Starting phenix.real_space_refine on Sat Aug 8 13:00:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11ok_72138/08_2026/11ok_72138.cif Found real_map, /net/cci-nas-00/data/ceres_data/11ok_72138/08_2026/11ok_72138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11ok_72138/08_2026/11ok_72138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11ok_72138/08_2026/11ok_72138.map" model { file = "/net/cci-nas-00/data/ceres_data/11ok_72138/08_2026/11ok_72138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11ok_72138/08_2026/11ok_72138.cif" } resolution = 3.5 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= 0.006 sd= 0.037 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: 5 Type Number sf(0) Gaussians S 72 5.16 5 C 8808 2.51 5 N 2268 2.21 5 O 2856 1.98 5 H 13752 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.02s 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: 27756 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 2313 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.42, per 1000 atoms: 0.12 Number of scatterers: 27756 At special positions: 0 Unit cell: (119.6, 118.56, 97.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2856 8.00 N 2268 7.00 C 8808 6.00 H 13752 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 952.4 milliseconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 12.3% alpha, 89.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.549A pdb=" N ASP A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 69 through 82 removed outlier: 3.549A pdb=" N ASP B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 69 through 82 removed outlier: 3.549A pdb=" N ASP C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 69 through 82 removed outlier: 3.550A pdb=" N ASP D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 69 through 82 removed outlier: 3.550A pdb=" N ASP E 73 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 69 through 82 removed outlier: 3.550A pdb=" N ASP F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 69 through 82 removed outlier: 3.550A pdb=" N ASP G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 69 through 82 removed outlier: 3.551A pdb=" N ASP H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 69 through 82 removed outlier: 3.549A pdb=" N ASP I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 69 through 82 removed outlier: 3.550A pdb=" N ASP J 73 " --> pdb=" O GLU J 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.549A pdb=" N ASP K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 69 through 82 removed outlier: 3.550A pdb=" N ASP L 73 " --> pdb=" O GLU L 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU A 91 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 108 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ASP A 98 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU A 106 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE A 107 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY A 143 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 109 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 141 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS A 111 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP A 139 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 113 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 131 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE A 121 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY A 129 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A 123 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 28 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP A 64 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE A 26 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU A 91 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 108 " --> pdb=" O ASP A 96 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ASP A 98 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU A 106 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE A 107 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY A 143 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA A 109 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 141 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS A 111 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP A 139 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 113 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR A 131 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE A 121 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY A 129 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A 123 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 151 " --> pdb=" O ASN A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 40 removed outlier: 3.548A pdb=" N GLY A 54 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 38 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 52 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS A 40 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS A 50 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU B 91 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 108 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP B 98 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU B 106 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE B 107 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY B 143 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA B 109 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 141 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS B 111 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP B 139 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 113 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 131 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE B 121 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY B 129 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN B 123 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 28 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 64 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE B 26 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU B 91 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS B 108 " --> pdb=" O ASP B 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP B 98 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU B 106 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE B 107 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY B 143 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA B 109 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 141 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS B 111 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP B 139 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 113 " --> pdb=" O LYS B 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 131 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE B 121 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY B 129 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN B 123 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 151 " --> pdb=" O ASN B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 40 removed outlier: 3.548A pdb=" N GLY B 54 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 38 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE B 52 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS B 40 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS B 50 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 21 removed outlier: 4.776A pdb=" N GLU C 91 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS C 108 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP C 98 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU C 106 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE C 107 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY C 143 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 109 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 141 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS C 111 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP C 139 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 113 " --> pdb=" O LYS C 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR C 131 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE C 121 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY C 129 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 123 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL C 127 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 28 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP C 64 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE C 26 " --> pdb=" O ASP C 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 18 through 21 removed outlier: 4.776A pdb=" N GLU C 91 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS C 108 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP C 98 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU C 106 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE C 107 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY C 143 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 109 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 141 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS C 111 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP C 139 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 113 " --> pdb=" O LYS C 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR C 131 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE C 121 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY C 129 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 123 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL C 127 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 151 " --> pdb=" O ASN C 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 40 removed outlier: 3.548A pdb=" N GLY C 54 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA C 38 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE C 52 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS C 40 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS C 50 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 18 through 21 removed outlier: 4.774A pdb=" N GLU D 91 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 108 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP D 98 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU D 106 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE D 107 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY D 143 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA D 109 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL D 141 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS D 111 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP D 139 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS D 113 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR D 131 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE D 121 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY D 129 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN D 123 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 28 " --> pdb=" O VAL D 62 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP D 64 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE D 26 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 21 removed outlier: 4.774A pdb=" N GLU D 91 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS D 108 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP D 98 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU D 106 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE D 107 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY D 143 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA D 109 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL D 141 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS D 111 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP D 139 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS D 113 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR D 131 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE D 121 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY D 129 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN D 123 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 151 " --> pdb=" O ASN D 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 35 through 40 removed outlier: 3.547A pdb=" N GLY D 54 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA D 38 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE D 52 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS D 40 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS D 50 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 18 through 21 removed outlier: 4.774A pdb=" N GLU E 91 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS E 108 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP E 98 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU E 106 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE E 107 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY E 143 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA E 109 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 141 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS E 111 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP E 139 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS E 113 " --> pdb=" O LYS E 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR E 131 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE E 121 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY E 129 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN E 123 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E 28 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP E 64 " --> pdb=" O PHE E 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE E 26 " --> pdb=" O ASP E 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 18 through 21 removed outlier: 4.774A pdb=" N GLU E 91 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS E 108 " --> pdb=" O ASP E 96 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP E 98 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU E 106 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE E 107 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY E 143 " --> pdb=" O PHE E 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA E 109 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 141 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS E 111 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP E 139 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS E 113 " --> pdb=" O LYS E 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR E 131 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE E 121 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY E 129 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN E 123 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 151 " --> pdb=" O ASN E 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 35 through 40 removed outlier: 3.547A pdb=" N GLY E 54 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA E 38 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE E 52 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS E 40 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS E 50 " --> pdb=" O LYS E 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU F 91 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS F 108 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ASP F 98 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU F 106 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE F 107 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY F 143 " --> pdb=" O PHE F 107 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA F 109 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL F 141 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS F 111 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP F 139 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS F 113 " --> pdb=" O LYS F 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR F 131 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE F 121 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY F 129 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN F 123 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP F 28 " --> pdb=" O VAL F 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP F 64 " --> pdb=" O PHE F 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE F 26 " --> pdb=" O ASP F 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU F 91 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS F 108 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ASP F 98 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU F 106 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE F 107 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY F 143 " --> pdb=" O PHE F 107 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA F 109 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL F 141 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS F 111 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP F 139 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS F 113 " --> pdb=" O LYS F 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR F 131 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE F 121 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY F 129 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN F 123 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR F 151 " --> pdb=" O ASN F 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 35 through 40 removed outlier: 3.546A pdb=" N GLY F 54 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA F 38 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE F 52 " --> pdb=" O ALA F 38 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS F 40 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS F 50 " --> pdb=" O LYS F 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU G 91 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS G 108 " --> pdb=" O ASP G 96 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP G 98 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N GLU G 106 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE G 107 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY G 143 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA G 109 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL G 141 " --> pdb=" O ALA G 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS G 111 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP G 139 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS G 113 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR G 131 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE G 121 " --> pdb=" O GLY G 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY G 129 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN G 123 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL G 127 " --> pdb=" O ASN G 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP G 28 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP G 64 " --> pdb=" O PHE G 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE G 26 " --> pdb=" O ASP G 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU G 91 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS G 108 " --> pdb=" O ASP G 96 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ASP G 98 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N GLU G 106 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N PHE G 107 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY G 143 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA G 109 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL G 141 " --> pdb=" O ALA G 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS G 111 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP G 139 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS G 113 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR G 131 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE G 121 " --> pdb=" O GLY G 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY G 129 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN G 123 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL G 127 " --> pdb=" O ASN G 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR G 151 " --> pdb=" O ASN G 146 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 35 through 40 removed outlier: 3.547A pdb=" N GLY G 54 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA G 38 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE G 52 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS G 40 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS G 50 " --> pdb=" O LYS G 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU H 91 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS H 108 " --> pdb=" O ASP H 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP H 98 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N GLU H 106 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE H 107 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY H 143 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA H 109 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL H 141 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS H 111 " --> pdb=" O ASP H 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP H 139 " --> pdb=" O LYS H 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS H 113 " --> pdb=" O LYS H 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR H 131 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE H 121 " --> pdb=" O GLY H 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY H 129 " --> pdb=" O PHE H 121 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN H 123 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL H 127 " --> pdb=" O ASN H 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP H 28 " --> pdb=" O VAL H 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP H 64 " --> pdb=" O PHE H 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE H 26 " --> pdb=" O ASP H 64 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU H 91 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS H 108 " --> pdb=" O ASP H 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP H 98 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N GLU H 106 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE H 107 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY H 143 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA H 109 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL H 141 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS H 111 " --> pdb=" O ASP H 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP H 139 " --> pdb=" O LYS H 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS H 113 " --> pdb=" O LYS H 137 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR H 131 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE H 121 " --> pdb=" O GLY H 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY H 129 " --> pdb=" O PHE H 121 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN H 123 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL H 127 " --> pdb=" O ASN H 123 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR H 151 " --> pdb=" O ASN H 146 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 35 through 40 removed outlier: 3.547A pdb=" N GLY H 54 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA H 38 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE H 52 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS H 40 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS H 50 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 18 through 21 removed outlier: 4.774A pdb=" N GLU I 91 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS I 108 " --> pdb=" O ASP I 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP I 98 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N GLU I 106 " --> pdb=" O ASP I 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE I 107 " --> pdb=" O GLY I 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY I 143 " --> pdb=" O PHE I 107 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA I 109 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL I 141 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS I 111 " --> pdb=" O ASP I 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP I 139 " --> pdb=" O LYS I 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS I 113 " --> pdb=" O LYS I 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR I 131 " --> pdb=" O ALA I 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE I 121 " --> pdb=" O GLY I 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY I 129 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN I 123 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL I 127 " --> pdb=" O ASN I 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP I 28 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP I 64 " --> pdb=" O PHE I 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE I 26 " --> pdb=" O ASP I 64 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 18 through 21 removed outlier: 4.774A pdb=" N GLU I 91 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS I 108 " --> pdb=" O ASP I 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP I 98 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N GLU I 106 " --> pdb=" O ASP I 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE I 107 " --> pdb=" O GLY I 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY I 143 " --> pdb=" O PHE I 107 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA I 109 " --> pdb=" O VAL I 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL I 141 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS I 111 " --> pdb=" O ASP I 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP I 139 " --> pdb=" O LYS I 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS I 113 " --> pdb=" O LYS I 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR I 131 " --> pdb=" O ALA I 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE I 121 " --> pdb=" O GLY I 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY I 129 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN I 123 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL I 127 " --> pdb=" O ASN I 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR I 151 " --> pdb=" O ASN I 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 35 through 40 removed outlier: 3.548A pdb=" N GLY I 54 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA I 38 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE I 52 " --> pdb=" O ALA I 38 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS I 40 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS I 50 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU J 91 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS J 108 " --> pdb=" O ASP J 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP J 98 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU J 106 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE J 107 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY J 143 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA J 109 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL J 141 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS J 111 " --> pdb=" O ASP J 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP J 139 " --> pdb=" O LYS J 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS J 113 " --> pdb=" O LYS J 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR J 131 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE J 121 " --> pdb=" O GLY J 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY J 129 " --> pdb=" O PHE J 121 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN J 123 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL J 127 " --> pdb=" O ASN J 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP J 28 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP J 64 " --> pdb=" O PHE J 26 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE J 26 " --> pdb=" O ASP J 64 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU J 91 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS J 108 " --> pdb=" O ASP J 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP J 98 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU J 106 " --> pdb=" O ASP J 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE J 107 " --> pdb=" O GLY J 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY J 143 " --> pdb=" O PHE J 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA J 109 " --> pdb=" O VAL J 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL J 141 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS J 111 " --> pdb=" O ASP J 139 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP J 139 " --> pdb=" O LYS J 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS J 113 " --> pdb=" O LYS J 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR J 131 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE J 121 " --> pdb=" O GLY J 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY J 129 " --> pdb=" O PHE J 121 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN J 123 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL J 127 " --> pdb=" O ASN J 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR J 151 " --> pdb=" O ASN J 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 35 through 40 removed outlier: 3.548A pdb=" N GLY J 54 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA J 38 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE J 52 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS J 40 " --> pdb=" O LYS J 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS J 50 " --> pdb=" O LYS J 40 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU K 91 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS K 108 " --> pdb=" O ASP K 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP K 98 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU K 106 " --> pdb=" O ASP K 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE K 107 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY K 143 " --> pdb=" O PHE K 107 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA K 109 " --> pdb=" O VAL K 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL K 141 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS K 111 " --> pdb=" O ASP K 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP K 139 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS K 113 " --> pdb=" O LYS K 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR K 131 " --> pdb=" O ALA K 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE K 121 " --> pdb=" O GLY K 129 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLY K 129 " --> pdb=" O PHE K 121 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN K 123 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL K 127 " --> pdb=" O ASN K 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP K 28 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP K 64 " --> pdb=" O PHE K 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE K 26 " --> pdb=" O ASP K 64 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU K 91 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS K 108 " --> pdb=" O ASP K 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP K 98 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU K 106 " --> pdb=" O ASP K 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE K 107 " --> pdb=" O GLY K 143 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY K 143 " --> pdb=" O PHE K 107 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA K 109 " --> pdb=" O VAL K 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL K 141 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS K 111 " --> pdb=" O ASP K 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP K 139 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS K 113 " --> pdb=" O LYS K 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR K 131 " --> pdb=" O ALA K 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE K 121 " --> pdb=" O GLY K 129 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLY K 129 " --> pdb=" O PHE K 121 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN K 123 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL K 127 " --> pdb=" O ASN K 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR K 151 " --> pdb=" O ASN K 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 35 through 40 removed outlier: 3.547A pdb=" N GLY K 54 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA K 38 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE K 52 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS K 40 " --> pdb=" O LYS K 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS K 50 " --> pdb=" O LYS K 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU L 91 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS L 108 " --> pdb=" O ASP L 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP L 98 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU L 106 " --> pdb=" O ASP L 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE L 107 " --> pdb=" O GLY L 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY L 143 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA L 109 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL L 141 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS L 111 " --> pdb=" O ASP L 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP L 139 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS L 113 " --> pdb=" O LYS L 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR L 131 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE L 121 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY L 129 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN L 123 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL L 127 " --> pdb=" O ASN L 123 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP L 28 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP L 64 " --> pdb=" O PHE L 26 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE L 26 " --> pdb=" O ASP L 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 18 through 21 removed outlier: 4.775A pdb=" N GLU L 91 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS L 108 " --> pdb=" O ASP L 96 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ASP L 98 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLU L 106 " --> pdb=" O ASP L 98 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE L 107 " --> pdb=" O GLY L 143 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY L 143 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA L 109 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL L 141 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LYS L 111 " --> pdb=" O ASP L 139 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP L 139 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS L 113 " --> pdb=" O LYS L 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR L 131 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE L 121 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLY L 129 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN L 123 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL L 127 " --> pdb=" O ASN L 123 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR L 151 " --> pdb=" O ASN L 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 35 through 40 removed outlier: 3.547A pdb=" N GLY L 54 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA L 38 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE L 52 " --> pdb=" O ALA L 38 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS L 40 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS L 50 " --> pdb=" O LYS L 40 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.24 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13740 1.03 - 1.23: 24 1.23 - 1.42: 5856 1.42 - 1.61: 8208 1.61 - 1.81: 132 Bond restraints: 27960 Sorted by residual: bond pdb=" CB LYS K 150 " pdb=" CG LYS K 150 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CB LYS L 150 " pdb=" CG LYS L 150 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.30e+00 bond pdb=" CB LYS C 150 " pdb=" CG LYS C 150 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB LYS B 150 " pdb=" CG LYS B 150 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB LYS A 150 " pdb=" CG LYS A 150 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 27955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 49619 1.86 - 3.73: 649 3.73 - 5.59: 72 5.59 - 7.46: 24 7.46 - 9.32: 12 Bond angle restraints: 50376 Sorted by residual: angle pdb=" CB MET K 81 " pdb=" CG MET K 81 " pdb=" SD MET K 81 " ideal model delta sigma weight residual 112.70 122.02 -9.32 3.00e+00 1.11e-01 9.66e+00 angle pdb=" CB MET H 81 " pdb=" CG MET H 81 " pdb=" SD MET H 81 " ideal model delta sigma weight residual 112.70 122.01 -9.31 3.00e+00 1.11e-01 9.63e+00 angle pdb=" CB MET E 81 " pdb=" CG MET E 81 " pdb=" SD MET E 81 " ideal model delta sigma weight residual 112.70 122.01 -9.31 3.00e+00 1.11e-01 9.63e+00 angle pdb=" CB MET I 81 " pdb=" CG MET I 81 " pdb=" SD MET I 81 " ideal model delta sigma weight residual 112.70 121.99 -9.29 3.00e+00 1.11e-01 9.60e+00 angle pdb=" CB MET F 81 " pdb=" CG MET F 81 " pdb=" SD MET F 81 " ideal model delta sigma weight residual 112.70 121.99 -9.29 3.00e+00 1.11e-01 9.58e+00 ... (remaining 50371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.68: 11138 13.68 - 27.36: 1219 27.36 - 41.04: 519 41.04 - 54.72: 192 54.72 - 68.40: 120 Dihedral angle restraints: 13188 sinusoidal: 7056 harmonic: 6132 Sorted by residual: dihedral pdb=" CA LYS E 4 " pdb=" C LYS E 4 " pdb=" N GLN E 5 " pdb=" CA GLN E 5 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LYS K 4 " pdb=" C LYS K 4 " pdb=" N GLN K 5 " pdb=" CA GLN K 5 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA LYS L 4 " pdb=" C LYS L 4 " pdb=" N GLN L 5 " pdb=" CA GLN L 5 " ideal model delta harmonic sigma weight residual 180.00 151.33 28.67 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 13185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1250 0.029 - 0.059: 624 0.059 - 0.088: 150 0.088 - 0.117: 127 0.117 - 0.147: 69 Chirality restraints: 2220 Sorted by residual: chirality pdb=" CA ILE J 66 " pdb=" N ILE J 66 " pdb=" C ILE J 66 " pdb=" CB ILE J 66 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA ILE D 66 " pdb=" N ILE D 66 " pdb=" C ILE D 66 " pdb=" CB ILE D 66 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE F 66 " pdb=" N ILE F 66 " pdb=" C ILE F 66 " pdb=" CB ILE F 66 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 2217 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU G 69 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" CD GLU G 69 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU G 69 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU G 69 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 69 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" CD GLU B 69 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU B 69 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 69 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 69 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" CD GLU A 69 " -0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 69 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 69 " 0.010 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 10123 2.35 - 2.92: 62517 2.92 - 3.48: 66994 3.48 - 4.04: 96517 4.04 - 4.60: 140929 Nonbonded interactions: 377080 Sorted by model distance: nonbonded pdb="HH12 ARG H 67 " pdb=" HE2 LYS L 4 " model vdw 1.793 2.270 nonbonded pdb="HH12 ARG B 67 " pdb=" HE2 LYS F 4 " model vdw 1.793 2.270 nonbonded pdb=" HE2 LYS I 4 " pdb="HH12 ARG L 67 " model vdw 1.810 2.270 nonbonded pdb=" HE2 LYS C 4 " pdb="HH12 ARG F 67 " model vdw 1.810 2.270 nonbonded pdb=" HE2 LYS H 4 " pdb="HH12 ARG K 67 " model vdw 1.821 2.270 ... (remaining 377075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.210 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.150 Find NCS groups from input model: 0.200 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 0.034 14208 Z= 0.156 Angle : 0.771 9.323 19188 Z= 0.425 Chirality : 0.046 0.147 2220 Planarity : 0.003 0.017 2460 Dihedral : 15.021 63.485 5076 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 17.89 % Favored : 82.11 % 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: -2.05 (0.18), residues: 1824 helix: -0.15 (0.39), residues: 228 sheet: -0.99 (0.19), residues: 744 loop : -1.99 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 6 TYR 0.009 0.001 TYR I 9 PHE 0.010 0.001 PHE B 145 TRP 0.005 0.001 TRP J 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (14208) covalent geometry : angle 0.77142 / 0.43 (19188) hydrogen bonds : bond 0.13842 / 8.96 ( 552) hydrogen bonds : angle 11.08192 / 7.63 ( 2196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7820 (ptpp) cc_final: 0.6909 (mmtp) REVERT: A 105 ASN cc_start: 0.4697 (m110) cc_final: 0.4160 (m-40) REVERT: A 122 ASP cc_start: 0.8578 (m-30) cc_final: 0.8254 (m-30) REVERT: B 7 LYS cc_start: 0.7822 (ptpp) cc_final: 0.6989 (mmtt) REVERT: B 81 MET cc_start: 0.7392 (mmm) cc_final: 0.6975 (mmm) REVERT: C 7 LYS cc_start: 0.8025 (ptpp) cc_final: 0.7308 (mmtt) REVERT: D 7 LYS cc_start: 0.7963 (ptpp) cc_final: 0.7176 (mmtt) REVERT: D 81 MET cc_start: 0.7327 (mmm) cc_final: 0.6954 (mmm) REVERT: E 7 LYS cc_start: 0.8091 (ptpp) cc_final: 0.7292 (mmtt) REVERT: F 7 LYS cc_start: 0.7880 (ptpp) cc_final: 0.7092 (mmtp) REVERT: H 9 TYR cc_start: 0.8003 (t80) cc_final: 0.7713 (t80) REVERT: H 98 ASP cc_start: 0.8300 (p0) cc_final: 0.7891 (p0) REVERT: J 98 ASP cc_start: 0.8329 (p0) cc_final: 0.7902 (p0) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.3131 time to fit residues: 225.0168 Evaluate side-chains 310 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0170 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 82 GLN B 11 ASN B 82 GLN C 11 ASN C 82 GLN D 11 ASN D 82 GLN E 11 ASN E 82 GLN F 11 ASN F 82 GLN G 11 ASN H 11 ASN I 11 ASN J 11 ASN K 11 ASN L 11 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117287 restraints weight = 67861.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.121313 restraints weight = 30208.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123987 restraints weight = 16514.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.125717 restraints weight = 10204.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126831 restraints weight = 6842.929| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14208 Z= 0.234 Angle : 0.622 5.318 19188 Z= 0.342 Chirality : 0.049 0.164 2220 Planarity : 0.003 0.043 2460 Dihedral : 5.443 26.078 1956 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.91 % Allowed : 20.53 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.18), residues: 1824 helix: -0.78 (0.36), residues: 228 sheet: -0.90 (0.18), residues: 756 loop : -2.07 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 67 TYR 0.016 0.002 TYR C 55 PHE 0.010 0.001 PHE G 26 TRP 0.006 0.002 TRP K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 (14208) covalent geometry : angle 0.62209 / 0.34 (19188) hydrogen bonds : bond 0.03522 / 2.34 ( 552) hydrogen bonds : angle 6.89378 / 4.75 ( 2196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7131 (mmtp) REVERT: A 105 ASN cc_start: 0.4570 (m110) cc_final: 0.4356 (m110) REVERT: B 7 LYS cc_start: 0.7778 (ptpp) cc_final: 0.7150 (mmtt) REVERT: C 7 LYS cc_start: 0.7941 (ptpp) cc_final: 0.7310 (mmtt) REVERT: C 123 ASN cc_start: 0.7412 (p0) cc_final: 0.6970 (p0) REVERT: D 7 LYS cc_start: 0.7774 (ptpp) cc_final: 0.7160 (mmtt) REVERT: E 7 LYS cc_start: 0.7926 (ptpp) cc_final: 0.7266 (mmtt) REVERT: E 123 ASN cc_start: 0.7313 (p0) cc_final: 0.6788 (p0) REVERT: F 7 LYS cc_start: 0.7876 (ptpp) cc_final: 0.7252 (mmtp) REVERT: F 105 ASN cc_start: 0.4732 (m110) cc_final: 0.4464 (m110) REVERT: H 9 TYR cc_start: 0.8010 (t80) cc_final: 0.7781 (t80) REVERT: J 9 TYR cc_start: 0.7921 (t80) cc_final: 0.7675 (t80) outliers start: 43 outliers final: 35 residues processed: 330 average time/residue: 0.2697 time to fit residues: 130.9873 Evaluate side-chains 315 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 133 ASN Chi-restraints excluded: chain L residue 133 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN H 5 GLN I 5 GLN ** I 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.123758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110066 restraints weight = 69412.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.114064 restraints weight = 30733.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116735 restraints weight = 16955.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118489 restraints weight = 10636.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119639 restraints weight = 7268.782| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14208 Z= 0.285 Angle : 0.628 5.717 19188 Z= 0.347 Chirality : 0.049 0.158 2220 Planarity : 0.004 0.054 2460 Dihedral : 5.432 19.211 1956 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.30 % Allowed : 17.55 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.17), residues: 1824 helix: -1.04 (0.36), residues: 216 sheet: -1.38 (0.18), residues: 744 loop : -2.57 (0.14), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 67 TYR 0.021 0.003 TYR I 55 PHE 0.013 0.002 PHE F 19 TRP 0.008 0.002 TRP K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.29 (14208) covalent geometry : angle 0.62840 / 0.35 (19188) hydrogen bonds : bond 0.03426 / 2.24 ( 552) hydrogen bonds : angle 6.34313 / 4.37 ( 2196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 305 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7973 (ptpp) cc_final: 0.7200 (mmtt) REVERT: B 7 LYS cc_start: 0.7902 (ptpp) cc_final: 0.7278 (mmtt) REVERT: C 7 LYS cc_start: 0.7958 (ptpp) cc_final: 0.7312 (mmtt) REVERT: D 7 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7276 (mmtt) REVERT: E 4 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7229 (mttt) REVERT: E 7 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7262 (mmtt) REVERT: F 7 LYS cc_start: 0.7998 (ptpp) cc_final: 0.7263 (mmtt) REVERT: G 21 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6738 (t80) REVERT: H 9 TYR cc_start: 0.8156 (t80) cc_final: 0.7847 (t80) REVERT: H 21 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6783 (t80) REVERT: I 21 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6808 (t80) REVERT: J 9 TYR cc_start: 0.8167 (t80) cc_final: 0.7883 (t80) REVERT: J 21 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6816 (t80) REVERT: K 21 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6874 (t80) REVERT: L 21 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6745 (t80) REVERT: L 81 MET cc_start: 0.7978 (mmm) cc_final: 0.7507 (mmm) outliers start: 93 outliers final: 71 residues processed: 363 average time/residue: 0.2985 time to fit residues: 153.9748 Evaluate side-chains 346 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 268 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 4 LYS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 21 PHE Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 PHE Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 21 PHE Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 21 PHE Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 133 ASN Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 21 PHE Chi-restraints excluded: chain K residue 50 LYS Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 133 ASN Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 PHE Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 133 ASN Chi-restraints excluded: chain L residue 137 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 162 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN B 123 ASN C 123 ASN D 123 ASN E 123 ASN F 123 ASN H 123 ASN I 123 ASN J 5 GLN J 123 ASN K 5 GLN K 123 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.112155 restraints weight = 68617.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116119 restraints weight = 30836.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.118757 restraints weight = 17017.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120478 restraints weight = 10634.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.121634 restraints weight = 7238.129| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14208 Z= 0.168 Angle : 0.529 6.454 19188 Z= 0.287 Chirality : 0.047 0.149 2220 Planarity : 0.003 0.025 2460 Dihedral : 5.028 18.971 1956 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.15 % Allowed : 18.09 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.17), residues: 1824 helix: -0.85 (0.37), residues: 216 sheet: -1.21 (0.18), residues: 732 loop : -2.16 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 67 TYR 0.015 0.002 TYR B 92 PHE 0.009 0.001 PHE C 21 TRP 0.006 0.002 TRP I 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (14208) covalent geometry : angle 0.52878 / 0.29 (19188) hydrogen bonds : bond 0.02895 / 1.92 ( 552) hydrogen bonds : angle 5.87600 / 4.04 ( 2196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 279 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7039 (mttt) REVERT: A 7 LYS cc_start: 0.7768 (ptpp) cc_final: 0.7106 (mmtt) REVERT: B 7 LYS cc_start: 0.7830 (ptpp) cc_final: 0.7210 (mmtp) REVERT: B 123 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7159 (p0) REVERT: C 7 LYS cc_start: 0.7860 (ptpp) cc_final: 0.7250 (mmtt) REVERT: C 123 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7240 (p0) REVERT: D 7 LYS cc_start: 0.7841 (ptpp) cc_final: 0.7200 (mmtp) REVERT: E 7 LYS cc_start: 0.7646 (ptpp) cc_final: 0.7225 (mmtt) REVERT: E 123 ASN cc_start: 0.7713 (OUTLIER) cc_final: 0.7304 (p0) REVERT: F 7 LYS cc_start: 0.7889 (ptpp) cc_final: 0.7232 (mmtt) REVERT: H 9 TYR cc_start: 0.8024 (t80) cc_final: 0.7792 (t80) REVERT: H 81 MET cc_start: 0.8037 (mmm) cc_final: 0.7292 (mmm) REVERT: J 9 TYR cc_start: 0.8014 (t80) cc_final: 0.7782 (t80) REVERT: K 4 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7491 (mttt) REVERT: K 127 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8736 (m) REVERT: L 69 GLU cc_start: 0.5511 (mp0) cc_final: 0.5247 (tp30) outliers start: 76 outliers final: 60 residues processed: 318 average time/residue: 0.2974 time to fit residues: 133.7061 Evaluate side-chains 334 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 123 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 133 ASN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 127 VAL Chi-restraints excluded: chain K residue 133 ASN Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 133 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 102 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN B 123 ASN C 123 ASN D 123 ASN E 123 ASN F 123 ASN H 123 ASN I 123 ASN J 123 ASN K 123 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.123389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109602 restraints weight = 69248.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113684 restraints weight = 30132.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116396 restraints weight = 16390.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118180 restraints weight = 10176.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119362 restraints weight = 6887.720| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14208 Z= 0.233 Angle : 0.555 6.671 19188 Z= 0.302 Chirality : 0.047 0.150 2220 Planarity : 0.003 0.032 2460 Dihedral : 5.070 18.825 1956 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 6.84 % Allowed : 17.28 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.17), residues: 1824 helix: -0.87 (0.37), residues: 216 sheet: -1.32 (0.18), residues: 732 loop : -2.22 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 67 TYR 0.013 0.002 TYR J 9 PHE 0.011 0.001 PHE C 21 TRP 0.007 0.002 TRP K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (14208) covalent geometry : angle 0.55475 / 0.30 (19188) hydrogen bonds : bond 0.03044 / 2.00 ( 552) hydrogen bonds : angle 5.81282 / 3.99 ( 2196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 273 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7239 (mttt) REVERT: A 7 LYS cc_start: 0.7935 (ptpp) cc_final: 0.7230 (mmtt) REVERT: A 123 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7982 (p0) REVERT: B 7 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7196 (mmtp) REVERT: C 4 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7375 (mttt) REVERT: C 7 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7182 (mmtt) REVERT: C 123 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7670 (p0) REVERT: D 7 LYS cc_start: 0.7958 (ptpp) cc_final: 0.7222 (mmtt) REVERT: E 7 LYS cc_start: 0.7806 (ptpp) cc_final: 0.7122 (mmtt) REVERT: E 123 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7660 (p0) REVERT: F 7 LYS cc_start: 0.8050 (ptpp) cc_final: 0.7289 (mmtt) REVERT: H 9 TYR cc_start: 0.8140 (t80) cc_final: 0.7857 (t80) REVERT: J 9 TYR cc_start: 0.8098 (t80) cc_final: 0.7856 (t80) REVERT: K 4 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7399 (mtmt) REVERT: L 75 ILE cc_start: 0.9059 (mm) cc_final: 0.8775 (mp) outliers start: 101 outliers final: 80 residues processed: 331 average time/residue: 0.2977 time to fit residues: 138.6006 Evaluate side-chains 351 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 265 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain H residue 4 LYS Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 133 ASN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 133 ASN Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 133 ASN Chi-restraints excluded: chain L residue 137 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 123 ASN I 123 ASN J 123 ASN K 123 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.124159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111005 restraints weight = 68829.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114915 restraints weight = 30743.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117496 restraints weight = 16900.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119195 restraints weight = 10561.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.120320 restraints weight = 7161.260| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14208 Z= 0.175 Angle : 0.522 5.558 19188 Z= 0.283 Chirality : 0.046 0.147 2220 Planarity : 0.003 0.025 2460 Dihedral : 4.930 19.317 1956 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 6.78 % Allowed : 17.21 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.17), residues: 1824 helix: -0.81 (0.38), residues: 216 sheet: -1.17 (0.18), residues: 708 loop : -2.27 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 67 TYR 0.011 0.002 TYR J 9 PHE 0.010 0.001 PHE E 21 TRP 0.006 0.002 TRP K 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (14208) covalent geometry : angle 0.52211 / 0.28 (19188) hydrogen bonds : bond 0.02858 / 1.89 ( 552) hydrogen bonds : angle 5.64255 / 3.88 ( 2196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 277 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7861 (ptpp) cc_final: 0.7233 (mmtt) REVERT: A 123 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7950 (p0) REVERT: B 4 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7461 (mttt) REVERT: B 7 LYS cc_start: 0.7853 (ptpp) cc_final: 0.7225 (mmtt) REVERT: B 123 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.7417 (p0) REVERT: B 137 LYS cc_start: 0.8541 (ptpp) cc_final: 0.8159 (ptpp) REVERT: C 7 LYS cc_start: 0.7868 (ptpp) cc_final: 0.7223 (mmtt) REVERT: C 137 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8399 (ptpp) REVERT: D 4 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7422 (mttt) REVERT: D 7 LYS cc_start: 0.7861 (ptpp) cc_final: 0.7129 (mmtm) REVERT: E 7 LYS cc_start: 0.7722 (ptpp) cc_final: 0.7107 (mmtt) REVERT: F 7 LYS cc_start: 0.7877 (ptpp) cc_final: 0.7258 (mmtt) REVERT: F 123 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7953 (p0) REVERT: G 4 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7675 (mtmt) REVERT: H 9 TYR cc_start: 0.8004 (t80) cc_final: 0.7802 (t80) REVERT: H 140 MET cc_start: 0.5708 (ptm) cc_final: 0.5378 (ptm) REVERT: J 9 TYR cc_start: 0.8007 (t80) cc_final: 0.7802 (t80) REVERT: K 4 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7488 (mttt) REVERT: L 4 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7645 (mtmt) REVERT: L 75 ILE cc_start: 0.9055 (mm) cc_final: 0.8770 (mp) outliers start: 100 outliers final: 74 residues processed: 335 average time/residue: 0.3176 time to fit residues: 149.7194 Evaluate side-chains 357 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 274 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 11 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 MET Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 133 ASN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 133 ASN Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 50 LYS Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 133 ASN Chi-restraints excluded: chain L residue 137 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN C 123 ASN E 123 ASN F 123 ASN G 11 ASN H 82 GLN H 123 ASN I 123 ASN J 123 ASN K 82 GLN K 123 ASN L 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107475 restraints weight = 69725.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.111409 restraints weight = 30724.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114001 restraints weight = 16846.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115708 restraints weight = 10510.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116848 restraints weight = 7139.066| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14208 Z= 0.257 Angle : 0.574 5.731 19188 Z= 0.315 Chirality : 0.048 0.148 2220 Planarity : 0.004 0.041 2460 Dihedral : 5.103 19.658 1956 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 7.25 % Allowed : 16.67 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.17), residues: 1824 helix: -0.89 (0.37), residues: 216 sheet: -1.28 (0.18), residues: 708 loop : -2.56 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 67 TYR 0.014 0.002 TYR I 55 PHE 0.015 0.002 PHE F 19 TRP 0.007 0.002 TRP H 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 (14208) covalent geometry : angle 0.57373 / 0.32 (19188) hydrogen bonds : bond 0.03152 / 2.06 ( 552) hydrogen bonds : angle 5.75567 / 3.95 ( 2196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 267 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7959 (ptpp) cc_final: 0.7306 (mmtt) REVERT: B 4 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7462 (mttt) REVERT: B 7 LYS cc_start: 0.7947 (ptpp) cc_final: 0.7211 (mmtm) REVERT: B 123 ASN cc_start: 0.7878 (p0) cc_final: 0.7540 (p0) REVERT: C 7 LYS cc_start: 0.7746 (ptpp) cc_final: 0.7144 (mmtt) REVERT: C 137 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8457 (ptpp) REVERT: D 4 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7378 (mttt) REVERT: D 7 LYS cc_start: 0.7946 (ptpp) cc_final: 0.7198 (mmtm) REVERT: E 7 LYS cc_start: 0.7738 (ptpp) cc_final: 0.7121 (mmtt) REVERT: F 7 LYS cc_start: 0.7929 (ptpp) cc_final: 0.7344 (mmtt) REVERT: G 4 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7694 (mtmt) REVERT: G 21 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.7044 (t80) REVERT: G 75 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8621 (mp) REVERT: H 9 TYR cc_start: 0.8053 (t80) cc_final: 0.7786 (t80) REVERT: H 65 MET cc_start: 0.8102 (mtp) cc_final: 0.7646 (tpp) REVERT: J 9 TYR cc_start: 0.8087 (t80) cc_final: 0.7817 (t80) REVERT: J 75 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8616 (mt) REVERT: K 4 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7613 (mtmt) REVERT: K 81 MET cc_start: 0.8694 (mmm) cc_final: 0.8211 (mmm) REVERT: L 4 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7649 (mtmt) REVERT: L 75 ILE cc_start: 0.9096 (mm) cc_final: 0.8848 (mp) outliers start: 107 outliers final: 78 residues processed: 329 average time/residue: 0.3052 time to fit residues: 143.2938 Evaluate side-chains 349 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 262 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain B residue 4 LYS Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 153 LYS Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 21 PHE Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 133 ASN Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 90 THR Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 123 ASN Chi-restraints excluded: chain J residue 133 ASN Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 133 ASN Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 133 ASN Chi-restraints excluded: chain L residue 137 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 123 ASN G 82 GLN J 123 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.126186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112772 restraints weight = 68248.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116732 restraints weight = 30650.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.119359 restraints weight = 16924.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.121075 restraints weight = 10602.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.122189 restraints weight = 7225.032| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 14208 Z= 0.106 Angle : 0.508 5.699 19188 Z= 0.272 Chirality : 0.046 0.144 2220 Planarity : 0.003 0.031 2460 Dihedral : 4.787 19.903 1956 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.32 % Allowed : 21.14 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.18), residues: 1824 helix: -0.76 (0.38), residues: 216 sheet: -1.27 (0.18), residues: 732 loop : -2.29 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 67 TYR 0.009 0.001 TYR L 92 PHE 0.022 0.001 PHE D 145 TRP 0.005 0.001 TRP J 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (14208) covalent geometry : angle 0.50771 / 0.27 (19188) hydrogen bonds : bond 0.02655 / 1.76 ( 552) hydrogen bonds : angle 5.45076 / 3.75 ( 2196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7801 (ptpp) cc_final: 0.7262 (mmtt) REVERT: B 7 LYS cc_start: 0.7864 (ptpp) cc_final: 0.7173 (mmtm) REVERT: B 137 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8191 (ptpp) REVERT: C 7 LYS cc_start: 0.7675 (ptpp) cc_final: 0.7267 (mmtt) REVERT: C 137 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8396 (ptpp) REVERT: D 7 LYS cc_start: 0.7860 (ptpp) cc_final: 0.7153 (mmtm) REVERT: D 137 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8181 (ptpp) REVERT: E 7 LYS cc_start: 0.7689 (ptpp) cc_final: 0.7149 (mmtt) REVERT: F 7 LYS cc_start: 0.7803 (ptpp) cc_final: 0.7294 (mmtt) REVERT: F 123 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8190 (p0) REVERT: G 4 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7634 (mttt) REVERT: H 6 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.6704 (ttt-90) REVERT: H 9 TYR cc_start: 0.7991 (t80) cc_final: 0.7735 (t80) REVERT: H 123 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8185 (p0) REVERT: J 6 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.6807 (ttt-90) REVERT: J 9 TYR cc_start: 0.7985 (t80) cc_final: 0.7749 (t80) REVERT: K 4 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7854 (mttt) REVERT: K 81 MET cc_start: 0.8479 (mmm) cc_final: 0.8249 (mmm) REVERT: K 140 MET cc_start: 0.5655 (ptm) cc_final: 0.5279 (ptm) REVERT: L 4 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7681 (mttt) REVERT: L 75 ILE cc_start: 0.9020 (mm) cc_final: 0.8751 (mp) outliers start: 49 outliers final: 34 residues processed: 305 average time/residue: 0.3172 time to fit residues: 137.0003 Evaluate side-chains 313 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 271 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 147 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 160 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN D 123 ASN F 123 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 ASN J 123 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.121551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108021 restraints weight = 69584.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.112062 restraints weight = 30299.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114721 restraints weight = 16455.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116447 restraints weight = 10200.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.117563 restraints weight = 6876.779| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 14208 Z= 0.221 Angle : 0.561 8.851 19188 Z= 0.301 Chirality : 0.047 0.144 2220 Planarity : 0.003 0.030 2460 Dihedral : 4.916 20.298 1956 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.79 % Allowed : 20.87 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.17), residues: 1824 helix: -0.82 (0.38), residues: 216 sheet: -1.34 (0.17), residues: 732 loop : -2.46 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 67 TYR 0.013 0.002 TYR I 55 PHE 0.020 0.002 PHE D 145 TRP 0.007 0.002 TRP J 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (14208) covalent geometry : angle 0.56076 / 0.30 (19188) hydrogen bonds : bond 0.02929 / 1.92 ( 552) hydrogen bonds : angle 5.53276 / 3.80 ( 2196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7979 (ptpp) cc_final: 0.7347 (mmtt) REVERT: B 7 LYS cc_start: 0.7966 (ptpp) cc_final: 0.7294 (mmtt) REVERT: B 123 ASN cc_start: 0.7908 (p0) cc_final: 0.7690 (p0) REVERT: C 7 LYS cc_start: 0.7806 (ptpp) cc_final: 0.7197 (mmtt) REVERT: D 7 LYS cc_start: 0.7961 (ptpp) cc_final: 0.7185 (mmtm) REVERT: E 7 LYS cc_start: 0.7824 (ptpp) cc_final: 0.7217 (mmtt) REVERT: F 7 LYS cc_start: 0.8013 (ptpp) cc_final: 0.7392 (mmtt) REVERT: G 4 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7792 (mtmt) REVERT: G 75 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8630 (mt) REVERT: H 6 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.6944 (ttt-90) REVERT: H 9 TYR cc_start: 0.8083 (t80) cc_final: 0.7782 (t80) REVERT: H 65 MET cc_start: 0.8135 (mtp) cc_final: 0.7714 (tpp) REVERT: H 123 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8099 (p0) REVERT: J 6 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.6938 (ttt-90) REVERT: J 9 TYR cc_start: 0.8080 (t80) cc_final: 0.7828 (t80) REVERT: J 75 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8566 (mt) REVERT: J 123 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8258 (p0) REVERT: K 81 MET cc_start: 0.8526 (mmm) cc_final: 0.8194 (mmm) REVERT: L 4 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7562 (mtmt) REVERT: L 75 ILE cc_start: 0.9075 (mm) cc_final: 0.8806 (mp) outliers start: 56 outliers final: 43 residues processed: 294 average time/residue: 0.3336 time to fit residues: 137.0734 Evaluate side-chains 314 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 123 ASN Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 123 ASN Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 123 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108166 restraints weight = 69579.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.112221 restraints weight = 30158.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114907 restraints weight = 16365.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116657 restraints weight = 10124.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117805 restraints weight = 6830.644| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 14208 Z= 0.227 Angle : 0.786 59.195 19188 Z= 0.464 Chirality : 0.047 0.213 2220 Planarity : 0.005 0.146 2460 Dihedral : 4.931 20.371 1956 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.59 % Allowed : 21.27 % Favored : 75.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.17), residues: 1824 helix: -0.82 (0.38), residues: 216 sheet: -1.34 (0.17), residues: 732 loop : -2.47 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 67 TYR 0.011 0.002 TYR A 9 PHE 0.018 0.001 PHE D 145 TRP 0.007 0.002 TRP J 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (14208) covalent geometry : angle 0.78614 / 0.46 (19188) hydrogen bonds : bond 0.02905 / 1.90 ( 552) hydrogen bonds : angle 5.53425 / 3.80 ( 2196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7975 (ptpp) cc_final: 0.7343 (mmtt) REVERT: B 7 LYS cc_start: 0.7963 (ptpp) cc_final: 0.7197 (mmtm) REVERT: B 123 ASN cc_start: 0.7943 (p0) cc_final: 0.7727 (p0) REVERT: C 7 LYS cc_start: 0.7808 (ptpp) cc_final: 0.7196 (mmtt) REVERT: D 7 LYS cc_start: 0.7960 (ptpp) cc_final: 0.7185 (mmtm) REVERT: E 7 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7213 (mmtt) REVERT: F 7 LYS cc_start: 0.8009 (ptpp) cc_final: 0.7387 (mmtt) REVERT: G 4 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7795 (mtmt) REVERT: H 6 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.6926 (ttt-90) REVERT: H 9 TYR cc_start: 0.8084 (t80) cc_final: 0.7779 (t80) REVERT: H 65 MET cc_start: 0.8138 (mtp) cc_final: 0.7707 (tpp) REVERT: H 123 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8088 (p0) REVERT: J 6 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.6925 (ttt-90) REVERT: J 9 TYR cc_start: 0.8077 (t80) cc_final: 0.7826 (t80) REVERT: K 81 MET cc_start: 0.8534 (mmm) cc_final: 0.8203 (mmm) REVERT: L 4 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7554 (mtmt) REVERT: L 75 ILE cc_start: 0.9070 (mm) cc_final: 0.8801 (mp) outliers start: 53 outliers final: 44 residues processed: 294 average time/residue: 0.3219 time to fit residues: 132.3201 Evaluate side-chains 311 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 262 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain G residue 4 LYS Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 123 ASN Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 11 ASN Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 137 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN D 123 ASN F 123 ASN ** G 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108242 restraints weight = 69256.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112315 restraints weight = 30151.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.114992 restraints weight = 16391.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116736 restraints weight = 10137.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117885 restraints weight = 6859.176| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 14208 Z= 0.227 Angle : 0.786 59.195 19188 Z= 0.464 Chirality : 0.047 0.213 2220 Planarity : 0.005 0.146 2460 Dihedral : 4.931 20.371 1956 Min Nonbonded Distance : 1.452 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.39 % Allowed : 21.41 % Favored : 75.20 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.17), residues: 1824 helix: -0.82 (0.38), residues: 216 sheet: -1.34 (0.17), residues: 732 loop : -2.47 (0.17), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 67 TYR 0.011 0.002 TYR A 9 PHE 0.018 0.001 PHE D 145 TRP 0.007 0.002 TRP J 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (14208) covalent geometry : angle 0.78614 / 0.46 (19188) hydrogen bonds : bond 0.02905 / 1.90 ( 552) hydrogen bonds : angle 5.53425 / 3.80 ( 2196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4395.07 seconds wall clock time: 75 minutes 47.17 seconds (4547.17 seconds total)