Starting phenix.real_space_refine on Fri Aug 7 02:49:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31es_58347/08_2026/31es_58347.cif Found real_map, /net/cci-nas-00/data/ceres_data/31es_58347/08_2026/31es_58347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/31es_58347/08_2026/31es_58347.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31es_58347/08_2026/31es_58347.map" model { file = "/net/cci-nas-00/data/ceres_data/31es_58347/08_2026/31es_58347.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31es_58347/08_2026/31es_58347.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 0.138 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 54 5.16 5 C 11736 2.51 5 N 3006 2.21 5 O 3726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18522 Number of models: 1 Model: "" Number of chains: 1 Chain: "G" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1029 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Restraints were copied for chains: A, B, C, D, E, F, H, I, J, K, L, M, N, O, P, Q, R Time building chain proxies: 1.57, per 1000 atoms: 0.08 Number of scatterers: 18522 At special positions: 0 Unit cell: (100.7, 101.76, 143.1, 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 54 16.00 O 3726 8.00 N 3006 7.00 C 11736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 804.3 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 54 sheets defined 11.5% alpha, 71.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'G' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE G 12 " --> pdb=" O GLU G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 16 No H-bonds generated for 'chain 'G' and resid 14 through 16' Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.523A pdb=" N PHE A 12 " --> pdb=" O GLU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.523A pdb=" N PHE B 12 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE C 12 " --> pdb=" O GLU C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 16 No H-bonds generated for 'chain 'C' and resid 14 through 16' Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'D' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE D 12 " --> pdb=" O GLU D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 16 No H-bonds generated for 'chain 'D' and resid 14 through 16' Processing helix chain 'D' and resid 72 through 78 Processing helix chain 'E' and resid 8 through 12 removed outlier: 3.523A pdb=" N PHE E 12 " --> pdb=" O GLU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 72 through 78 Processing helix chain 'F' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE F 12 " --> pdb=" O GLU F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 72 through 78 Processing helix chain 'H' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE H 12 " --> pdb=" O GLU H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 16 No H-bonds generated for 'chain 'H' and resid 14 through 16' Processing helix chain 'H' and resid 72 through 78 Processing helix chain 'I' and resid 8 through 12 removed outlier: 3.523A pdb=" N PHE I 12 " --> pdb=" O GLU I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 16 No H-bonds generated for 'chain 'I' and resid 14 through 16' Processing helix chain 'I' and resid 72 through 78 Processing helix chain 'J' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE J 12 " --> pdb=" O GLU J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 72 through 78 Processing helix chain 'K' and resid 8 through 12 removed outlier: 3.523A pdb=" N PHE K 12 " --> pdb=" O GLU K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 16 No H-bonds generated for 'chain 'K' and resid 14 through 16' Processing helix chain 'K' and resid 72 through 78 Processing helix chain 'L' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE L 12 " --> pdb=" O GLU L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 16 No H-bonds generated for 'chain 'L' and resid 14 through 16' Processing helix chain 'L' and resid 72 through 78 Processing helix chain 'M' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE M 12 " --> pdb=" O GLU M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 16 No H-bonds generated for 'chain 'M' and resid 14 through 16' Processing helix chain 'M' and resid 72 through 78 Processing helix chain 'N' and resid 8 through 12 removed outlier: 3.523A pdb=" N PHE N 12 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 16 No H-bonds generated for 'chain 'N' and resid 14 through 16' Processing helix chain 'N' and resid 72 through 78 Processing helix chain 'O' and resid 8 through 12 removed outlier: 3.523A pdb=" N PHE O 12 " --> pdb=" O GLU O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 16 No H-bonds generated for 'chain 'O' and resid 14 through 16' Processing helix chain 'O' and resid 72 through 78 Processing helix chain 'P' and resid 8 through 12 removed outlier: 3.523A pdb=" N PHE P 12 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 16 No H-bonds generated for 'chain 'P' and resid 14 through 16' Processing helix chain 'P' and resid 72 through 78 Processing helix chain 'Q' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE Q 12 " --> pdb=" O GLU Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 16 No H-bonds generated for 'chain 'Q' and resid 14 through 16' Processing helix chain 'Q' and resid 72 through 78 Processing helix chain 'R' and resid 8 through 12 removed outlier: 3.524A pdb=" N PHE R 12 " --> pdb=" O GLU R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 16 No H-bonds generated for 'chain 'R' and resid 14 through 16' Processing helix chain 'R' and resid 72 through 78 Processing sheet with id=AA1, first strand: chain 'G' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE G 20 " --> pdb=" O GLU G 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE G 82 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN G 103 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER G 98 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY G 130 " --> pdb=" O LYS G 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE G 20 " --> pdb=" O GLU G 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE G 82 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN G 103 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS G 60 " --> pdb=" O PHE G 37 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE G 37 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER G 62 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA G 35 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER G 64 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE G 33 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN G 66 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE G 37 " --> pdb=" O PRO A 110 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN G 39 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LYS A 108 " --> pdb=" O GLN G 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 44 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 115 removed outlier: 6.315A pdb=" N LYS G 108 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN R 39 " --> pdb=" O LYS G 108 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE R 37 " --> pdb=" O PRO G 110 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN R 66 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE R 33 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER R 64 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA R 35 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER R 62 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE R 37 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS R 60 " --> pdb=" O PHE R 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN R 103 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE R 82 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE R 20 " --> pdb=" O GLU R 27 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 115 removed outlier: 6.315A pdb=" N LYS G 108 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN R 39 " --> pdb=" O LYS G 108 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE R 37 " --> pdb=" O PRO G 110 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN R 66 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE R 33 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER R 64 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA R 35 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER R 62 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE R 37 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS R 60 " --> pdb=" O PHE R 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER R 98 " --> pdb=" O LEU R 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY R 130 " --> pdb=" O LYS R 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE A 20 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE A 82 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 103 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER A 98 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 130 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE A 20 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE A 82 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 103 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS A 60 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE A 37 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 62 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA A 35 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER A 64 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE A 33 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASN A 66 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE A 37 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLN A 39 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS B 108 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE B 20 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE B 82 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 103 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER B 98 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 130 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE B 20 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE B 82 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 103 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS B 60 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE B 37 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER B 62 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 35 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER B 64 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE B 33 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN B 66 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHE B 37 " --> pdb=" O PRO D 110 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN B 39 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 108 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE C 20 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE C 82 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 103 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER C 98 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY C 130 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE C 20 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE C 82 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN C 103 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS C 60 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE C 37 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER C 62 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA C 35 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER C 64 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE C 33 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN C 66 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N PHE C 37 " --> pdb=" O PRO R 110 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN C 39 " --> pdb=" O LYS R 108 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS R 108 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 44 Processing sheet with id=AB6, first strand: chain 'C' and resid 108 through 115 removed outlier: 6.275A pdb=" N LYS C 108 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLN D 39 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE D 37 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN D 66 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE D 33 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER D 64 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 35 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER D 62 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE D 37 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS D 60 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN D 103 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE D 82 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE D 20 " --> pdb=" O GLU D 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 108 through 115 removed outlier: 6.275A pdb=" N LYS C 108 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLN D 39 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE D 37 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN D 66 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE D 33 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER D 64 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA D 35 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER D 62 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE D 37 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS D 60 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER D 98 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY D 130 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 42 through 44 Processing sheet with id=AB9, first strand: chain 'E' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE E 20 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE E 82 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 103 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER E 98 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY E 130 " --> pdb=" O LYS E 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE E 20 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE E 82 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 103 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS E 60 " --> pdb=" O PHE E 37 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE E 37 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER E 62 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA E 35 " --> pdb=" O SER E 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER E 64 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE E 33 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN E 66 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N PHE E 37 " --> pdb=" O PRO F 110 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLN E 39 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS F 108 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AC3, first strand: chain 'E' and resid 108 through 115 removed outlier: 6.294A pdb=" N LYS E 108 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN J 39 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE J 37 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN J 66 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE J 33 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER J 64 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA J 35 " --> pdb=" O SER J 62 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER J 62 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE J 37 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS J 60 " --> pdb=" O PHE J 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN J 103 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE J 82 " --> pdb=" O ASN J 103 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE J 20 " --> pdb=" O GLU J 27 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 108 through 115 removed outlier: 6.294A pdb=" N LYS E 108 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN J 39 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE J 37 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN J 66 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE J 33 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER J 64 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA J 35 " --> pdb=" O SER J 62 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER J 62 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE J 37 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS J 60 " --> pdb=" O PHE J 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER J 98 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY J 130 " --> pdb=" O LYS J 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE F 20 " --> pdb=" O GLU F 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE F 82 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN F 103 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER F 98 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY F 130 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE F 20 " --> pdb=" O GLU F 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE F 82 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN F 103 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS F 60 " --> pdb=" O PHE F 37 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE F 37 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER F 62 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA F 35 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER F 64 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE F 33 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN F 66 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE F 37 " --> pdb=" O PRO H 110 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLN F 39 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS H 108 " --> pdb=" O GLN F 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 42 through 44 Processing sheet with id=AC8, first strand: chain 'H' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE H 20 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE H 82 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN H 103 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER H 98 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY H 130 " --> pdb=" O LYS H 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE H 20 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE H 82 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN H 103 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS H 60 " --> pdb=" O PHE H 37 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE H 37 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER H 62 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA H 35 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER H 64 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE H 33 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN H 66 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N PHE H 37 " --> pdb=" O PRO I 110 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN H 39 " --> pdb=" O LYS I 108 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS I 108 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 42 through 44 Processing sheet with id=AD2, first strand: chain 'I' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE I 20 " --> pdb=" O GLU I 27 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE I 82 " --> pdb=" O ASN I 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN I 103 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER I 98 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY I 130 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE I 20 " --> pdb=" O GLU I 27 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE I 82 " --> pdb=" O ASN I 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN I 103 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS I 60 " --> pdb=" O PHE I 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE I 37 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER I 62 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA I 35 " --> pdb=" O SER I 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER I 64 " --> pdb=" O ILE I 33 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE I 33 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN I 66 " --> pdb=" O GLU I 31 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE I 37 " --> pdb=" O PRO K 110 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLN I 39 " --> pdb=" O LYS K 108 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS K 108 " --> pdb=" O GLN I 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AD5, first strand: chain 'J' and resid 42 through 44 Processing sheet with id=AD6, first strand: chain 'J' and resid 108 through 115 removed outlier: 6.283A pdb=" N LYS J 108 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN K 39 " --> pdb=" O LYS J 108 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE K 37 " --> pdb=" O PRO J 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN K 66 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE K 33 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER K 64 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA K 35 " --> pdb=" O SER K 62 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER K 62 " --> pdb=" O ALA K 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE K 37 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS K 60 " --> pdb=" O PHE K 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN K 103 " --> pdb=" O PHE K 82 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE K 82 " --> pdb=" O ASN K 103 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE K 20 " --> pdb=" O GLU K 27 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 108 through 115 removed outlier: 6.283A pdb=" N LYS J 108 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN K 39 " --> pdb=" O LYS J 108 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE K 37 " --> pdb=" O PRO J 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN K 66 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE K 33 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER K 64 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA K 35 " --> pdb=" O SER K 62 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER K 62 " --> pdb=" O ALA K 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE K 37 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS K 60 " --> pdb=" O PHE K 37 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER K 98 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY K 130 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 42 through 44 Processing sheet with id=AD9, first strand: chain 'L' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE L 20 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE L 82 " --> pdb=" O ASN L 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN L 103 " --> pdb=" O PHE L 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER L 98 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY L 130 " --> pdb=" O LYS L 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE L 20 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE L 82 " --> pdb=" O ASN L 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN L 103 " --> pdb=" O PHE L 82 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS L 60 " --> pdb=" O PHE L 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE L 37 " --> pdb=" O LYS L 60 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER L 62 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA L 35 " --> pdb=" O SER L 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER L 64 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE L 33 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN L 66 " --> pdb=" O GLU L 31 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE L 37 " --> pdb=" O PRO M 110 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN L 39 " --> pdb=" O LYS M 108 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS M 108 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 42 through 44 Processing sheet with id=AE3, first strand: chain 'L' and resid 108 through 115 removed outlier: 6.321A pdb=" N LYS L 108 " --> pdb=" O GLN P 39 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLN P 39 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE P 37 " --> pdb=" O PRO L 110 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN P 66 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE P 33 " --> pdb=" O SER P 64 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER P 64 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA P 35 " --> pdb=" O SER P 62 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER P 62 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE P 37 " --> pdb=" O LYS P 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS P 60 " --> pdb=" O PHE P 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN P 103 " --> pdb=" O PHE P 82 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE P 82 " --> pdb=" O ASN P 103 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE P 20 " --> pdb=" O GLU P 27 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 108 through 115 removed outlier: 6.321A pdb=" N LYS L 108 " --> pdb=" O GLN P 39 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N GLN P 39 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE P 37 " --> pdb=" O PRO L 110 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN P 66 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE P 33 " --> pdb=" O SER P 64 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER P 64 " --> pdb=" O ILE P 33 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA P 35 " --> pdb=" O SER P 62 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER P 62 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE P 37 " --> pdb=" O LYS P 60 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS P 60 " --> pdb=" O PHE P 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER P 98 " --> pdb=" O LEU P 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY P 130 " --> pdb=" O LYS P 102 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 25 through 27 removed outlier: 4.672A pdb=" N ILE M 20 " --> pdb=" O GLU M 27 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE M 82 " --> pdb=" O ASN M 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN M 103 " --> pdb=" O PHE M 82 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER M 98 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY M 130 " --> pdb=" O LYS M 102 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 25 through 27 removed outlier: 4.672A pdb=" N ILE M 20 " --> pdb=" O GLU M 27 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE M 82 " --> pdb=" O ASN M 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN M 103 " --> pdb=" O PHE M 82 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS M 60 " --> pdb=" O PHE M 37 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE M 37 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER M 62 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA M 35 " --> pdb=" O SER M 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER M 64 " --> pdb=" O ILE M 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE M 33 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN M 66 " --> pdb=" O GLU M 31 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE M 37 " --> pdb=" O PRO N 110 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLN M 39 " --> pdb=" O LYS N 108 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS N 108 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 42 through 44 Processing sheet with id=AE8, first strand: chain 'N' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE N 20 " --> pdb=" O GLU N 27 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE N 82 " --> pdb=" O ASN N 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN N 103 " --> pdb=" O PHE N 82 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER N 98 " --> pdb=" O LEU N 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY N 130 " --> pdb=" O LYS N 102 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE N 20 " --> pdb=" O GLU N 27 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE N 82 " --> pdb=" O ASN N 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN N 103 " --> pdb=" O PHE N 82 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS N 60 " --> pdb=" O PHE N 37 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE N 37 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER N 62 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA N 35 " --> pdb=" O SER N 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER N 64 " --> pdb=" O ILE N 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE N 33 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN N 66 " --> pdb=" O GLU N 31 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N PHE N 37 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN N 39 " --> pdb=" O LYS O 108 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS O 108 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 42 through 44 Processing sheet with id=AF2, first strand: chain 'O' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE O 20 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE O 82 " --> pdb=" O ASN O 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN O 103 " --> pdb=" O PHE O 82 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER O 98 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY O 130 " --> pdb=" O LYS O 102 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 25 through 27 removed outlier: 4.673A pdb=" N ILE O 20 " --> pdb=" O GLU O 27 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE O 82 " --> pdb=" O ASN O 103 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN O 103 " --> pdb=" O PHE O 82 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS O 60 " --> pdb=" O PHE O 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE O 37 " --> pdb=" O LYS O 60 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER O 62 " --> pdb=" O ALA O 35 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA O 35 " --> pdb=" O SER O 62 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER O 64 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE O 33 " --> pdb=" O SER O 64 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN O 66 " --> pdb=" O GLU O 31 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE O 37 " --> pdb=" O PRO Q 110 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLN O 39 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS Q 108 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AF5, first strand: chain 'P' and resid 42 through 44 Processing sheet with id=AF6, first strand: chain 'P' and resid 108 through 115 removed outlier: 6.275A pdb=" N LYS P 108 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN Q 39 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE Q 37 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN Q 66 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE Q 33 " --> pdb=" O SER Q 64 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER Q 64 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA Q 35 " --> pdb=" O SER Q 62 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER Q 62 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE Q 37 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS Q 60 " --> pdb=" O PHE Q 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN Q 103 " --> pdb=" O PHE Q 82 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE Q 82 " --> pdb=" O ASN Q 103 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE Q 20 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 108 through 115 removed outlier: 6.275A pdb=" N LYS P 108 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN Q 39 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE Q 37 " --> pdb=" O PRO P 110 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN Q 66 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE Q 33 " --> pdb=" O SER Q 64 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER Q 64 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA Q 35 " --> pdb=" O SER Q 62 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER Q 62 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE Q 37 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LYS Q 60 " --> pdb=" O PHE Q 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER Q 98 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY Q 130 " --> pdb=" O LYS Q 102 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 42 through 44 Processing sheet with id=AF9, first strand: chain 'R' and resid 42 through 44 966 hydrogen bonds defined for protein. 2646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6120 1.34 - 1.46: 3678 1.46 - 1.57: 8868 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 18738 Sorted by residual: bond pdb=" CG GLU Q 27 " pdb=" CD GLU Q 27 " ideal model delta sigma weight residual 1.516 1.500 0.016 2.50e-02 1.60e+03 3.94e-01 bond pdb=" CG GLU D 27 " pdb=" CD GLU D 27 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.80e-01 bond pdb=" CG GLU O 27 " pdb=" CD GLU O 27 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.62e-01 bond pdb=" CG GLU L 27 " pdb=" CD GLU L 27 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.57e-01 bond pdb=" CG GLU G 27 " pdb=" CD GLU G 27 " ideal model delta sigma weight residual 1.516 1.501 0.015 2.50e-02 1.60e+03 3.50e-01 ... (remaining 18733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 23928 1.06 - 2.12: 966 2.12 - 3.19: 162 3.19 - 4.25: 18 4.25 - 5.31: 18 Bond angle restraints: 25092 Sorted by residual: angle pdb=" C LEU N 47 " pdb=" N GLY N 48 " pdb=" CA GLY N 48 " ideal model delta sigma weight residual 122.46 117.15 5.31 2.70e+00 1.37e-01 3.87e+00 angle pdb=" C LEU C 47 " pdb=" N GLY C 48 " pdb=" CA GLY C 48 " ideal model delta sigma weight residual 122.46 117.18 5.28 2.70e+00 1.37e-01 3.83e+00 angle pdb=" C LEU L 47 " pdb=" N GLY L 48 " pdb=" CA GLY L 48 " ideal model delta sigma weight residual 122.46 117.18 5.28 2.70e+00 1.37e-01 3.83e+00 angle pdb=" C LEU Q 47 " pdb=" N GLY Q 48 " pdb=" CA GLY Q 48 " ideal model delta sigma weight residual 122.46 117.19 5.27 2.70e+00 1.37e-01 3.81e+00 angle pdb=" C LEU M 47 " pdb=" N GLY M 48 " pdb=" CA GLY M 48 " ideal model delta sigma weight residual 122.46 117.19 5.27 2.70e+00 1.37e-01 3.81e+00 ... (remaining 25087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 9522 15.42 - 30.83: 1116 30.83 - 46.25: 558 46.25 - 61.67: 180 61.67 - 77.08: 54 Dihedral angle restraints: 11430 sinusoidal: 4734 harmonic: 6696 Sorted by residual: dihedral pdb=" CB LYS K 121 " pdb=" CG LYS K 121 " pdb=" CD LYS K 121 " pdb=" CE LYS K 121 " ideal model delta sinusoidal sigma weight residual -60.00 -116.07 56.07 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CB LYS M 121 " pdb=" CG LYS M 121 " pdb=" CD LYS M 121 " pdb=" CE LYS M 121 " ideal model delta sinusoidal sigma weight residual -60.00 -116.06 56.06 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CB LYS B 121 " pdb=" CG LYS B 121 " pdb=" CD LYS B 121 " pdb=" CE LYS B 121 " ideal model delta sinusoidal sigma weight residual -60.00 -116.04 56.04 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 11427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1504 0.026 - 0.052: 770 0.052 - 0.078: 291 0.078 - 0.104: 135 0.104 - 0.130: 108 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA ILE C 99 " pdb=" N ILE C 99 " pdb=" C ILE C 99 " pdb=" CB ILE C 99 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE J 99 " pdb=" N ILE J 99 " pdb=" C ILE J 99 " pdb=" CB ILE J 99 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE L 99 " pdb=" N ILE L 99 " pdb=" C ILE L 99 " pdb=" CB ILE L 99 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 2805 not shown) Planarity restraints: 3240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 68 " 0.008 2.00e-02 2.50e+03 7.42e-03 1.10e+00 pdb=" CG TYR R 68 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR R 68 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR R 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 68 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR R 68 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR R 68 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 68 " 0.009 2.00e-02 2.50e+03 7.41e-03 1.10e+00 pdb=" CG TYR N 68 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR N 68 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR N 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR N 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR N 68 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR N 68 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 68 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 68 " 0.008 2.00e-02 2.50e+03 7.36e-03 1.08e+00 pdb=" CG TYR P 68 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR P 68 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR P 68 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR P 68 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR P 68 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR P 68 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR P 68 " 0.000 2.00e-02 2.50e+03 ... (remaining 3237 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 7922 2.94 - 3.43: 16465 3.43 - 3.92: 32449 3.92 - 4.41: 36738 4.41 - 4.90: 62603 Nonbonded interactions: 156177 Sorted by model distance: nonbonded pdb=" O GLY D 15 " pdb=" O LEU H 47 " model vdw 2.452 3.040 nonbonded pdb=" O GLY H 15 " pdb=" O LEU N 47 " model vdw 2.454 3.040 nonbonded pdb=" O GLY B 15 " pdb=" O LEU F 47 " model vdw 2.459 3.040 nonbonded pdb=" O GLY A 15 " pdb=" O LEU E 47 " model vdw 2.461 3.040 nonbonded pdb=" O GLY J 15 " pdb=" O LEU P 47 " model vdw 2.462 3.040 ... (remaining 156172 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: 0.04 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.780 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.003 0.016 18738 Z= 0.144 Angle : 0.526 5.310 25092 Z= 0.288 Chirality : 0.043 0.130 2808 Planarity : 0.002 0.011 3240 Dihedral : 18.112 77.084 7146 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.00 % Allowed : 27.83 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2304 helix: -0.73 (0.36), residues: 126 sheet: 0.47 (0.15), residues: 1242 loop : -0.88 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 100 TYR 0.018 0.002 TYR R 68 PHE 0.012 0.001 PHE O 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (18738) covalent geometry : angle 0.52627 / 0.29 (25092) hydrogen bonds : bond 0.13270 / 8.60 ( 720) hydrogen bonds : angle 7.97813 / 5.31 ( 2646) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 776 time to evaluate : 0.719 Fit side-chains REVERT: G 32 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 32 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 100 ARG cc_start: 0.8995 (ttm-80) cc_final: 0.8605 (ttp-110) REVERT: C 100 ARG cc_start: 0.9036 (ttm-80) cc_final: 0.8828 (ttp-170) REVERT: D 34 LYS cc_start: 0.8363 (mmmt) cc_final: 0.8043 (tptt) REVERT: D 38 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8200 (mp0) REVERT: D 87 ASN cc_start: 0.8915 (m110) cc_final: 0.8670 (m110) REVERT: E 17 ASP cc_start: 0.8314 (m-30) cc_final: 0.8035 (m-30) REVERT: E 34 LYS cc_start: 0.8349 (mmmt) cc_final: 0.8057 (mttm) REVERT: E 42 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8426 (mm-40) REVERT: E 76 LYS cc_start: 0.8355 (mmpt) cc_final: 0.8144 (mttt) REVERT: E 80 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7619 (mtm-85) REVERT: E 105 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8159 (ttm-80) REVERT: F 8 GLU cc_start: 0.6281 (tt0) cc_final: 0.5654 (mm-30) REVERT: F 34 LYS cc_start: 0.8317 (mmmt) cc_final: 0.8006 (mttp) REVERT: F 76 LYS cc_start: 0.8332 (mmpt) cc_final: 0.8024 (mttt) REVERT: F 80 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7495 (mtm-85) REVERT: F 96 TYR cc_start: 0.8915 (p90) cc_final: 0.8680 (p90) REVERT: F 135 ASN cc_start: 0.8800 (t0) cc_final: 0.8510 (t0) REVERT: H 80 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7481 (mtm-85) REVERT: H 108 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8224 (mtmm) REVERT: I 17 ASP cc_start: 0.8333 (m-30) cc_final: 0.8057 (m-30) REVERT: I 34 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8038 (mttm) REVERT: I 42 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8451 (mm-40) REVERT: I 80 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7603 (mtm-85) REVERT: I 103 ASN cc_start: 0.8326 (m-40) cc_final: 0.8124 (m110) REVERT: I 105 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8191 (ttm-80) REVERT: J 80 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: K 8 GLU cc_start: 0.6281 (tt0) cc_final: 0.5658 (mm-30) REVERT: K 34 LYS cc_start: 0.8347 (mmmt) cc_final: 0.8051 (mttp) REVERT: K 39 GLN cc_start: 0.8765 (pp30) cc_final: 0.8559 (pp30) REVERT: K 55 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8034 (mmp-170) REVERT: K 76 LYS cc_start: 0.8333 (mmpt) cc_final: 0.8054 (mttt) REVERT: K 80 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7598 (mtm-85) REVERT: L 11 SER cc_start: 0.8978 (m) cc_final: 0.8758 (t) REVERT: L 80 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: L 103 ASN cc_start: 0.8469 (m-40) cc_final: 0.8268 (m-40) REVERT: M 11 SER cc_start: 0.8864 (m) cc_final: 0.8586 (t) REVERT: M 17 ASP cc_start: 0.8228 (m-30) cc_final: 0.7913 (m-30) REVERT: M 34 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8268 (tptt) REVERT: M 41 GLU cc_start: 0.7730 (tt0) cc_final: 0.7509 (tt0) REVERT: M 80 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7378 (mtm-85) REVERT: M 100 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8542 (ttm110) REVERT: N 8 GLU cc_start: 0.5658 (tt0) cc_final: 0.5385 (tt0) REVERT: N 11 SER cc_start: 0.8867 (m) cc_final: 0.8613 (t) REVERT: N 80 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7546 (mtm-85) REVERT: O 11 SER cc_start: 0.8984 (m) cc_final: 0.8710 (t) REVERT: O 34 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8328 (tptt) REVERT: O 80 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7525 (mtm-85) REVERT: P 8 GLU cc_start: 0.5683 (tt0) cc_final: 0.5352 (tt0) REVERT: P 11 SER cc_start: 0.8911 (m) cc_final: 0.8663 (t) REVERT: P 80 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7566 (mtm-85) REVERT: Q 11 SER cc_start: 0.8921 (m) cc_final: 0.8673 (t) REVERT: Q 17 ASP cc_start: 0.8160 (m-30) cc_final: 0.7872 (m-30) REVERT: Q 29 TYR cc_start: 0.9042 (m-80) cc_final: 0.8836 (m-80) REVERT: Q 34 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8261 (tptt) REVERT: Q 80 ARG cc_start: 0.7722 (mtm-85) cc_final: 0.7396 (mtm-85) REVERT: R 32 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7635 (tm-30) REVERT: R 41 GLU cc_start: 0.7708 (tt0) cc_final: 0.7482 (tt0) outliers start: 0 outliers final: 1 residues processed: 776 average time/residue: 0.8243 time to fit residues: 691.7147 Evaluate side-chains 552 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 551 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.0870 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 2.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 14 ASN A 14 ASN A 66 ASN A 87 ASN A 103 ASN B 14 ASN B 135 ASN C 14 ASN C 66 ASN C 87 ASN C 103 ASN D 14 ASN D 87 ASN E 14 ASN E 103 ASN E 135 ASN F 14 ASN F 103 ASN F 135 ASN H 14 ASN H 103 ASN H 135 ASN I 14 ASN I 135 ASN J 14 ASN J 103 ASN J 135 ASN K 14 ASN K 103 ASN K 135 ASN L 42 GLN M 14 ASN M 42 GLN M 50 GLN M 90 ASN N 14 ASN N 42 GLN N 103 ASN O 42 GLN O 103 ASN P 42 GLN P 103 ASN Q 14 ASN Q 42 GLN Q 50 GLN Q 90 ASN R 90 ASN R 103 ASN R 135 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.129879 restraints weight = 16838.061| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 0.91 r_work: 0.3291 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 18738 Z= 0.191 Angle : 0.597 8.209 25092 Z= 0.327 Chirality : 0.045 0.126 2808 Planarity : 0.003 0.035 3240 Dihedral : 5.948 164.415 2505 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.09 % Allowed : 24.15 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2304 helix: -0.06 (0.43), residues: 126 sheet: 0.90 (0.16), residues: 1134 loop : -0.26 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 129 TYR 0.019 0.002 TYR D 68 PHE 0.013 0.002 PHE A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (18738) covalent geometry : angle 0.59686 / 0.33 (25092) hydrogen bonds : bond 0.04540 / 2.99 ( 720) hydrogen bonds : angle 6.77138 / 4.54 ( 2646) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 566 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8118 (tptt) REVERT: A 50 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7239 (mm-40) REVERT: B 8 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6288 (tt0) REVERT: B 32 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 100 ARG cc_start: 0.8964 (ttm-80) cc_final: 0.8668 (ttp-110) REVERT: C 50 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7205 (mm-40) REVERT: D 8 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6037 (tm-30) REVERT: D 34 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8093 (tptt) REVERT: D 137 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6298 (mm) REVERT: E 34 LYS cc_start: 0.8420 (mmmt) cc_final: 0.8132 (mttm) REVERT: E 50 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.6826 (tm-30) REVERT: E 76 LYS cc_start: 0.8619 (mmpt) cc_final: 0.7850 (mttt) REVERT: E 77 LEU cc_start: 0.9107 (tp) cc_final: 0.8887 (tp) REVERT: E 80 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7713 (mtm-85) REVERT: E 105 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8307 (ttm-80) REVERT: E 123 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: F 27 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7198 (tp30) REVERT: F 50 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: F 80 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7740 (mtm-85) REVERT: F 123 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: F 137 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6161 (mt) REVERT: H 27 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7427 (tm-30) REVERT: H 34 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8221 (tptp) REVERT: H 50 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: H 76 LYS cc_start: 0.8556 (mttt) cc_final: 0.8179 (mmmm) REVERT: H 80 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7716 (mtm-85) REVERT: H 135 ASN cc_start: 0.8856 (t0) cc_final: 0.8621 (t0) REVERT: I 34 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8145 (mttm) REVERT: I 50 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7713 (tm-30) REVERT: I 80 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7700 (mtm-85) REVERT: I 123 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: J 27 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7387 (tm-30) REVERT: J 50 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: J 76 LYS cc_start: 0.8423 (mttt) cc_final: 0.8100 (mmmm) REVERT: J 80 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7664 (mtm-85) REVERT: J 135 ASN cc_start: 0.8820 (t0) cc_final: 0.8583 (t0) REVERT: K 9 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7277 (tt0) REVERT: K 27 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7125 (tp30) REVERT: K 50 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: K 60 LYS cc_start: 0.8085 (tttm) cc_final: 0.7589 (tppt) REVERT: K 80 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7734 (mtm-85) REVERT: K 123 GLU cc_start: 0.7172 (mp0) cc_final: 0.6892 (mp0) REVERT: L 11 SER cc_start: 0.8892 (m) cc_final: 0.8641 (t) REVERT: L 73 LYS cc_start: 0.8294 (pttp) cc_final: 0.8062 (pttm) REVERT: L 80 ARG cc_start: 0.8103 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: L 123 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: M 11 SER cc_start: 0.9142 (m) cc_final: 0.8765 (t) REVERT: M 17 ASP cc_start: 0.8282 (m-30) cc_final: 0.7999 (m-30) REVERT: M 80 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7321 (mtm-85) REVERT: M 100 ARG cc_start: 0.8828 (ttm-80) cc_final: 0.8615 (ttm110) REVERT: N 11 SER cc_start: 0.8957 (m) cc_final: 0.8633 (t) REVERT: N 73 LYS cc_start: 0.8340 (ptmm) cc_final: 0.8131 (pttm) REVERT: O 34 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8482 (tptt) REVERT: O 80 ARG cc_start: 0.8075 (mtm-85) cc_final: 0.7602 (mtm-85) REVERT: O 123 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: P 11 SER cc_start: 0.9017 (m) cc_final: 0.8688 (t) REVERT: P 73 LYS cc_start: 0.8299 (ptmm) cc_final: 0.8087 (pttm) REVERT: Q 11 SER cc_start: 0.9134 (m) cc_final: 0.8779 (t) REVERT: Q 17 ASP cc_start: 0.8268 (m-30) cc_final: 0.7987 (m-30) REVERT: Q 27 GLU cc_start: 0.6634 (mm-30) cc_final: 0.6348 (mm-30) REVERT: Q 80 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7322 (mtm-85) REVERT: R 8 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6336 (tt0) REVERT: R 32 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7727 (tm-30) REVERT: R 100 ARG cc_start: 0.8937 (ttm-80) cc_final: 0.8639 (ttp-110) outliers start: 64 outliers final: 14 residues processed: 601 average time/residue: 0.6823 time to fit residues: 446.8435 Evaluate side-chains 560 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 528 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 102 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 68 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 66 ASN A 135 ASN B 14 ASN B 66 ASN B 135 ASN C 14 ASN C 66 ASN C 103 ASN C 135 ASN E 14 ASN E 66 ASN E 103 ASN F 14 ASN F 135 ASN H 14 ASN H 66 ASN H 103 ASN I 14 ASN I 66 ASN I 103 ASN I 135 ASN J 14 ASN J 103 ASN K 14 ASN K 135 ASN L 42 GLN L 135 ASN N 103 ASN O 42 GLN O 103 ASN O 135 ASN P 103 ASN Q 42 GLN Q 50 GLN R 90 ASN R 135 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.138040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126048 restraints weight = 17076.712| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 0.91 r_work: 0.3248 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 18738 Z= 0.274 Angle : 0.688 10.099 25092 Z= 0.371 Chirality : 0.047 0.135 2808 Planarity : 0.004 0.032 3240 Dihedral : 5.526 20.931 2502 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.12 % Allowed : 22.32 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2304 helix: -0.36 (0.40), residues: 126 sheet: 0.84 (0.16), residues: 1134 loop : -0.26 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 129 TYR 0.021 0.003 TYR D 68 PHE 0.014 0.002 PHE A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.27 (18738) covalent geometry : angle 0.68763 / 0.37 (25092) hydrogen bonds : bond 0.04923 / 3.25 ( 720) hydrogen bonds : angle 7.13036 / 4.79 ( 2646) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 540 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8544 (mmmt) cc_final: 0.8207 (tptt) REVERT: G 50 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7295 (mm-40) REVERT: A 50 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7402 (mm-40) REVERT: B 8 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6426 (tt0) REVERT: B 32 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 100 ARG cc_start: 0.9014 (ttm-80) cc_final: 0.8736 (ttp-110) REVERT: B 105 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7856 (ttp80) REVERT: B 107 LYS cc_start: 0.9007 (tptp) cc_final: 0.8761 (tptt) REVERT: C 50 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7384 (mm-40) REVERT: D 8 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: D 34 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8253 (tptt) REVERT: D 50 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7263 (mm-40) REVERT: D 137 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6676 (mm) REVERT: E 34 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8196 (mttm) REVERT: E 50 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.6857 (tm-30) REVERT: E 76 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8135 (mttt) REVERT: E 80 ARG cc_start: 0.8071 (mtm-85) cc_final: 0.7841 (mtm-85) REVERT: E 105 ARG cc_start: 0.8639 (tpp80) cc_final: 0.8340 (ttm-80) REVERT: E 123 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: F 27 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7455 (tp30) REVERT: F 50 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: F 66 ASN cc_start: 0.9059 (m-40) cc_final: 0.8770 (m-40) REVERT: F 76 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8159 (mmmt) REVERT: F 80 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7930 (mtm-85) REVERT: F 123 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: H 27 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7772 (tm-30) REVERT: H 50 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: H 76 LYS cc_start: 0.8494 (mttt) cc_final: 0.7648 (tmmt) REVERT: H 80 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7779 (mtm-85) REVERT: H 105 ARG cc_start: 0.8448 (tpp80) cc_final: 0.8181 (ttm-80) REVERT: H 135 ASN cc_start: 0.8918 (t0) cc_final: 0.8646 (t0) REVERT: I 34 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8218 (mttm) REVERT: I 50 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: I 80 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7787 (mtm-85) REVERT: I 123 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7576 (mt-10) REVERT: J 27 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7779 (tm-30) REVERT: J 50 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: J 76 LYS cc_start: 0.8474 (mttt) cc_final: 0.7953 (mmmm) REVERT: J 80 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7764 (mtm-85) REVERT: J 125 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: J 135 ASN cc_start: 0.8873 (t0) cc_final: 0.8555 (t0) REVERT: K 27 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7456 (tp30) REVERT: K 50 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: K 60 LYS cc_start: 0.8144 (tttm) cc_final: 0.7693 (tppt) REVERT: K 80 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7936 (mtm-85) REVERT: K 123 GLU cc_start: 0.7366 (mp0) cc_final: 0.7146 (mp0) REVERT: L 9 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6602 (tt0) REVERT: L 80 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7629 (mtm-85) REVERT: L 123 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: L 125 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: M 9 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: M 17 ASP cc_start: 0.8357 (m-30) cc_final: 0.8079 (m-30) REVERT: M 80 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7485 (mtm-85) REVERT: N 50 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7614 (mm-40) REVERT: O 9 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6601 (tt0) REVERT: O 80 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7613 (mtm-85) REVERT: O 123 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: P 50 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7598 (mm-40) REVERT: Q 9 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7011 (tp30) REVERT: Q 17 ASP cc_start: 0.8348 (m-30) cc_final: 0.8074 (m-30) REVERT: Q 80 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7495 (mtm-85) REVERT: R 8 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: R 32 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7686 (tm-30) REVERT: R 100 ARG cc_start: 0.9007 (ttm-80) cc_final: 0.8724 (ttp-110) REVERT: R 105 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8467 (ttm-80) REVERT: R 107 LYS cc_start: 0.8994 (tptp) cc_final: 0.8740 (tptt) outliers start: 106 outliers final: 33 residues processed: 598 average time/residue: 0.7538 time to fit residues: 489.7495 Evaluate side-chains 566 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 502 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 50 GLN Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 118 GLU Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 123 GLU Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 9 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain Q residue 137 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 105 ARG Chi-restraints excluded: chain R residue 118 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 217 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 135 ASN B 14 ASN B 66 ASN B 103 ASN B 135 ASN C 66 ASN C 135 ASN E 14 ASN E 103 ASN F 14 ASN F 103 ASN F 135 ASN H 14 ASN H 66 ASN I 14 ASN I 103 ASN J 14 ASN J 66 ASN J 103 ASN K 14 ASN K 103 ASN K 135 ASN L 14 ASN L 42 GLN L 135 ASN N 14 ASN N 103 ASN O 14 ASN O 42 GLN O 103 ASN O 135 ASN P 103 ASN R 66 ASN R 90 ASN R 135 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.128042 restraints weight = 17577.356| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 0.91 r_work: 0.3284 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18738 Z= 0.167 Angle : 0.559 6.439 25092 Z= 0.308 Chirality : 0.044 0.126 2808 Planarity : 0.003 0.032 3240 Dihedral : 5.026 20.353 2502 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 4.64 % Allowed : 23.38 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.17), residues: 2304 helix: 0.36 (0.43), residues: 126 sheet: 0.82 (0.16), residues: 1134 loop : -0.30 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 80 TYR 0.015 0.002 TYR D 68 PHE 0.013 0.002 PHE R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (18738) covalent geometry : angle 0.55904 / 0.31 (25092) hydrogen bonds : bond 0.04267 / 2.81 ( 720) hydrogen bonds : angle 6.58274 / 4.42 ( 2646) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 529 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8252 (tptt) REVERT: G 50 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7239 (mm-40) REVERT: G 136 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: A 50 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7304 (mm-40) REVERT: A 76 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8604 (mmmt) REVERT: A 105 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7910 (ttp80) REVERT: B 100 ARG cc_start: 0.8980 (ttm-80) cc_final: 0.8685 (ttp-110) REVERT: C 50 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: C 105 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7895 (ttp80) REVERT: D 34 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8277 (tptt) REVERT: D 50 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7213 (mm-40) REVERT: E 34 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8170 (mttm) REVERT: E 50 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: E 76 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8147 (mttt) REVERT: E 80 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7772 (mtm-85) REVERT: E 105 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8258 (ttm-80) REVERT: E 123 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: F 27 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7393 (tp30) REVERT: F 60 LYS cc_start: 0.8113 (tttm) cc_final: 0.7620 (tppt) REVERT: F 66 ASN cc_start: 0.9051 (m-40) cc_final: 0.8829 (m-40) REVERT: F 71 ASP cc_start: 0.8879 (p0) cc_final: 0.8644 (p0) REVERT: F 76 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8325 (mmmm) REVERT: F 80 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7847 (mtm-85) REVERT: F 123 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: H 27 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7740 (tm-30) REVERT: H 50 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: H 71 ASP cc_start: 0.8858 (p0) cc_final: 0.8584 (p0) REVERT: H 76 LYS cc_start: 0.8359 (mttt) cc_final: 0.8093 (mmmm) REVERT: H 80 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7658 (mtm-85) REVERT: H 105 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8181 (ttm-80) REVERT: H 135 ASN cc_start: 0.8874 (t0) cc_final: 0.8596 (t0) REVERT: I 34 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8169 (mttm) REVERT: I 50 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: I 80 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7727 (mtm-85) REVERT: I 105 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8291 (ttm-80) REVERT: I 123 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: J 27 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7745 (tm-30) REVERT: J 50 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: J 71 ASP cc_start: 0.8823 (p0) cc_final: 0.8570 (p0) REVERT: J 76 LYS cc_start: 0.8328 (mttt) cc_final: 0.8021 (mmmm) REVERT: J 80 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7674 (mtm-85) REVERT: J 96 TYR cc_start: 0.9008 (p90) cc_final: 0.8747 (p90) REVERT: J 105 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8224 (ttm-80) REVERT: J 135 ASN cc_start: 0.8797 (t0) cc_final: 0.8444 (t0) REVERT: K 27 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7390 (tp30) REVERT: K 60 LYS cc_start: 0.7866 (tttm) cc_final: 0.7365 (tppt) REVERT: K 76 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8391 (mmmt) REVERT: K 80 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7940 (mtm-85) REVERT: L 80 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7644 (mtm-85) REVERT: L 123 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: L 125 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: M 17 ASP cc_start: 0.8333 (m-30) cc_final: 0.8099 (m-30) REVERT: M 80 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7611 (mtm-85) REVERT: N 73 LYS cc_start: 0.8191 (ptmm) cc_final: 0.7939 (pttm) REVERT: N 107 LYS cc_start: 0.8882 (tptp) cc_final: 0.8672 (tptp) REVERT: O 9 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: O 80 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7619 (mtm-85) REVERT: O 123 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: P 73 LYS cc_start: 0.8188 (ptmm) cc_final: 0.7932 (pttm) REVERT: P 76 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7953 (mmmm) REVERT: Q 9 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6756 (tp30) REVERT: Q 17 ASP cc_start: 0.8290 (m-30) cc_final: 0.8049 (m-30) REVERT: Q 80 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7606 (mtm-85) REVERT: R 32 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7765 (tm-30) REVERT: R 100 ARG cc_start: 0.8949 (ttm-80) cc_final: 0.8645 (ttp-110) REVERT: R 105 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8444 (ttm-80) REVERT: R 107 LYS cc_start: 0.8961 (tptp) cc_final: 0.8744 (tptt) outliers start: 96 outliers final: 32 residues processed: 573 average time/residue: 0.7323 time to fit residues: 456.7533 Evaluate side-chains 566 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 509 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain Q residue 137 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 102 LYS Chi-restraints excluded: chain R residue 105 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 194 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 135 ASN B 66 ASN B 135 ASN C 66 ASN C 135 ASN E 66 ASN E 103 ASN F 14 ASN F 135 ASN H 14 ASN I 14 ASN I 66 ASN I 103 ASN I 135 ASN J 14 ASN J 66 ASN J 103 ASN K 14 ASN K 66 ASN K 135 ASN L 14 ASN L 42 GLN L 103 ASN L 135 ASN N 103 ASN O 14 ASN O 42 GLN O 103 ASN O 135 ASN P 103 ASN Q 50 GLN R 66 ASN R 135 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127158 restraints weight = 17142.134| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 0.92 r_work: 0.3267 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 18738 Z= 0.203 Angle : 0.602 7.526 25092 Z= 0.328 Chirality : 0.045 0.130 2808 Planarity : 0.003 0.030 3240 Dihedral : 5.181 20.861 2502 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 5.70 % Allowed : 22.32 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2304 helix: 0.21 (0.42), residues: 126 sheet: 0.81 (0.16), residues: 1134 loop : -0.31 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 80 TYR 0.017 0.003 TYR H 96 PHE 0.013 0.002 PHE R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (18738) covalent geometry : angle 0.60228 / 0.33 (25092) hydrogen bonds : bond 0.04440 / 2.93 ( 720) hydrogen bonds : angle 6.72307 / 4.52 ( 2646) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 505 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8274 (tptt) REVERT: G 50 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7238 (mm-40) REVERT: A 50 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7338 (mm-40) REVERT: A 105 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7922 (ttp80) REVERT: B 28 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8846 (mt) REVERT: B 100 ARG cc_start: 0.8979 (ttm-80) cc_final: 0.8683 (ttp-110) REVERT: B 105 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8512 (ttm-80) REVERT: C 50 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7349 (mm-40) REVERT: C 105 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7903 (ttp80) REVERT: D 8 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6064 (tm-30) REVERT: D 34 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8201 (tptt) REVERT: D 50 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7218 (mm-40) REVERT: D 118 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: E 34 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8156 (mttm) REVERT: E 50 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: E 76 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8130 (mttt) REVERT: E 80 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7696 (mtm-85) REVERT: E 105 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: E 123 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: F 27 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7425 (tp30) REVERT: F 66 ASN cc_start: 0.9069 (m-40) cc_final: 0.8800 (m-40) REVERT: F 71 ASP cc_start: 0.8940 (p0) cc_final: 0.8671 (p0) REVERT: F 80 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: F 123 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: H 27 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7793 (tm-30) REVERT: H 50 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: H 80 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7672 (mtm-85) REVERT: H 135 ASN cc_start: 0.8827 (t0) cc_final: 0.8618 (t0) REVERT: I 34 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8148 (mttm) REVERT: I 50 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: I 80 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7730 (mtm-85) REVERT: I 105 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8285 (ttm-80) REVERT: I 123 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: J 27 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7761 (tm-30) REVERT: J 50 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: J 80 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7677 (mtm-85) REVERT: J 135 ASN cc_start: 0.8819 (t0) cc_final: 0.8568 (t0) REVERT: K 27 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7475 (tp30) REVERT: K 60 LYS cc_start: 0.7911 (tttm) cc_final: 0.7394 (tppt) REVERT: K 76 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8445 (mmmt) REVERT: K 80 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7936 (mtm-85) REVERT: K 123 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: K 136 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: L 9 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: L 80 ARG cc_start: 0.8050 (mtm-85) cc_final: 0.7585 (mtm-85) REVERT: L 123 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: L 125 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7846 (pm20) REVERT: M 9 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: M 17 ASP cc_start: 0.8311 (m-30) cc_final: 0.8046 (m-30) REVERT: M 27 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6424 (mm-30) REVERT: M 28 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8732 (mt) REVERT: M 50 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: M 80 ARG cc_start: 0.7958 (mtm-85) cc_final: 0.7613 (mtm-85) REVERT: N 50 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7655 (mm-40) REVERT: N 73 LYS cc_start: 0.8188 (ptmm) cc_final: 0.7886 (pttm) REVERT: O 9 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6658 (tt0) REVERT: O 80 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: O 123 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: P 50 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7660 (mm-40) REVERT: Q 9 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: Q 17 ASP cc_start: 0.8308 (m-30) cc_final: 0.8046 (m-30) REVERT: Q 27 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6410 (mm-30) REVERT: Q 80 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7606 (mtm-85) REVERT: R 28 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8797 (mt) REVERT: R 32 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7647 (tm-30) REVERT: R 100 ARG cc_start: 0.8944 (ttm-80) cc_final: 0.8642 (ttp-110) REVERT: R 105 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8478 (ttm-80) outliers start: 118 outliers final: 35 residues processed: 568 average time/residue: 0.7324 time to fit residues: 452.8227 Evaluate side-chains 571 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 498 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 123 GLU Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 9 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain M residue 27 GLU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 50 GLN Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain Q residue 137 LEU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 105 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 138 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 166 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN B 14 ASN B 66 ASN B 135 ASN C 66 ASN C 135 ASN E 103 ASN F 14 ASN F 135 ASN H 14 ASN H 66 ASN I 103 ASN J 14 ASN J 66 ASN J 103 ASN K 14 ASN K 135 ASN L 14 ASN L 103 ASN L 135 ASN N 103 ASN O 14 ASN O 103 ASN O 135 ASN P 103 ASN R 135 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.139936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.128069 restraints weight = 17070.546| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 0.92 r_work: 0.3279 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 18738 Z= 0.184 Angle : 0.576 7.028 25092 Z= 0.315 Chirality : 0.044 0.130 2808 Planarity : 0.003 0.038 3240 Dihedral : 5.075 20.701 2502 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 5.85 % Allowed : 22.37 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2304 helix: 0.26 (0.42), residues: 126 sheet: 0.82 (0.16), residues: 1134 loop : -0.31 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 80 TYR 0.018 0.002 TYR H 96 PHE 0.012 0.002 PHE R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 (18738) covalent geometry : angle 0.57578 / 0.32 (25092) hydrogen bonds : bond 0.04281 / 2.82 ( 720) hydrogen bonds : angle 6.56673 / 4.41 ( 2646) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 498 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8115 (tptt) REVERT: G 50 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7226 (mm-40) REVERT: G 118 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7916 (pt0) REVERT: A 50 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7319 (mm-40) REVERT: A 105 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7909 (ttp80) REVERT: B 8 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6548 (tt0) REVERT: B 28 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8840 (mt) REVERT: B 100 ARG cc_start: 0.8965 (ttm-80) cc_final: 0.8667 (ttp-110) REVERT: B 105 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8496 (ttm-80) REVERT: C 50 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7303 (mm-40) REVERT: C 105 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7888 (ttp80) REVERT: D 8 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6036 (tm-30) REVERT: D 34 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8276 (tptt) REVERT: D 50 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7187 (mm-40) REVERT: E 34 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8154 (mttm) REVERT: E 50 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: E 76 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8100 (mttt) REVERT: E 80 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7739 (mtm-85) REVERT: E 105 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8254 (ttm-80) REVERT: E 123 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: F 27 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7441 (tp30) REVERT: F 60 LYS cc_start: 0.8139 (tttm) cc_final: 0.7668 (tppt) REVERT: F 71 ASP cc_start: 0.8929 (p0) cc_final: 0.8658 (p0) REVERT: F 80 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: F 123 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7126 (mm-30) REVERT: H 27 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7774 (tm-30) REVERT: H 50 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: H 80 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: H 125 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: H 135 ASN cc_start: 0.8839 (t0) cc_final: 0.8618 (t0) REVERT: I 34 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8151 (mttm) REVERT: I 50 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: I 105 ARG cc_start: 0.8547 (tpp80) cc_final: 0.8266 (ttm-80) REVERT: I 123 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: J 27 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7746 (tm-30) REVERT: J 50 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7360 (tm-30) REVERT: J 80 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7809 (mtm-85) REVERT: J 96 TYR cc_start: 0.8986 (p90) cc_final: 0.8733 (p90) REVERT: J 135 ASN cc_start: 0.8796 (t0) cc_final: 0.8533 (t0) REVERT: K 27 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7428 (tp30) REVERT: K 66 ASN cc_start: 0.9035 (m110) cc_final: 0.8604 (m-40) REVERT: K 71 ASP cc_start: 0.8933 (p0) cc_final: 0.8716 (p0) REVERT: K 80 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7931 (mtm-85) REVERT: K 123 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7073 (mm-30) REVERT: L 80 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7607 (mtm-85) REVERT: L 123 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: L 125 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: M 9 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7043 (tt0) REVERT: M 17 ASP cc_start: 0.8287 (m-30) cc_final: 0.8035 (m-30) REVERT: M 50 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: M 80 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7601 (mtm-85) REVERT: M 102 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8856 (mtpt) REVERT: N 50 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7544 (mm-40) REVERT: N 73 LYS cc_start: 0.8199 (ptmm) cc_final: 0.7959 (pttm) REVERT: O 9 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: O 80 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7600 (mtm-85) REVERT: O 123 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: P 50 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7534 (mm-40) REVERT: P 73 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7914 (pttm) REVERT: Q 9 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: Q 17 ASP cc_start: 0.8307 (m-30) cc_final: 0.8067 (m-30) REVERT: Q 27 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6424 (mm-30) REVERT: Q 28 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8742 (mt) REVERT: Q 80 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7601 (mtm-85) REVERT: R 8 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6645 (tt0) REVERT: R 28 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8779 (mt) REVERT: R 100 ARG cc_start: 0.8914 (ttm-80) cc_final: 0.8611 (ttp-110) REVERT: R 105 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8435 (ttm-80) REVERT: R 107 LYS cc_start: 0.8984 (tptp) cc_final: 0.8757 (tptt) outliers start: 121 outliers final: 40 residues processed: 564 average time/residue: 0.6882 time to fit residues: 424.0312 Evaluate side-chains 567 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 489 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 123 GLU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain M residue 50 GLN Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain Q residue 137 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 102 LYS Chi-restraints excluded: chain R residue 105 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 135 ASN B 66 ASN B 135 ASN C 66 ASN E 103 ASN F 14 ASN F 66 ASN F 135 ASN H 14 ASN I 103 ASN J 14 ASN J 66 ASN J 103 ASN K 14 ASN K 135 ASN L 14 ASN L 103 ASN L 135 ASN N 103 ASN O 14 ASN O 103 ASN O 135 ASN P 103 ASN Q 103 ASN R 135 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.140438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.128522 restraints weight = 17146.792| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 0.92 r_work: 0.3283 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 18738 Z= 0.173 Angle : 0.565 6.415 25092 Z= 0.310 Chirality : 0.044 0.162 2808 Planarity : 0.003 0.043 3240 Dihedral : 5.008 20.573 2502 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.41 % Allowed : 22.90 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2304 helix: 0.39 (0.43), residues: 126 sheet: 0.82 (0.16), residues: 1134 loop : -0.32 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 80 TYR 0.017 0.002 TYR L 86 PHE 0.012 0.002 PHE R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (18738) covalent geometry : angle 0.56465 / 0.31 (25092) hydrogen bonds : bond 0.04209 / 2.77 ( 720) hydrogen bonds : angle 6.50308 / 4.37 ( 2646) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 508 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8087 (tptt) REVERT: G 50 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7210 (mm-40) REVERT: G 118 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7948 (pt0) REVERT: A 50 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7286 (mm-40) REVERT: A 105 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7899 (ttp80) REVERT: B 8 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6537 (tt0) REVERT: B 28 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8839 (mt) REVERT: B 100 ARG cc_start: 0.8955 (ttm-80) cc_final: 0.8654 (ttp-110) REVERT: B 105 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7845 (ttp80) REVERT: C 50 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7276 (mm-40) REVERT: C 105 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7883 (ttp80) REVERT: D 8 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6086 (tm-30) REVERT: D 34 LYS cc_start: 0.8494 (mmmt) cc_final: 0.8281 (tptt) REVERT: D 50 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7176 (mm-40) REVERT: D 118 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: D 133 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8508 (tp) REVERT: E 34 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8152 (mttm) REVERT: E 50 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.6712 (tm-30) REVERT: E 76 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8164 (mttt) REVERT: E 105 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8250 (ttm-80) REVERT: E 123 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: F 27 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7440 (tp30) REVERT: F 60 LYS cc_start: 0.8111 (tttm) cc_final: 0.7650 (tppt) REVERT: F 66 ASN cc_start: 0.9049 (m110) cc_final: 0.8759 (m-40) REVERT: F 71 ASP cc_start: 0.8935 (p0) cc_final: 0.8664 (p0) REVERT: F 80 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: F 123 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: H 27 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7767 (tm-30) REVERT: H 50 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: H 71 ASP cc_start: 0.8919 (p0) cc_final: 0.8709 (p0) REVERT: H 80 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7820 (mtm-85) REVERT: H 125 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: H 135 ASN cc_start: 0.8830 (t0) cc_final: 0.8606 (t0) REVERT: I 34 LYS cc_start: 0.8420 (mmmt) cc_final: 0.8154 (mttm) REVERT: I 50 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: I 105 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8279 (ttm-80) REVERT: I 123 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7449 (mt-10) REVERT: J 27 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7728 (tm-30) REVERT: J 50 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: J 76 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8398 (mmmt) REVERT: J 80 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: K 27 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7434 (tp30) REVERT: K 66 ASN cc_start: 0.9047 (m110) cc_final: 0.8601 (m-40) REVERT: K 80 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7922 (mtm-85) REVERT: K 123 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: L 11 SER cc_start: 0.8964 (m) cc_final: 0.8609 (t) REVERT: L 80 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7625 (mtm-85) REVERT: L 123 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: L 125 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: M 17 ASP cc_start: 0.8287 (m-30) cc_final: 0.8049 (m-30) REVERT: M 50 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7166 (tm-30) REVERT: M 80 ARG cc_start: 0.7957 (mtm-85) cc_final: 0.7607 (mtm-85) REVERT: M 102 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8876 (mtpt) REVERT: N 50 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7528 (mm-40) REVERT: N 73 LYS cc_start: 0.8266 (ptmm) cc_final: 0.8011 (pttm) REVERT: O 9 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: O 80 ARG cc_start: 0.8028 (mtm-85) cc_final: 0.7608 (mtm-85) REVERT: O 123 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7257 (mt-10) REVERT: P 50 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7531 (mm-40) REVERT: P 73 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7892 (pttm) REVERT: Q 17 ASP cc_start: 0.8329 (m-30) cc_final: 0.8102 (m-30) REVERT: Q 27 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6391 (mm-30) REVERT: Q 80 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7596 (mtm-85) REVERT: R 8 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6538 (tt0) REVERT: R 28 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8776 (mt) REVERT: R 100 ARG cc_start: 0.8901 (ttm-80) cc_final: 0.8597 (ttp-110) REVERT: R 105 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7836 (ttp80) REVERT: R 107 LYS cc_start: 0.8962 (tptp) cc_final: 0.8756 (tptt) outliers start: 112 outliers final: 44 residues processed: 567 average time/residue: 0.7297 time to fit residues: 451.4681 Evaluate side-chains 588 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 506 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 76 LYS Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 123 GLU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain M residue 50 GLN Chi-restraints excluded: chain M residue 60 LYS Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain O residue 137 LEU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 27 GLU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain Q residue 137 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 102 LYS Chi-restraints excluded: chain R residue 105 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 105 optimal weight: 9.9990 chunk 201 optimal weight: 0.0980 chunk 195 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN B 66 ASN B 135 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN E 14 ASN E 103 ASN E 135 ASN F 14 ASN F 135 ASN H 14 ASN H 66 ASN I 14 ASN I 103 ASN J 14 ASN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN J 135 ASN K 14 ASN K 135 ASN L 14 ASN L 103 ASN L 135 ASN N 103 ASN O 103 ASN O 135 ASN P 103 ASN R 66 ASN R 135 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.135886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123794 restraints weight = 17734.995| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 0.92 r_work: 0.3244 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 18738 Z= 0.372 Angle : 0.791 11.834 25092 Z= 0.422 Chirality : 0.050 0.191 2808 Planarity : 0.005 0.041 3240 Dihedral : 5.766 21.968 2502 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.46 % Allowed : 22.75 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2304 helix: -0.74 (0.38), residues: 126 sheet: 0.86 (0.16), residues: 1134 loop : -0.42 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 80 TYR 0.030 0.004 TYR P 68 PHE 0.017 0.003 PHE R 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00795 / 0.37 (18738) covalent geometry : angle 0.79090 / 0.42 (25092) hydrogen bonds : bond 0.05267 / 3.49 ( 720) hydrogen bonds : angle 7.30067 / 4.90 ( 2646) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 489 time to evaluate : 0.694 Fit side-chains REVERT: G 34 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8139 (tptt) REVERT: G 50 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7268 (mm-40) REVERT: G 118 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: A 105 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8010 (ttp80) REVERT: B 8 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6648 (tt0) REVERT: B 28 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8928 (mt) REVERT: B 100 ARG cc_start: 0.9014 (ttm-80) cc_final: 0.8735 (ttp-110) REVERT: B 105 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7946 (ttp80) REVERT: C 105 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7970 (ttp80) REVERT: D 8 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6146 (tm-30) REVERT: D 23 ASP cc_start: 0.8191 (m-30) cc_final: 0.7973 (m-30) REVERT: D 50 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7266 (mm-40) REVERT: D 118 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: D 133 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8718 (tp) REVERT: D 137 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6969 (mm) REVERT: E 50 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: E 105 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8235 (ttp80) REVERT: E 123 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: F 27 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7391 (tp30) REVERT: F 80 ARG cc_start: 0.8207 (mtm-85) cc_final: 0.7979 (mtm-85) REVERT: F 123 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: H 27 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7803 (tm-30) REVERT: H 50 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: H 71 ASP cc_start: 0.8889 (p0) cc_final: 0.8603 (p0) REVERT: H 80 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7839 (mtm-85) REVERT: I 50 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: I 123 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: J 27 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7777 (tm-30) REVERT: J 50 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: J 80 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7753 (mtm-85) REVERT: K 27 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7431 (tp30) REVERT: K 39 GLN cc_start: 0.8821 (pp30) cc_final: 0.8584 (pp30) REVERT: K 76 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8462 (mmmm) REVERT: K 80 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7976 (mtm-85) REVERT: K 123 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: L 80 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7639 (mtm-85) REVERT: L 123 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: M 8 GLU cc_start: 0.6214 (tt0) cc_final: 0.5643 (tt0) REVERT: M 17 ASP cc_start: 0.8332 (m-30) cc_final: 0.8069 (m-30) REVERT: M 50 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: M 123 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: N 9 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: N 50 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7786 (mm-40) REVERT: O 9 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: O 27 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7169 (mm-30) REVERT: O 80 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7668 (mtm-85) REVERT: O 123 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: Q 17 ASP cc_start: 0.8345 (m-30) cc_final: 0.8095 (m-30) REVERT: Q 123 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: R 8 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6638 (tt0) REVERT: R 28 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8906 (mt) REVERT: R 100 ARG cc_start: 0.9002 (ttm-80) cc_final: 0.8723 (ttp-110) REVERT: R 105 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7954 (ttp80) REVERT: R 131 TYR cc_start: 0.9017 (p90) cc_final: 0.8807 (p90) outliers start: 113 outliers final: 48 residues processed: 556 average time/residue: 0.7639 time to fit residues: 463.5067 Evaluate side-chains 578 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 495 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 118 GLU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 118 GLU Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain F residue 136 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 43 SER Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 76 LYS Chi-restraints excluded: chain K residue 123 GLU Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain M residue 50 GLN Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 9 GLU Chi-restraints excluded: chain N residue 49 CYS Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain O residue 9 GLU Chi-restraints excluded: chain O residue 27 GLU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain P residue 49 CYS Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain Q residue 137 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 93 THR Chi-restraints excluded: chain R residue 105 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 143 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 211 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN A 103 ASN A 135 ASN B 135 ASN C 66 ASN C 103 ASN C 135 ASN E 103 ASN F 14 ASN F 135 ASN H 14 ASN H 66 ASN H 135 ASN I 14 ASN I 103 ASN J 14 ASN J 66 ASN J 103 ASN J 135 ASN K 14 ASN K 135 ASN L 14 ASN L 103 ASN L 135 ASN N 103 ASN O 14 ASN O 50 GLN O 103 ASN O 135 ASN P 103 ASN R 135 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.131908 restraints weight = 17765.669| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 0.89 r_work: 0.3323 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 2.34 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18738 Z= 0.139 Angle : 0.539 5.073 25092 Z= 0.299 Chirality : 0.044 0.145 2808 Planarity : 0.003 0.059 3240 Dihedral : 4.928 20.162 2502 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.11 % Allowed : 24.35 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2304 helix: 0.21 (0.43), residues: 126 sheet: 0.85 (0.16), residues: 1134 loop : -0.35 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 80 TYR 0.018 0.002 TYR L 86 PHE 0.013 0.002 PHE Q 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (18738) covalent geometry : angle 0.53883 / 0.30 (25092) hydrogen bonds : bond 0.04087 / 2.68 ( 720) hydrogen bonds : angle 6.38223 / 4.29 ( 2646) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 527 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 34 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8099 (tptt) REVERT: A 105 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7882 (ttp80) REVERT: B 8 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6610 (tt0) REVERT: B 28 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8828 (mt) REVERT: B 100 ARG cc_start: 0.8943 (ttm-80) cc_final: 0.8627 (ttp-110) REVERT: B 105 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7801 (ttp80) REVERT: C 105 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7812 (ttp80) REVERT: E 34 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8150 (mttm) REVERT: E 50 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: E 76 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8208 (mttt) REVERT: E 105 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8279 (ttm-80) REVERT: E 123 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: F 27 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7209 (tp30) REVERT: F 60 LYS cc_start: 0.8095 (tttm) cc_final: 0.7686 (tppt) REVERT: F 66 ASN cc_start: 0.8976 (m110) cc_final: 0.8690 (m-40) REVERT: F 71 ASP cc_start: 0.8958 (p0) cc_final: 0.8686 (p0) REVERT: F 76 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8159 (mmmm) REVERT: F 123 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: H 27 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7722 (tm-30) REVERT: H 50 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: H 71 ASP cc_start: 0.8885 (p0) cc_final: 0.8677 (p0) REVERT: I 34 LYS cc_start: 0.8360 (mmmt) cc_final: 0.8150 (mttm) REVERT: I 50 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: I 105 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8285 (ttm-80) REVERT: I 123 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: J 27 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7716 (tm-30) REVERT: J 50 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7265 (tm-30) REVERT: J 105 ARG cc_start: 0.8400 (tpp80) cc_final: 0.8182 (ttm-80) REVERT: K 27 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7379 (tp30) REVERT: K 39 GLN cc_start: 0.8800 (pp30) cc_final: 0.8554 (pp30) REVERT: K 66 ASN cc_start: 0.8976 (m110) cc_final: 0.8438 (m-40) REVERT: K 71 ASP cc_start: 0.8906 (p0) cc_final: 0.8657 (p0) REVERT: K 80 ARG cc_start: 0.8116 (mtm-85) cc_final: 0.7896 (mtm-85) REVERT: K 123 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6997 (mm-30) REVERT: L 11 SER cc_start: 0.8909 (m) cc_final: 0.8569 (t) REVERT: L 80 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7629 (mtm-85) REVERT: L 123 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7062 (mt-10) REVERT: M 8 GLU cc_start: 0.6131 (tt0) cc_final: 0.5513 (tt0) REVERT: M 17 ASP cc_start: 0.8299 (m-30) cc_final: 0.8094 (m-30) REVERT: M 50 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: M 76 LYS cc_start: 0.8289 (mmmm) cc_final: 0.7954 (mmtp) REVERT: M 80 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7610 (mtm-85) REVERT: N 50 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7601 (mm-40) REVERT: N 73 LYS cc_start: 0.8252 (ptmm) cc_final: 0.8007 (pttm) REVERT: O 80 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7652 (mtm-85) REVERT: O 123 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: P 9 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6682 (tt0) REVERT: P 50 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7606 (mm-40) REVERT: P 73 LYS cc_start: 0.8190 (ptmm) cc_final: 0.7951 (pttm) REVERT: Q 17 ASP cc_start: 0.8309 (m-30) cc_final: 0.8106 (m-30) REVERT: Q 76 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7949 (mmtp) REVERT: Q 80 ARG cc_start: 0.7900 (mtm-85) cc_final: 0.7590 (mtm-85) REVERT: R 8 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6662 (tt0) REVERT: R 100 ARG cc_start: 0.8875 (ttm-80) cc_final: 0.8556 (ttp-110) outliers start: 85 outliers final: 36 residues processed: 570 average time/residue: 0.7710 time to fit residues: 478.7297 Evaluate side-chains 559 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 499 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 123 GLU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain M residue 50 GLN Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 49 CYS Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain P residue 49 CYS Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain Q residue 137 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 73 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 171 optimal weight: 4.9990 chunk 232 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN B 66 ASN B 135 ASN C 66 ASN E 103 ASN F 14 ASN F 135 ASN H 14 ASN H 66 ASN H 135 ASN I 103 ASN J 14 ASN J 66 ASN J 135 ASN K 14 ASN K 135 ASN L 14 ASN L 103 ASN L 135 ASN N 103 ASN O 14 ASN O 50 GLN O 103 ASN O 135 ASN R 135 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.143975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132388 restraints weight = 17310.925| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.89 r_work: 0.3337 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18738 Z= 0.150 Angle : 0.551 5.578 25092 Z= 0.303 Chirality : 0.044 0.138 2808 Planarity : 0.003 0.058 3240 Dihedral : 4.873 20.113 2502 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.19 % Allowed : 25.41 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2304 helix: 0.47 (0.43), residues: 126 sheet: 0.81 (0.16), residues: 1134 loop : -0.33 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 80 TYR 0.019 0.002 TYR L 86 PHE 0.012 0.002 PHE B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (18738) covalent geometry : angle 0.55074 / 0.30 (25092) hydrogen bonds : bond 0.04071 / 2.67 ( 720) hydrogen bonds : angle 6.34552 / 4.26 ( 2646) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 512 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7833 (ttp80) REVERT: B 8 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6535 (tt0) REVERT: B 100 ARG cc_start: 0.8926 (ttm-80) cc_final: 0.8610 (ttp-110) REVERT: B 105 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7797 (ttp80) REVERT: C 105 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7828 (ttp80) REVERT: E 34 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8109 (mttm) REVERT: E 50 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: E 76 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8231 (mttt) REVERT: E 105 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8248 (ttm-80) REVERT: E 123 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: F 27 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7197 (tp30) REVERT: F 60 LYS cc_start: 0.8052 (tttm) cc_final: 0.7671 (tppt) REVERT: F 66 ASN cc_start: 0.8979 (m110) cc_final: 0.8697 (m-40) REVERT: F 71 ASP cc_start: 0.8931 (p0) cc_final: 0.8692 (p0) REVERT: F 123 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7079 (mm-30) REVERT: H 50 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: H 71 ASP cc_start: 0.8904 (p0) cc_final: 0.8652 (p0) REVERT: I 34 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8111 (mttm) REVERT: I 50 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: I 105 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8276 (ttm-80) REVERT: I 123 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: J 27 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7685 (tm-30) REVERT: J 50 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.6926 (tm-30) REVERT: J 105 ARG cc_start: 0.8414 (tpp80) cc_final: 0.8198 (ttm-80) REVERT: K 27 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7232 (tp30) REVERT: K 66 ASN cc_start: 0.8998 (m110) cc_final: 0.8596 (m-40) REVERT: K 71 ASP cc_start: 0.8918 (p0) cc_final: 0.8680 (p0) REVERT: K 123 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: L 11 SER cc_start: 0.8913 (m) cc_final: 0.8559 (t) REVERT: L 80 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7608 (mtm-85) REVERT: L 123 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: L 132 ASP cc_start: 0.8441 (m-30) cc_final: 0.8238 (m-30) REVERT: M 8 GLU cc_start: 0.6122 (tt0) cc_final: 0.5397 (tt0) REVERT: M 17 ASP cc_start: 0.8322 (m-30) cc_final: 0.8115 (m-30) REVERT: M 50 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: M 76 LYS cc_start: 0.8306 (mmmm) cc_final: 0.7950 (mmtp) REVERT: M 80 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7577 (mtm-85) REVERT: M 123 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: N 50 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7613 (mm-40) REVERT: N 73 LYS cc_start: 0.8258 (ptmm) cc_final: 0.8026 (pttm) REVERT: O 11 SER cc_start: 0.8915 (m) cc_final: 0.8586 (t) REVERT: O 80 ARG cc_start: 0.7997 (mtm-85) cc_final: 0.7619 (mtm-85) REVERT: O 123 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: P 50 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7617 (mm-40) REVERT: P 73 LYS cc_start: 0.8212 (ptmm) cc_final: 0.7975 (pttm) REVERT: Q 8 GLU cc_start: 0.6016 (tt0) cc_final: 0.5486 (tt0) REVERT: Q 76 LYS cc_start: 0.8275 (mmmm) cc_final: 0.7938 (mmtp) REVERT: Q 80 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7542 (mtm-85) REVERT: R 8 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6622 (tt0) REVERT: R 100 ARG cc_start: 0.8836 (ttm-80) cc_final: 0.8514 (ttp-110) outliers start: 66 outliers final: 34 residues processed: 545 average time/residue: 0.7210 time to fit residues: 428.4910 Evaluate side-chains 559 residues out of total 2070 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 504 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 123 GLU Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 123 GLU Chi-restraints excluded: chain J residue 50 GLN Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 118 GLU Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 123 GLU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 123 GLU Chi-restraints excluded: chain M residue 50 GLN Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 123 GLU Chi-restraints excluded: chain M residue 137 LEU Chi-restraints excluded: chain N residue 49 CYS Chi-restraints excluded: chain N residue 50 GLN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain O residue 93 THR Chi-restraints excluded: chain O residue 123 GLU Chi-restraints excluded: chain P residue 49 CYS Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 93 THR Chi-restraints excluded: chain P residue 123 GLU Chi-restraints excluded: chain P residue 137 LEU Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain Q residue 123 GLU Chi-restraints excluded: chain Q residue 137 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 51 ASN Chi-restraints excluded: chain R residue 73 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 85 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 153 optimal weight: 0.0000 chunk 158 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 228 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 135 ASN ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN E 103 ASN F 14 ASN F 135 ASN H 14 ASN H 135 ASN I 14 ASN I 103 ASN J 14 ASN ** J 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 ASN K 14 ASN K 135 ASN L 14 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN L 135 ASN N 103 ASN O 50 GLN O 103 ASN O 135 ASN R 135 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.138302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126471 restraints weight = 16999.756| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 0.90 r_work: 0.3246 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 18738 Z= 0.283 Angle : 0.707 9.859 25092 Z= 0.380 Chirality : 0.047 0.162 2808 Planarity : 0.004 0.052 3240 Dihedral : 5.461 21.823 2502 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.62 % Allowed : 25.27 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.17), residues: 2304 helix: -0.32 (0.40), residues: 126 sheet: 0.84 (0.16), residues: 1134 loop : -0.38 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 80 TYR 0.030 0.004 TYR P 68 PHE 0.014 0.002 PHE B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.28 (18738) covalent geometry : angle 0.70661 / 0.38 (25092) hydrogen bonds : bond 0.04849 / 3.21 ( 720) hydrogen bonds : angle 6.98486 / 4.69 ( 2646) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8746.76 seconds wall clock time: 149 minutes 10.11 seconds (8950.11 seconds total)