.5153 (mm) REVERT: F 112 MET cc_start: 0.5780 (mtm) cc_final: 0.5275 (tpp) REVERT: F 216 HIS cc_start: 0.7512 (t-90) cc_final: 0.7156 (t-170) REVERT: F 291 MET cc_start: 0.8016 (mmp) cc_final: 0.7392 (ttt) REVERT: F 301 ASN cc_start: 0.8951 (t0) cc_final: 0.8603 (t0) REVERT: F 455 MET cc_start: 0.3810 (tpp) cc_final: 0.3423 (tpt) REVERT: G 39 ILE cc_start: 0.9081 (tp) cc_final: 0.8679 (tt) REVERT: G 273 LEU cc_start: 0.8105 (tp) cc_final: 0.7727 (tp) REVERT: G 357 MET cc_start: 0.6929 (tpt) cc_final: 0.6502 (tpt) REVERT: G 465 MET cc_start: 0.4777 (mmt) cc_final: 0.3982 (mmm) REVERT: G 470 ILE cc_start: 0.5602 (mm) cc_final: 0.5301 (mm) REVERT: H 132 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8258 (tp30) REVERT: H 301 ASN cc_start: 0.8825 (t0) cc_final: 0.8227 (p0) REVERT: H 408 LEU cc_start: 0.8041 (mp) cc_final: 0.6850 (tp) REVERT: I 58 TRP cc_start: 0.7287 (m100) cc_final: 0.6779 (m100) REVERT: I 208 ASP cc_start: 0.7967 (m-30) cc_final: 0.7611 (p0) REVERT: J 291 MET cc_start: 0.7875 (mmp) cc_final: 0.6804 (ttt) REVERT: J 301 ASN cc_start: 0.8708 (t0) cc_final: 0.8466 (t0) REVERT: J 376 TYR cc_start: 0.7070 (t80) cc_final: 0.6567 (t80) REVERT: K 74 MET cc_start: 0.8297 (tpp) cc_final: 0.7370 (tpp) REVERT: K 108 GLU cc_start: 0.7271 (pt0) cc_final: 0.6827 (tp30) REVERT: K 134 LEU cc_start: 0.8060 (tp) cc_final: 0.7570 (tt) REVERT: K 138 VAL cc_start: 0.8041 (p) cc_final: 0.7818 (p) REVERT: K 465 MET cc_start: 0.3511 (mmt) cc_final: 0.3248 (mpp) REVERT: L 260 ASP cc_start: 0.5796 (p0) cc_final: 0.5532 (p0) REVERT: L 291 MET cc_start: 0.8171 (mmp) cc_final: 0.7344 (ttt) REVERT: L 301 ASN cc_start: 0.8834 (t0) cc_final: 0.8526 (t0) REVERT: L 455 MET cc_start: 0.3896 (tpp) cc_final: 0.3471 (tpt) outliers start: 1 outliers final: 0 residues processed: 747 average time/residue: 0.5420 time to fit residues: 685.1421 Evaluate side-chains 535 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 5.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 329 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 317 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 338 optimal weight: 6.9990 chunk 362 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 418 optimal weight: 0.0060 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 178 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 178 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 HIS K 32 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.7087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44736 Z= 0.193 Angle : 0.647 14.917 60588 Z= 0.327 Chirality : 0.043 0.180 6876 Planarity : 0.004 0.042 7932 Dihedral : 4.353 22.436 6204 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 5580 helix: 0.96 (0.10), residues: 2604 sheet: -1.08 (0.16), residues: 912 loop : -1.70 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP J 449 HIS 0.007 0.002 HIS A 216 PHE 0.021 0.001 PHE H 131 TYR 0.019 0.001 TYR L 268 ARG 0.009 0.000 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 754 time to evaluate : 4.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8996 (tp) cc_final: 0.8593 (tt) REVERT: A 273 LEU cc_start: 0.8019 (tp) cc_final: 0.7672 (tp) REVERT: A 289 MET cc_start: 0.7380 (ttm) cc_final: 0.7161 (ttm) REVERT: A 465 MET cc_start: 0.4449 (mmt) cc_final: 0.3598 (mmm) REVERT: B 54 TYR cc_start: 0.5944 (m-10) cc_final: 0.5731 (m-10) REVERT: B 114 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7998 (pp20) REVERT: B 235 MET cc_start: 0.7343 (ptp) cc_final: 0.6839 (ptt) REVERT: B 289 MET cc_start: 0.8265 (ttm) cc_final: 0.7944 (ttm) REVERT: B 291 MET cc_start: 0.8217 (mmp) cc_final: 0.7630 (mmt) REVERT: B 301 ASN cc_start: 0.8925 (t0) cc_final: 0.8374 (p0) REVERT: B 326 ASP cc_start: 0.8302 (m-30) cc_final: 0.8090 (m-30) REVERT: B 376 TYR cc_start: 0.6396 (t80) cc_final: 0.6021 (t80) REVERT: B 408 LEU cc_start: 0.8138 (mp) cc_final: 0.6898 (tp) REVERT: C 68 ASN cc_start: 0.8862 (t0) cc_final: 0.8623 (t0) REVERT: C 112 MET cc_start: 0.8188 (mtt) cc_final: 0.7913 (mtm) REVERT: C 383 ASP cc_start: 0.6660 (t0) cc_final: 0.5986 (m-30) REVERT: C 470 ILE cc_start: 0.5434 (mm) cc_final: 0.5061 (mm) REVERT: D 37 TYR cc_start: 0.7372 (m-80) cc_final: 0.7164 (m-10) REVERT: D 114 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7796 (tp30) REVERT: D 291 MET cc_start: 0.7865 (mmp) cc_final: 0.6798 (ttt) REVERT: D 301 ASN cc_start: 0.8820 (t0) cc_final: 0.8600 (t0) REVERT: D 376 TYR cc_start: 0.7010 (t80) cc_final: 0.6445 (t80) REVERT: E 74 MET cc_start: 0.8288 (tpp) cc_final: 0.7380 (tpp) REVERT: E 118 MET cc_start: 0.7610 (mmm) cc_final: 0.7330 (mmt) REVERT: E 179 MET cc_start: 0.6854 (ptt) cc_final: 0.6626 (ptp) REVERT: E 279 LEU cc_start: 0.9155 (tp) cc_final: 0.8807 (tt) REVERT: E 358 LEU cc_start: 0.6824 (tp) cc_final: 0.6374 (tt) REVERT: E 470 ILE cc_start: 0.5263 (mm) cc_final: 0.4892 (mm) REVERT: F 291 MET cc_start: 0.8049 (mmp) cc_final: 0.7382 (ttt) REVERT: F 301 ASN cc_start: 0.9011 (t0) cc_final: 0.8662 (t0) REVERT: G 39 ILE cc_start: 0.9024 (tp) cc_final: 0.8691 (tt) REVERT: G 273 LEU cc_start: 0.8119 (tp) cc_final: 0.7784 (tp) REVERT: G 465 MET cc_start: 0.4683 (mmt) cc_final: 0.3862 (mmm) REVERT: G 470 ILE cc_start: 0.5733 (mm) cc_final: 0.5477 (mm) REVERT: H 132 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8219 (tp30) REVERT: H 301 ASN cc_start: 0.8891 (t0) cc_final: 0.8343 (p0) REVERT: H 408 LEU cc_start: 0.8102 (mp) cc_final: 0.6860 (tp) REVERT: I 58 TRP cc_start: 0.7071 (m100) cc_final: 0.6801 (m100) REVERT: I 208 ASP cc_start: 0.7983 (m-30) cc_final: 0.7600 (p0) REVERT: I 465 MET cc_start: 0.3125 (mpp) cc_final: 0.2877 (mpp) REVERT: I 470 ILE cc_start: 0.5304 (mm) cc_final: 0.4917 (mm) REVERT: J 291 MET cc_start: 0.7828 (mmp) cc_final: 0.6740 (ttt) REVERT: J 301 ASN cc_start: 0.8700 (t0) cc_final: 0.8443 (t0) REVERT: J 376 TYR cc_start: 0.6976 (t80) cc_final: 0.6281 (t80) REVERT: K 74 MET cc_start: 0.8259 (tpp) cc_final: 0.7375 (tpp) REVERT: K 118 MET cc_start: 0.7630 (mmm) cc_final: 0.7333 (mmt) REVERT: K 134 LEU cc_start: 0.8079 (tp) cc_final: 0.7680 (tt) REVERT: K 465 MET cc_start: 0.3323 (mmt) cc_final: 0.3058 (mpp) REVERT: K 470 ILE cc_start: 0.5294 (mm) cc_final: 0.4946 (mm) REVERT: L 112 MET cc_start: 0.6599 (ptp) cc_final: 0.5039 (tpp) REVERT: L 260 ASP cc_start: 0.5762 (p0) cc_final: 0.5426 (p0) REVERT: L 291 MET cc_start: 0.8076 (mmp) cc_final: 0.7196 (ttt) REVERT: L 301 ASN cc_start: 0.8876 (t0) cc_final: 0.8559 (t0) REVERT: L 385 LEU cc_start: 0.7397 (mp) cc_final: 0.7080 (mp) outliers start: 0 outliers final: 0 residues processed: 754 average time/residue: 0.5402 time to fit residues: 690.0717 Evaluate side-chains 532 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 4.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 483 optimal weight: 20.0000 chunk 509 optimal weight: 5.9990 chunk 465 optimal weight: 5.9990 chunk 495 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 389 optimal weight: 6.9990 chunk 152 optimal weight: 0.1980 chunk 448 optimal weight: 1.9990 chunk 468 optimal weight: 10.0000 chunk 494 optimal weight: 4.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN E 409 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 124 ASN G 409 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 281 ASN ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 409 GLN K 409 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 44736 Z= 0.291 Angle : 0.703 9.850 60588 Z= 0.362 Chirality : 0.045 0.217 6876 Planarity : 0.005 0.041 7932 Dihedral : 4.701 22.211 6204 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.04 % Allowed : 0.78 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.11), residues: 5580 helix: 0.72 (0.10), residues: 2604 sheet: -1.11 (0.16), residues: 912 loop : -1.70 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 58 HIS 0.009 0.004 HIS K 216 PHE 0.026 0.002 PHE B 131 TYR 0.025 0.002 TYR C 91 ARG 0.009 0.001 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 699 time to evaluate : 4.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.9064 (tp) cc_final: 0.8698 (tt) REVERT: A 273 LEU cc_start: 0.8059 (tp) cc_final: 0.7835 (tp) REVERT: A 465 MET cc_start: 0.4547 (mmt) cc_final: 0.3679 (mmm) REVERT: A 470 ILE cc_start: 0.5887 (mm) cc_final: 0.5657 (mm) REVERT: B 54 TYR cc_start: 0.6182 (m-10) cc_final: 0.5797 (m-10) REVERT: B 256 MET cc_start: 0.7335 (tmm) cc_final: 0.6978 (tpp) REVERT: B 301 ASN cc_start: 0.8856 (t0) cc_final: 0.8617 (t0) REVERT: B 408 LEU cc_start: 0.8161 (mp) cc_final: 0.6957 (tp) REVERT: C 112 MET cc_start: 0.8317 (mtt) cc_final: 0.7953 (mtm) REVERT: C 381 LEU cc_start: 0.8204 (tp) cc_final: 0.7979 (tp) REVERT: D 37 TYR cc_start: 0.7437 (m-80) cc_final: 0.7096 (m-10) REVERT: D 78 PHE cc_start: 0.8621 (m-10) cc_final: 0.8413 (m-10) REVERT: D 84 MET cc_start: 0.5629 (pmm) cc_final: 0.5140 (ppp) REVERT: D 291 MET cc_start: 0.8057 (mmp) cc_final: 0.6912 (ttt) REVERT: D 376 TYR cc_start: 0.6963 (t80) cc_final: 0.6496 (t80) REVERT: D 472 ASN cc_start: 0.7530 (t0) cc_final: 0.6930 (m-40) REVERT: E 74 MET cc_start: 0.8301 (tpp) cc_final: 0.7360 (tpp) REVERT: E 108 GLU cc_start: 0.7289 (pt0) cc_final: 0.6805 (tp30) REVERT: E 112 MET cc_start: 0.8288 (mtm) cc_final: 0.8016 (mtm) REVERT: E 275 ASP cc_start: 0.8525 (m-30) cc_final: 0.7981 (m-30) REVERT: E 351 ARG cc_start: 0.6948 (ttp-110) cc_final: 0.6225 (ttm170) REVERT: E 465 MET cc_start: 0.3944 (mpp) cc_final: 0.2854 (mpp) REVERT: E 470 ILE cc_start: 0.5259 (mm) cc_final: 0.4899 (mm) REVERT: F 291 MET cc_start: 0.8166 (mmp) cc_final: 0.7454 (ttt) REVERT: F 301 ASN cc_start: 0.9030 (t0) cc_final: 0.8653 (t0) REVERT: G 39 ILE cc_start: 0.9129 (tp) cc_final: 0.8775 (tt) REVERT: G 137 LEU cc_start: 0.7954 (tt) cc_final: 0.7704 (tt) REVERT: G 273 LEU cc_start: 0.8295 (tp) cc_final: 0.7846 (tp) REVERT: G 465 MET cc_start: 0.4738 (mmt) cc_final: 0.3863 (mmm) REVERT: G 470 ILE cc_start: 0.5923 (mm) cc_final: 0.5654 (mm) REVERT: H 54 TYR cc_start: 0.6230 (m-10) cc_final: 0.5918 (m-10) REVERT: H 114 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7770 (tm-30) REVERT: H 132 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8315 (tp30) REVERT: H 256 MET cc_start: 0.7327 (tmm) cc_final: 0.6854 (tpp) REVERT: H 301 ASN cc_start: 0.8881 (t0) cc_final: 0.8233 (p0) REVERT: H 326 ASP cc_start: 0.8476 (m-30) cc_final: 0.8212 (m-30) REVERT: H 408 LEU cc_start: 0.8094 (mp) cc_final: 0.6873 (tp) REVERT: I 470 ILE cc_start: 0.5508 (mm) cc_final: 0.5098 (mm) REVERT: J 78 PHE cc_start: 0.7887 (m-10) cc_final: 0.7647 (m-10) REVERT: J 179 MET cc_start: 0.7596 (ptt) cc_final: 0.7118 (ptt) REVERT: J 291 MET cc_start: 0.7980 (mmp) cc_final: 0.6847 (ttt) REVERT: J 301 ASN cc_start: 0.8756 (t0) cc_final: 0.8553 (t0) REVERT: J 376 TYR cc_start: 0.6971 (t80) cc_final: 0.6520 (t80) REVERT: K 74 MET cc_start: 0.8348 (tpp) cc_final: 0.7477 (tpp) REVERT: K 108 GLU cc_start: 0.7304 (pt0) cc_final: 0.6812 (tp30) REVERT: K 112 MET cc_start: 0.8234 (mtm) cc_final: 0.7965 (mtm) REVERT: K 134 LEU cc_start: 0.8112 (tp) cc_final: 0.7705 (tt) REVERT: K 275 ASP cc_start: 0.8606 (m-30) cc_final: 0.8319 (m-30) REVERT: K 465 MET cc_start: 0.3271 (mmt) cc_final: 0.2874 (mpp) REVERT: K 470 ILE cc_start: 0.5214 (mm) cc_final: 0.4962 (mm) REVERT: L 218 TYR cc_start: 0.4945 (p90) cc_final: 0.4716 (p90) REVERT: L 260 ASP cc_start: 0.6110 (p0) cc_final: 0.5860 (p0) REVERT: L 291 MET cc_start: 0.8351 (mmp) cc_final: 0.7657 (mmm) REVERT: L 301 ASN cc_start: 0.8965 (t0) cc_final: 0.8665 (t0) outliers start: 2 outliers final: 0 residues processed: 700 average time/residue: 0.5262 time to fit residues: 626.5674 Evaluate side-chains 509 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 5.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 325 optimal weight: 0.9990 chunk 524 optimal weight: 20.0000 chunk 319 optimal weight: 0.0170 chunk 248 optimal weight: 2.9990 chunk 364 optimal weight: 6.9990 chunk 549 optimal weight: 4.9990 chunk 506 optimal weight: 0.3980 chunk 437 optimal weight: 2.9990 chunk 45 optimal weight: 0.0000 chunk 338 optimal weight: 1.9990 chunk 268 optimal weight: 6.9990 overall best weight: 0.6826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN C 409 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 124 ASN G 178 GLN G 409 GLN ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN I 409 GLN J 472 ASN K 409 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 44736 Z= 0.190 Angle : 0.654 11.535 60588 Z= 0.331 Chirality : 0.043 0.167 6876 Planarity : 0.004 0.041 7932 Dihedral : 4.319 21.375 6204 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.02 % Allowed : 0.27 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 5580 helix: 0.94 (0.10), residues: 2604 sheet: -1.04 (0.16), residues: 912 loop : -1.71 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 58 HIS 0.005 0.002 HIS I 216 PHE 0.021 0.001 PHE B 131 TYR 0.031 0.001 TYR I 91 ARG 0.008 0.000 ARG K 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11160 Ramachandran restraints generated. 5580 Oldfield, 0 Emsley, 5580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 725 time to evaluate : 5.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.8786 (tp) cc_final: 0.8409 (tt) REVERT: A 273 LEU cc_start: 0.8071 (tp) cc_final: 0.7734 (tp) REVERT: A 289 MET cc_start: 0.7403 (ttm) cc_final: 0.7189 (ttm) REVERT: A 384 THR cc_start: 0.7667 (p) cc_final: 0.7437 (p) REVERT: A 465 MET cc_start: 0.4525 (mmt) cc_final: 0.3708 (mmm) REVERT: B 112 MET cc_start: 0.5572 (tpt) cc_final: 0.5161 (tpp) REVERT: B 235 MET cc_start: 0.7262 (ptp) cc_final: 0.6761 (ptt) REVERT: B 256 MET cc_start: 0.7044 (tmm) cc_final: 0.6597 (tpp) REVERT: B 268 TYR cc_start: 0.7840 (t80) cc_final: 0.7585 (t80) REVERT: B 291 MET cc_start: 0.7848 (mmp) cc_final: 0.7377 (ttt) REVERT: B 301 ASN cc_start: 0.8919 (t0) cc_final: 0.8409 (p0) REVERT: B 376 TYR cc_start: 0.6022 (t80) cc_final: 0.5633 (t80) REVERT: B 455 MET cc_start: 0.5824 (tpp) cc_final: 0.5296 (tpp) REVERT: C 112 MET cc_start: 0.8200 (mtt) cc_final: 0.7953 (mtm) REVERT: C 383 ASP cc_start: 0.6758 (t0) cc_final: 0.6266 (m-30) REVERT: C 470 ILE cc_start: 0.5358 (mm) cc_final: 0.5019 (mm) REVERT: D 37 TYR cc_start: 0.7250 (m-80) cc_final: 0.6975 (m-10) REVERT: D 84 MET cc_start: 0.5549 (pmm) cc_final: 0.5198 (ppp) REVERT: D 179 MET cc_start: 0.7570 (ptp) cc_final: 0.7303 (ptt) REVERT: D 291 MET cc_start: 0.7719 (mmp) cc_final: 0.6784 (ttt) REVERT: D 301 ASN cc_start: 0.8800 (t0) cc_final: 0.8528 (t0) REVERT: D 376 TYR cc_start: 0.7022 (t80) cc_final: 0.6606 (t80) REVERT: E 61 VAL cc_start: 0.8882 (t) cc_final: 0.8555 (t) REVERT: E 74 MET cc_start: 0.8258 (tpp) cc_final: 0.7391 (tpp) REVERT: E 108 GLU cc_start: 0.7262 (pt0) cc_final: 0.6797 (tp30) REVERT: E 179 MET cc_start: 0.6984 (ptt) cc_final: 0.6766 (ptp) REVERT: E 279 LEU cc_start: 0.9166 (tp) cc_final: 0.8776 (tt) REVERT: E 465 MET cc_start: 0.4009 (mpp) cc_final: 0.3108 (mpp) REVERT: E 470 ILE cc_start: 0.5056 (mm) cc_final: 0.4774 (mm) REVERT: F 291 MET cc_start: 0.7989 (mmp) cc_final: 0.7242 (ttt) REVERT: F 301 ASN cc_start: 0.8969 (t0) cc_final: 0.8610 (t0) REVERT: G 39 ILE cc_start: 0.8992 (tp) cc_final: 0.8528 (tt) REVERT: G 134 LEU cc_start: 0.8275 (tp) cc_final: 0.8068 (tp) REVERT: G 146 TYR cc_start: 0.7732 (t80) cc_final: 0.7468 (t80) REVERT: G 273 LEU cc_start: 0.8236 (tp) cc_final: 0.7721 (tp) REVERT: G 465 MET cc_start: 0.4596 (mmt) cc_final: 0.3886 (mmm) REVERT: H 54 TYR cc_start: 0.6135 (m-10) cc_final: 0.5842 (m-10) REVERT: H 114 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7864 (tm-30) REVERT: H 118 MET cc_start: 0.7123 (mtt) cc_final: 0.6462 (mtt) REVERT: H 132 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8202 (tp30) REVERT: H 235 MET cc_start: 0.7454 (ptp) cc_final: 0.7199 (ptt) REVERT: H 256 MET cc_start: 0.6886 (tmm) cc_final: 0.6611 (tpp) REVERT: H 268 TYR cc_start: 0.7720 (t80) cc_final: 0.7489 (t80) REVERT: H 301 ASN cc_start: 0.8888 (t0) cc_final: 0.8374 (p0) REVERT: H 408 LEU cc_start: 0.8040 (mp) cc_final: 0.6817 (tp) REVERT: I 58 TRP cc_start: 0.7093 (m100) cc_final: 0.6834 (m100) REVERT: J 192 GLU cc_start: 0.4322 (tp30) cc_final: 0.4091 (tp30) REVERT: J 291 MET cc_start: 0.7723 (mmp) cc_final: 0.6597 (ttt) REVERT: J 301 ASN cc_start: 0.8636 (t0) cc_final: 0.8431 (t0) REVERT: J 376 TYR cc_start: 0.6906 (t80) cc_final: 0.6471 (t80) REVERT: K 74 MET cc_start: 0.8252 (tpp) cc_final: 0.7439 (tpp) REVERT: K 108 GLU cc_start: 0.7287 (pt0) cc_final: 0.6815 (tp30) REVERT: K 134 LEU cc_start: 0.8104 (tp) cc_final: 0.7695 (tt) REVERT: K 465 MET cc_start: 0.3376 (mmt) cc_final: 0.2961 (mpp) REVERT: K 470 ILE cc_start: 0.4844 (mm) cc_final: 0.4551 (mm) REVERT: L 260 ASP cc_start: 0.5582 (p0) cc_final: 0.5259 (p0) REVERT: L 291 MET cc_start: 0.8042 (mmp) cc_final: 0.7295 (ttt) REVERT: L 301 ASN cc_start: 0.8873 (t0) cc_final: 0.8569 (t0) outliers start: 1 outliers final: 0 residues processed: 726 average time/residue: 0.5305 time to fit residues: 650.9132 Evaluate side-chains 535 residues out of total 4752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 5.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 347 optimal weight: 6.9990 chunk 466 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 403 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 438 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 450 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN ** E 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 ASN ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN ** K 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.141408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.131213 restraints weight = 101594.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.130841 restraints weight = 107778.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130245 restraints weight = 88842.798| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 580 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44736 Z= 0.224 Angle : 0.662 8.303 60588 Z= 0.338 Chirality : 0.043 0.163 6876 Planarity : 0.004 0.056 7932 Dihedral : 4.348 21.122 6204 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.11), residues: 5580 helix: 0.93 (0.10), residues: 2604 sheet: -0.87 (0.16), residues: 888 loop : -1.69 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 58 HIS 0.007 0.003 HIS E 216 PHE 0.029 0.002 PHE A 329 TYR 0.028 0.002 TYR I 91 ARG 0.009 0.001 ARG E 64 =============================================================================== Job complete usr+sys time: 12758.17 seconds wall clock time: 230 minutes 53.82 seconds (13853.82 seconds total)