Starting phenix.real_space_refine on Fri Mar 22 07:26:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/03_2024/6e9z_9021.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/03_2024/6e9z_9021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/03_2024/6e9z_9021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/03_2024/6e9z_9021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/03_2024/6e9z_9021.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e9z_9021/03_2024/6e9z_9021.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 126 atoms to isotropic. 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 18 5.16 5 C 9846 2.51 5 N 2925 2.21 5 O 3033 1.98 5 H 16830 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32652 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "A" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "C" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "F" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "D" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "H" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "G" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "E" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain: "I" Number of atoms: 3628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 3628 Classifications: {'peptide': 225} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Time building chain proxies: 13.44, per 1000 atoms: 0.41 Number of scatterers: 32652 At special positions: 0 Unit cell: (152.25, 152.25, 75.6, 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 18 16.00 O 3033 8.00 N 2925 7.00 C 9846 6.00 H 16830 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 - 3.50 Amino acid : False - 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: 25.97 Conformation dependent library (CDL) restraints added in 3.7 seconds 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'B' and resid 1 through 26 removed outlier: 3.611A pdb=" N ARG B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 8 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 45 removed outlier: 3.784A pdb=" N ARG B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 41 " --> pdb=" O THR B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.657A pdb=" N GLN B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 108 " --> pdb=" O MET B 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 195 removed outlier: 3.907A pdb=" N ALA B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 183 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 215 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'A' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN A 51 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 140 removed outlier: 3.588A pdb=" N ARG A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 195 removed outlier: 3.908A pdb=" N ALA A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 181 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'C' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 8 " --> pdb=" O GLU C 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 17 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU C 81 " --> pdb=" O ARG C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU C 108 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG C 120 " --> pdb=" O GLU C 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 removed outlier: 3.907A pdb=" N ALA C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 215 Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'F' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU F 18 " --> pdb=" O GLU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 54 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU F 55 " --> pdb=" O GLN F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 83 removed outlier: 3.812A pdb=" N ARG F 63 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU F 81 " --> pdb=" O ARG F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 113 removed outlier: 3.503A pdb=" N LEU F 92 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE F 93 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU F 108 " --> pdb=" O MET F 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 140 removed outlier: 3.590A pdb=" N ARG F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG F 134 " --> pdb=" O GLU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 170 removed outlier: 4.394A pdb=" N LEU F 158 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 195 removed outlier: 3.908A pdb=" N ALA F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 176 " --> pdb=" O PRO F 172 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU F 181 " --> pdb=" O MET F 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 183 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 188 " --> pdb=" O ARG F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 215 Processing helix chain 'F' and resid 218 through 222 Processing helix chain 'D' and resid 2 through 26 removed outlier: 3.612A pdb=" N ARG D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 17 " --> pdb=" O LYS D 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 108 " --> pdb=" O MET D 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 140 removed outlier: 3.588A pdb=" N ARG D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 195 removed outlier: 3.908A pdb=" N ALA D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 181 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 215 Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL H 8 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA H 41 " --> pdb=" O THR H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.657A pdb=" N GLN H 51 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU H 54 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU H 55 " --> pdb=" O GLN H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU H 81 " --> pdb=" O ARG H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU H 92 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 108 " --> pdb=" O MET H 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 122 " --> pdb=" O ALA H 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU H 133 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU H 158 " --> pdb=" O GLU H 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU H 168 " --> pdb=" O GLU H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 195 removed outlier: 3.906A pdb=" N ALA H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS H 176 " --> pdb=" O PRO H 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU H 181 " --> pdb=" O MET H 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS H 183 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU H 188 " --> pdb=" O ARG H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 215 Processing helix chain 'H' and resid 218 through 222 Processing helix chain 'G' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL G 8 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA G 17 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU G 18 " --> pdb=" O GLU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 45 removed outlier: 3.784A pdb=" N ARG G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA G 41 " --> pdb=" O THR G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 54 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU G 55 " --> pdb=" O GLN G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 83 removed outlier: 3.810A pdb=" N ARG G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE G 93 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET G 104 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS G 111 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG G 120 " --> pdb=" O GLU G 116 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU G 133 " --> pdb=" O ALA G 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG G 134 " --> pdb=" O GLU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 170 removed outlier: 4.394A pdb=" N LEU G 158 " --> pdb=" O GLU G 154 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS G 160 " --> pdb=" O ALA G 156 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 195 removed outlier: 3.907A pdb=" N ALA G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS G 176 " --> pdb=" O PRO G 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU G 181 " --> pdb=" O MET G 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS G 183 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 188 " --> pdb=" O ARG G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 215 Processing helix chain 'G' and resid 218 through 222 Processing helix chain 'E' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.656A pdb=" N GLN E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU E 55 " --> pdb=" O GLN E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 108 " --> pdb=" O MET E 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 140 removed outlier: 3.588A pdb=" N ARG E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA E 121 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG E 134 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 170 removed outlier: 4.393A pdb=" N LEU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 160 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 195 removed outlier: 3.907A pdb=" N ALA E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS E 176 " --> pdb=" O PRO E 172 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU E 181 " --> pdb=" O MET E 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU E 188 " --> pdb=" O ARG E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 215 Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'I' and resid 2 through 26 removed outlier: 3.611A pdb=" N ARG I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL I 8 " --> pdb=" O GLU I 4 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA I 17 " --> pdb=" O LYS I 13 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU I 18 " --> pdb=" O GLU I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 45 removed outlier: 3.785A pdb=" N ARG I 36 " --> pdb=" O GLU I 32 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU I 40 " --> pdb=" O ARG I 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 41 " --> pdb=" O THR I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 55 removed outlier: 3.657A pdb=" N GLN I 51 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU I 55 " --> pdb=" O GLN I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 83 removed outlier: 3.811A pdb=" N ARG I 63 " --> pdb=" O GLU I 59 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU I 81 " --> pdb=" O ARG I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 113 removed outlier: 3.502A pdb=" N LEU I 92 " --> pdb=" O LEU I 88 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE I 93 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 140 removed outlier: 3.589A pdb=" N ARG I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL I 122 " --> pdb=" O ALA I 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I 133 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG I 134 " --> pdb=" O GLU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 170 removed outlier: 4.392A pdb=" N LEU I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS I 160 " --> pdb=" O ALA I 156 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU I 165 " --> pdb=" O ARG I 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 195 removed outlier: 3.906A pdb=" N ALA I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS I 176 " --> pdb=" O PRO I 172 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU I 181 " --> pdb=" O MET I 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS I 183 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU I 188 " --> pdb=" O ARG I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 215 Processing helix chain 'I' and resid 218 through 222 1207 hydrogen bonds defined for protein. 3567 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: 11.08 Time building geometry restraints manager: 26.95 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: 16830 1.03 - 1.23: 9 1.23 - 1.42: 5769 1.42 - 1.62: 10035 1.62 - 1.81: 36 Bond restraints: 32679 Sorted by residual: bond pdb=" CB VAL F 68 " pdb=" CG1 VAL F 68 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CG1 ILE G 78 " pdb=" CD1 ILE G 78 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.68e+00 bond pdb=" CB VAL B 68 " pdb=" CG1 VAL B 68 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.67e+00 bond pdb=" CG1 ILE F 78 " pdb=" CD1 ILE F 78 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.67e+00 bond pdb=" CG1 ILE I 78 " pdb=" CD1 ILE I 78 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.65e+00 ... (remaining 32674 not shown) Histogram of bond angle deviations from ideal: 99.42 - 105.43: 151 105.43 - 111.44: 39352 111.44 - 117.45: 7195 117.45 - 123.46: 10810 123.46 - 129.47: 2270 Bond angle restraints: 59778 Sorted by residual: angle pdb=" CA ARG E 90 " pdb=" CB ARG E 90 " pdb=" CG ARG E 90 " ideal model delta sigma weight residual 114.10 109.21 4.89 2.00e+00 2.50e-01 5.98e+00 angle pdb=" CA ARG D 90 " pdb=" CB ARG D 90 " pdb=" CG ARG D 90 " ideal model delta sigma weight residual 114.10 109.22 4.88 2.00e+00 2.50e-01 5.96e+00 angle pdb=" CA ARG A 90 " pdb=" CB ARG A 90 " pdb=" CG ARG A 90 " ideal model delta sigma weight residual 114.10 109.23 4.87 2.00e+00 2.50e-01 5.93e+00 angle pdb=" CA ARG G 90 " pdb=" CB ARG G 90 " pdb=" CG ARG G 90 " ideal model delta sigma weight residual 114.10 109.25 4.85 2.00e+00 2.50e-01 5.88e+00 angle pdb=" CA ARG H 90 " pdb=" CB ARG H 90 " pdb=" CG ARG H 90 " ideal model delta sigma weight residual 114.10 109.25 4.85 2.00e+00 2.50e-01 5.88e+00 ... (remaining 59773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.81: 12728 11.81 - 23.61: 1231 23.61 - 35.42: 522 35.42 - 47.22: 87 47.22 - 59.03: 48 Dihedral angle restraints: 14616 sinusoidal: 8676 harmonic: 5940 Sorted by residual: dihedral pdb=" CA GLU C 217 " pdb=" C GLU C 217 " pdb=" N ARG C 218 " pdb=" CA ARG C 218 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU G 217 " pdb=" C GLU G 217 " pdb=" N ARG G 218 " pdb=" CA ARG G 218 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU E 217 " pdb=" C GLU E 217 " pdb=" N ARG E 218 " pdb=" CA ARG E 218 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1267 0.033 - 0.066: 974 0.066 - 0.098: 222 0.098 - 0.131: 93 0.131 - 0.164: 27 Chirality restraints: 2583 Sorted by residual: chirality pdb=" CB VAL C 174 " pdb=" CA VAL C 174 " pdb=" CG1 VAL C 174 " pdb=" CG2 VAL C 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CB VAL E 174 " pdb=" CA VAL E 174 " pdb=" CG1 VAL E 174 " pdb=" CG2 VAL E 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CB VAL A 174 " pdb=" CA VAL A 174 " pdb=" CG1 VAL A 174 " pdb=" CG2 VAL A 174 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 2580 not shown) Planarity restraints: 4743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 211 " -0.036 2.00e-02 2.50e+03 7.20e-02 5.18e+01 pdb=" C GLU F 211 " 0.125 2.00e-02 2.50e+03 pdb=" O GLU F 211 " -0.047 2.00e-02 2.50e+03 pdb=" N ALA F 212 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 211 " -0.036 2.00e-02 2.50e+03 7.18e-02 5.15e+01 pdb=" C GLU B 211 " 0.124 2.00e-02 2.50e+03 pdb=" O GLU B 211 " -0.047 2.00e-02 2.50e+03 pdb=" N ALA B 212 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 211 " 0.036 2.00e-02 2.50e+03 7.17e-02 5.14e+01 pdb=" C GLU A 211 " -0.124 2.00e-02 2.50e+03 pdb=" O GLU A 211 " 0.047 2.00e-02 2.50e+03 pdb=" N ALA A 212 " 0.041 2.00e-02 2.50e+03 ... (remaining 4740 not shown) Histogram of nonbonded interaction distances: 0.65 - 1.44: 39 1.44 - 2.23: 2820 2.23 - 3.02: 101635 3.02 - 3.81: 129088 3.81 - 4.60: 221276 Warning: very small nonbonded interaction distances. Nonbonded interactions: 454858 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 100 " pdb=" O ILE H 24 " model vdw 0.652 1.850 nonbonded pdb=" HZ2 LYS C 100 " pdb=" O ILE F 24 " model vdw 0.653 1.850 nonbonded pdb=" HZ2 LYS B 100 " pdb=" O ILE D 24 " model vdw 0.653 1.850 nonbonded pdb=" HB3 LYS H 176 " pdb="HD21 LEU I 89 " model vdw 0.862 2.440 nonbonded pdb="HD21 LEU C 89 " pdb=" HB3 LYS I 176 " model vdw 0.862 2.440 ... (remaining 454853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.480 Extract box with map and model: 5.570 Check model and map are aligned: 0.460 Set scattering table: 0.310 Process input model: 97.490 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.011 0.075 15849 Z= 0.713 Angle : 0.847 6.581 21222 Z= 0.440 Chirality : 0.048 0.164 2583 Planarity : 0.006 0.072 2763 Dihedral : 10.267 51.911 6471 Min Nonbonded Distance : 1.132 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.48 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.29 (0.13), residues: 2007 helix: -4.32 (0.07), residues: 1719 sheet: None (None), residues: 0 loop : -0.54 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.652 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 outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 1.2710 time to fit residues: 527.9529 Evaluate side-chains 119 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN A 112 GLN C 112 GLN F 112 GLN D 112 GLN H 112 GLN E 112 GLN I 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15849 Z= 0.190 Angle : 0.603 7.496 21222 Z= 0.329 Chirality : 0.031 0.113 2583 Planarity : 0.004 0.059 2763 Dihedral : 4.949 19.611 2250 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.64 % Favored : 98.21 % Rotamer: Outliers : 0.68 % Allowed : 8.95 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.16), residues: 2007 helix: -1.95 (0.11), residues: 1800 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 2.714 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 206 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6662 (pt0) outliers start: 11 outliers final: 1 residues processed: 189 average time/residue: 0.9504 time to fit residues: 245.0198 Evaluate side-chains 113 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 206 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15849 Z= 0.276 Angle : 0.590 7.881 21222 Z= 0.320 Chirality : 0.032 0.123 2583 Planarity : 0.005 0.039 2763 Dihedral : 4.778 17.714 2250 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.48 % Allowed : 10.31 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 2007 helix: -0.65 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -0.73 (0.52), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.7904 (m-30) cc_final: 0.7478 (m-30) REVERT: A 30 ASP cc_start: 0.7663 (m-30) cc_final: 0.7396 (m-30) REVERT: A 114 ASP cc_start: 0.7830 (m-30) cc_final: 0.7439 (m-30) REVERT: C 114 ASP cc_start: 0.7981 (m-30) cc_final: 0.7659 (m-30) REVERT: G 32 GLU cc_start: 0.7379 (tp30) cc_final: 0.7110 (tp30) REVERT: G 114 ASP cc_start: 0.8000 (m-30) cc_final: 0.7696 (m-30) outliers start: 24 outliers final: 8 residues processed: 171 average time/residue: 0.9043 time to fit residues: 218.0096 Evaluate side-chains 115 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain E residue 14 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 171 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15849 Z= 0.209 Angle : 0.522 7.838 21222 Z= 0.283 Chirality : 0.030 0.114 2583 Planarity : 0.003 0.057 2763 Dihedral : 4.465 17.775 2250 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.86 % Allowed : 11.30 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 2007 helix: 0.11 (0.12), residues: 1809 sheet: None (None), residues: 0 loop : -0.75 (0.51), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.7839 (m-30) cc_final: 0.7472 (m-30) REVERT: A 30 ASP cc_start: 0.7749 (m-30) cc_final: 0.7524 (m-30) REVERT: A 114 ASP cc_start: 0.7799 (m-30) cc_final: 0.7466 (m-30) REVERT: C 114 ASP cc_start: 0.7935 (m-30) cc_final: 0.7632 (m-30) REVERT: F 114 ASP cc_start: 0.7644 (m-30) cc_final: 0.7373 (m-30) REVERT: G 114 ASP cc_start: 0.7954 (m-30) cc_final: 0.7675 (m-30) REVERT: I 171 ASP cc_start: 0.7677 (t0) cc_final: 0.7441 (t70) outliers start: 14 outliers final: 6 residues processed: 135 average time/residue: 0.7743 time to fit residues: 147.6257 Evaluate side-chains 111 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain E residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15849 Z= 0.158 Angle : 0.489 7.466 21222 Z= 0.265 Chirality : 0.029 0.111 2583 Planarity : 0.003 0.038 2763 Dihedral : 4.243 15.832 2250 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.74 % Allowed : 11.11 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.19), residues: 2007 helix: 0.77 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.46 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.7789 (m-30) cc_final: 0.7445 (m-30) REVERT: A 30 ASP cc_start: 0.7754 (m-30) cc_final: 0.7501 (m-30) REVERT: A 114 ASP cc_start: 0.7793 (m-30) cc_final: 0.7488 (m-30) REVERT: C 114 ASP cc_start: 0.7937 (m-30) cc_final: 0.7674 (m-30) REVERT: F 114 ASP cc_start: 0.7636 (m-30) cc_final: 0.7361 (m-30) REVERT: G 114 ASP cc_start: 0.7880 (m-30) cc_final: 0.7649 (m-30) REVERT: E 114 ASP cc_start: 0.7669 (m-30) cc_final: 0.7392 (m-30) REVERT: I 171 ASP cc_start: 0.7661 (t0) cc_final: 0.7458 (t0) outliers start: 12 outliers final: 8 residues processed: 126 average time/residue: 0.8191 time to fit residues: 143.8537 Evaluate side-chains 110 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain E residue 46 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15849 Z= 0.293 Angle : 0.559 7.863 21222 Z= 0.299 Chirality : 0.031 0.118 2583 Planarity : 0.004 0.072 2763 Dihedral : 4.397 17.895 2250 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.86 % Allowed : 11.60 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2007 helix: 0.91 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.50 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.7894 (m-30) cc_final: 0.7575 (m-30) REVERT: A 30 ASP cc_start: 0.7730 (m-30) cc_final: 0.7466 (m-30) REVERT: A 114 ASP cc_start: 0.7884 (m-30) cc_final: 0.7581 (m-30) REVERT: C 114 ASP cc_start: 0.7956 (m-30) cc_final: 0.7715 (m-30) REVERT: D 202 LYS cc_start: 0.7196 (mmtt) cc_final: 0.6982 (mmtt) REVERT: G 114 ASP cc_start: 0.7889 (m-30) cc_final: 0.7635 (m-30) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.7595 time to fit residues: 141.1673 Evaluate side-chains 114 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 GLN ** H 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15849 Z= 0.240 Angle : 0.530 8.464 21222 Z= 0.283 Chirality : 0.030 0.126 2583 Planarity : 0.003 0.055 2763 Dihedral : 4.307 17.973 2250 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.86 % Allowed : 11.98 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.19), residues: 2007 helix: 1.23 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.51 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.7896 (m-30) cc_final: 0.7582 (m-30) REVERT: A 30 ASP cc_start: 0.7785 (m-30) cc_final: 0.7530 (m-30) REVERT: A 114 ASP cc_start: 0.7870 (m-30) cc_final: 0.7601 (m-30) REVERT: C 114 ASP cc_start: 0.7960 (m-30) cc_final: 0.7714 (m-30) REVERT: D 202 LYS cc_start: 0.7198 (mmtt) cc_final: 0.6934 (mmtt) REVERT: G 114 ASP cc_start: 0.7921 (m-30) cc_final: 0.7643 (m-30) REVERT: G 214 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7652 (tm-30) outliers start: 14 outliers final: 11 residues processed: 117 average time/residue: 0.8546 time to fit residues: 139.9897 Evaluate side-chains 108 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 176 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 130 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15849 Z= 0.178 Angle : 0.502 8.893 21222 Z= 0.269 Chirality : 0.030 0.135 2583 Planarity : 0.003 0.074 2763 Dihedral : 4.158 17.287 2250 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.80 % Allowed : 12.04 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 2007 helix: 1.62 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.39 (0.48), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 2.746 Fit side-chains revert: symmetry clash REVERT: B 114 ASP cc_start: 0.7877 (m-30) cc_final: 0.7616 (m-30) REVERT: A 30 ASP cc_start: 0.7812 (m-30) cc_final: 0.7545 (m-30) REVERT: A 114 ASP cc_start: 0.7854 (m-30) cc_final: 0.7609 (m-30) REVERT: C 114 ASP cc_start: 0.7934 (m-30) cc_final: 0.7700 (m-30) REVERT: D 202 LYS cc_start: 0.7240 (mmtt) cc_final: 0.7026 (mmtt) REVERT: G 114 ASP cc_start: 0.7926 (m-30) cc_final: 0.7666 (m-30) REVERT: G 214 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7547 (tm-30) REVERT: E 114 ASP cc_start: 0.7587 (m-30) cc_final: 0.7254 (m-30) outliers start: 13 outliers final: 10 residues processed: 128 average time/residue: 0.8477 time to fit residues: 150.2408 Evaluate side-chains 112 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 177 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15849 Z= 0.132 Angle : 0.494 9.426 21222 Z= 0.265 Chirality : 0.030 0.163 2583 Planarity : 0.003 0.060 2763 Dihedral : 3.988 13.659 2250 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.74 % Allowed : 12.16 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.19), residues: 2007 helix: 1.97 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.25 (0.50), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.7845 (m-30) cc_final: 0.7561 (m-30) REVERT: A 30 ASP cc_start: 0.7747 (m-30) cc_final: 0.7466 (m-30) REVERT: A 114 ASP cc_start: 0.7820 (m-30) cc_final: 0.7585 (m-30) REVERT: C 50 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8679 (t) REVERT: C 114 ASP cc_start: 0.7885 (m-30) cc_final: 0.7677 (m-30) REVERT: F 114 ASP cc_start: 0.7682 (m-30) cc_final: 0.7412 (m-30) REVERT: D 202 LYS cc_start: 0.7311 (mmtt) cc_final: 0.7005 (mmtt) REVERT: G 114 ASP cc_start: 0.7860 (m-30) cc_final: 0.7635 (m-30) REVERT: E 114 ASP cc_start: 0.7695 (m-30) cc_final: 0.7407 (m-30) outliers start: 12 outliers final: 9 residues processed: 132 average time/residue: 0.7926 time to fit residues: 146.8803 Evaluate side-chains 118 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 176 LYS Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 181 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.7198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15849 Z= 0.197 Angle : 0.539 10.676 21222 Z= 0.287 Chirality : 0.030 0.151 2583 Planarity : 0.004 0.128 2763 Dihedral : 4.046 17.998 2250 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.80 % Allowed : 12.47 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.19), residues: 2007 helix: 2.00 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.43 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4014 Ramachandran restraints generated. 2007 Oldfield, 0 Emsley, 2007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Residue MET 177 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 ASP cc_start: 0.7869 (m-30) cc_final: 0.7588 (m-30) REVERT: A 30 ASP cc_start: 0.7855 (m-30) cc_final: 0.7589 (m-30) REVERT: A 114 ASP cc_start: 0.7860 (m-30) cc_final: 0.7623 (m-30) REVERT: C 114 ASP cc_start: 0.7896 (m-30) cc_final: 0.7675 (m-30) REVERT: F 114 ASP cc_start: 0.7697 (m-30) cc_final: 0.7441 (m-30) REVERT: D 202 LYS cc_start: 0.7505 (mmtt) cc_final: 0.7202 (mmtt) REVERT: G 114 ASP cc_start: 0.7879 (m-30) cc_final: 0.7657 (m-30) REVERT: E 114 ASP cc_start: 0.7643 (m-30) cc_final: 0.7333 (m-30) outliers start: 13 outliers final: 9 residues processed: 128 average time/residue: 0.7988 time to fit residues: 144.0277 Evaluate side-chains 119 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain H residue 165 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain E residue 176 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 161 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111252 restraints weight = 68101.293| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.20 r_work: 0.3209 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15849 Z= 0.138 Angle : 0.514 10.959 21222 Z= 0.273 Chirality : 0.029 0.160 2583 Planarity : 0.003 0.102 2763 Dihedral : 3.947 15.393 2250 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.62 % Allowed : 12.78 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.19), residues: 2007 helix: 2.20 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -1.40 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 147 =============================================================================== Job complete usr+sys time: 6038.85 seconds wall clock time: 106 minutes 59.76 seconds (6419.76 seconds total)