Starting phenix.real_space_refine on Wed Aug 7 19:48:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/08_2024/6nud_0516.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/08_2024/6nud_0516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/08_2024/6nud_0516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/08_2024/6nud_0516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/08_2024/6nud_0516.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nud_0516/08_2024/6nud_0516.cif" } resolution = 3.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 39 5.16 5 C 13003 2.51 5 N 3532 2.21 5 O 4188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 370": "NH1" <-> "NH2" Residue "J ARG 383": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "J ARG 397": "NH1" <-> "NH2" Residue "J ARG 421": "NH1" <-> "NH2" Residue "J ARG 515": "NH1" <-> "NH2" Residue "J ARG 531": "NH1" <-> "NH2" Residue "J ARG 655": "NH1" <-> "NH2" Residue "J ARG 678": "NH1" <-> "NH2" Residue "J ARG 720": "NH1" <-> "NH2" Residue "M ARG 65": "NH1" <-> "NH2" Residue "M ARG 74": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 171": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 171": "NH1" <-> "NH2" Residue "E ARG 188": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "N ARG 143": "NH1" <-> "NH2" Residue "N ARG 171": "NH1" <-> "NH2" Residue "N ARG 188": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 143": "NH1" <-> "NH2" Residue "O ARG 171": "NH1" <-> "NH2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "P ARG 81": "NH1" <-> "NH2" Residue "P ARG 115": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 143": "NH1" <-> "NH2" Residue "P ARG 171": "NH1" <-> "NH2" Residue "P ARG 188": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20831 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "B" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "H" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 832 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 14, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 19} Chain: "I" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2352 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 283} Chain: "J" Number of atoms: 5997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5997 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 8, 'TRANS': 732} Chain breaks: 1 Chain: "M" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Link IDs: {'TRANS': 107} Chain: "U" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 602 Classifications: {'RNA': 28} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 21} Chain: "C" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "E" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "N" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "O" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "P" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1667 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.47, per 1000 atoms: 0.60 Number of scatterers: 20831 At special positions: 0 Unit cell: (93.28, 119.78, 212, 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 39 16.00 P 69 15.00 O 4188 8.00 N 3532 7.00 C 13003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 7.73 Conformation dependent library (CDL) restraints added in 3.5 seconds 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4544 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 26 sheets defined 33.7% alpha, 10.0% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.760A pdb=" N LEU A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 47 removed outlier: 4.156A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 46 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 71 removed outlier: 3.579A pdb=" N TYR A 63 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 removed outlier: 4.038A pdb=" N LYS A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.884A pdb=" N ALA A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 94' Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.832A pdb=" N ARG A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU A 108 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.709A pdb=" N TYR A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.547A pdb=" N LEU B 19 " --> pdb=" O ARG B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 removed outlier: 4.153A pdb=" N CYS B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 46 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.823A pdb=" N ARG B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 71 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 75 through 86 removed outlier: 4.087A pdb=" N LYS B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LEU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 removed outlier: 4.137A pdb=" N ALA B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 94' Processing helix chain 'B' and resid 96 through 107 removed outlier: 3.771A pdb=" N ARG B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.501A pdb=" N TYR B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.947A pdb=" N PHE I 33 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA I 35 " --> pdb=" O ARG I 31 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL I 37 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 42 " --> pdb=" O LEU I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 54 removed outlier: 3.875A pdb=" N LEU I 50 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU I 52 " --> pdb=" O ALA I 48 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 102 removed outlier: 3.922A pdb=" N ARG I 95 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS I 98 " --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU I 99 " --> pdb=" O ARG I 95 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 118 removed outlier: 3.534A pdb=" N GLY I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU I 118 " --> pdb=" O TYR I 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 113 through 118' Processing helix chain 'I' and resid 165 through 169 Processing helix chain 'I' and resid 172 through 176 removed outlier: 3.564A pdb=" N TYR I 175 " --> pdb=" O SER I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 230 removed outlier: 3.663A pdb=" N GLU I 230 " --> pdb=" O GLU I 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 12 removed outlier: 3.575A pdb=" N PHE J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR J 10 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA J 12 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 25 removed outlier: 4.013A pdb=" N ILE J 21 " --> pdb=" O ILE J 17 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA J 24 " --> pdb=" O VAL J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 43 removed outlier: 4.187A pdb=" N GLY J 35 " --> pdb=" O HIS J 31 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE J 42 " --> pdb=" O TRP J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 54 removed outlier: 3.573A pdb=" N ASP J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN J 51 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR J 54 " --> pdb=" O ASP J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 81 removed outlier: 3.570A pdb=" N ILE J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER J 81 " --> pdb=" O ASP J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 114 Processing helix chain 'J' and resid 173 through 178 removed outlier: 3.840A pdb=" N GLU J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 184 removed outlier: 4.170A pdb=" N PHE J 183 " --> pdb=" O ILE J 180 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 184 " --> pdb=" O LEU J 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 180 through 184' Processing helix chain 'J' and resid 197 through 219 removed outlier: 3.857A pdb=" N ARG J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA J 207 " --> pdb=" O ARG J 203 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 238 removed outlier: 3.829A pdb=" N GLU J 237 " --> pdb=" O SER J 233 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU J 238 " --> pdb=" O ALA J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 290 removed outlier: 4.175A pdb=" N LEU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP J 275 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE J 276 " --> pdb=" O LEU J 272 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET J 277 " --> pdb=" O TYR J 273 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER J 278 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU J 279 " --> pdb=" O ASP J 275 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE J 281 " --> pdb=" O MET J 277 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA J 282 " --> pdb=" O SER J 278 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU J 285 " --> pdb=" O ILE J 281 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU J 286 " --> pdb=" O ALA J 282 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY J 290 " --> pdb=" O LEU J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 296 removed outlier: 4.333A pdb=" N ASN J 295 " --> pdb=" O ASN J 292 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 296 " --> pdb=" O ARG J 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 292 through 296' Processing helix chain 'J' and resid 312 through 326 removed outlier: 4.123A pdb=" N GLU J 316 " --> pdb=" O GLU J 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR J 317 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU J 318 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL J 319 " --> pdb=" O VAL J 315 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS J 323 " --> pdb=" O VAL J 319 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN J 326 " --> pdb=" O GLU J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 351 removed outlier: 3.673A pdb=" N ASP J 350 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE J 351 " --> pdb=" O ALA J 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 347 through 351' Processing helix chain 'J' and resid 357 through 367 removed outlier: 4.177A pdb=" N TYR J 361 " --> pdb=" O SER J 357 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE J 364 " --> pdb=" O SER J 360 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR J 365 " --> pdb=" O TYR J 361 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 376 Processing helix chain 'J' and resid 384 through 388 Processing helix chain 'J' and resid 420 through 428 removed outlier: 4.278A pdb=" N TYR J 424 " --> pdb=" O CYS J 420 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN J 425 " --> pdb=" O ARG J 421 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS J 428 " --> pdb=" O TYR J 424 " (cutoff:3.500A) Processing helix chain 'J' and resid 539 through 552 removed outlier: 3.572A pdb=" N SER J 543 " --> pdb=" O THR J 539 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET J 550 " --> pdb=" O PHE J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 555 through 561 removed outlier: 3.908A pdb=" N ASN J 559 " --> pdb=" O LYS J 555 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN J 560 " --> pdb=" O VAL J 556 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 601 removed outlier: 3.824A pdb=" N ILE J 586 " --> pdb=" O SER J 582 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE J 587 " --> pdb=" O TRP J 583 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ALA J 588 " --> pdb=" O GLN J 584 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL J 591 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG J 594 " --> pdb=" O THR J 590 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN J 595 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN J 596 " --> pdb=" O GLU J 592 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE J 597 " --> pdb=" O LEU J 593 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS J 599 " --> pdb=" O GLN J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 627 removed outlier: 4.304A pdb=" N HIS J 625 " --> pdb=" O SER J 621 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR J 627 " --> pdb=" O MET J 623 " (cutoff:3.500A) Processing helix chain 'J' and resid 628 through 634 removed outlier: 3.830A pdb=" N GLU J 632 " --> pdb=" O GLY J 628 " (cutoff:3.500A) Processing helix chain 'J' and resid 635 through 637 No H-bonds generated for 'chain 'J' and resid 635 through 637' Processing helix chain 'J' and resid 654 through 659 Processing helix chain 'J' and resid 662 through 667 removed outlier: 3.621A pdb=" N GLU J 666 " --> pdb=" O ASP J 662 " (cutoff:3.500A) Processing helix chain 'J' and resid 672 through 676 Processing helix chain 'J' and resid 679 through 682 Processing helix chain 'J' and resid 683 through 690 removed outlier: 3.557A pdb=" N ILE J 687 " --> pdb=" O ILE J 683 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU J 690 " --> pdb=" O LEU J 686 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 708 removed outlier: 3.502A pdb=" N VAL J 701 " --> pdb=" O GLU J 697 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA J 702 " --> pdb=" O LYS J 698 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 704 " --> pdb=" O ASN J 700 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR J 706 " --> pdb=" O ALA J 702 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR J 707 " --> pdb=" O ARG J 703 " (cutoff:3.500A) Processing helix chain 'J' and resid 709 through 714 removed outlier: 4.302A pdb=" N GLU J 713 " --> pdb=" O THR J 709 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU J 714 " --> pdb=" O ARG J 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 709 through 714' Processing helix chain 'J' and resid 719 through 722 removed outlier: 3.527A pdb=" N LYS J 722 " --> pdb=" O GLU J 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 719 through 722' Processing helix chain 'J' and resid 723 through 733 removed outlier: 3.668A pdb=" N LEU J 729 " --> pdb=" O GLN J 725 " (cutoff:3.500A) Processing helix chain 'J' and resid 740 through 755 removed outlier: 3.804A pdb=" N ALA J 744 " --> pdb=" O ASP J 740 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR J 751 " --> pdb=" O ALA J 747 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL J 752 " --> pdb=" O LEU J 748 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR J 753 " --> pdb=" O LEU J 749 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE J 755 " --> pdb=" O TYR J 751 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 20 removed outlier: 3.516A pdb=" N LEU M 19 " --> pdb=" O ARG M 15 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU M 20 " --> pdb=" O ALA M 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 15 through 20' Processing helix chain 'M' and resid 39 through 50 removed outlier: 3.764A pdb=" N SER M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER M 44 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR M 46 " --> pdb=" O CYS M 42 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP M 47 " --> pdb=" O SER M 43 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS M 50 " --> pdb=" O TYR M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 71 removed outlier: 4.125A pdb=" N SER M 62 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG M 65 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL M 66 " --> pdb=" O SER M 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN M 67 " --> pdb=" O TYR M 63 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL M 69 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN M 71 " --> pdb=" O GLN M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 86 removed outlier: 3.991A pdb=" N LYS M 79 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP M 80 " --> pdb=" O ILE M 76 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 94 removed outlier: 4.145A pdb=" N ALA M 90 " --> pdb=" O GLN M 86 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU M 91 " --> pdb=" O ILE M 87 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU M 93 " --> pdb=" O GLU M 89 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 86 through 94' Processing helix chain 'M' and resid 96 through 108 removed outlier: 3.769A pdb=" N ARG M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE M 103 " --> pdb=" O THR M 99 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG M 105 " --> pdb=" O GLN M 101 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU M 108 " --> pdb=" O CYS M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 113 Processing helix chain 'C' and resid 50 through 61 removed outlier: 3.636A pdb=" N GLY C 54 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 110 removed outlier: 3.834A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 179 removed outlier: 3.591A pdb=" N PHE C 167 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.629A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 removed outlier: 3.861A pdb=" N PHE E 83 " --> pdb=" O LEU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 110 removed outlier: 4.275A pdb=" N ASP E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 163 through 178 removed outlier: 3.742A pdb=" N LYS E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 61 removed outlier: 3.666A pdb=" N LYS N 53 " --> pdb=" O GLY N 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG N 57 " --> pdb=" O LYS N 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR N 58 " --> pdb=" O GLY N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.531A pdb=" N LEU N 82 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 79 through 83' Processing helix chain 'N' and resid 105 through 113 removed outlier: 4.166A pdb=" N ASP N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU N 112 " --> pdb=" O GLU N 108 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY N 113 " --> pdb=" O LEU N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 179 removed outlier: 3.922A pdb=" N LYS N 168 " --> pdb=" O GLU N 164 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL N 169 " --> pdb=" O GLU N 165 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU N 178 " --> pdb=" O LEU N 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU N 179 " --> pdb=" O LYS N 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 189 removed outlier: 4.250A pdb=" N ARG N 188 " --> pdb=" O SER N 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 61 removed outlier: 3.608A pdb=" N GLY O 54 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 84 removed outlier: 3.977A pdb=" N PHE O 83 " --> pdb=" O LEU O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 110 removed outlier: 4.449A pdb=" N ASP O 110 " --> pdb=" O ALA O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 113 No H-bonds generated for 'chain 'O' and resid 111 through 113' Processing helix chain 'O' and resid 162 through 178 removed outlier: 4.532A pdb=" N LYS O 168 " --> pdb=" O GLU O 164 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL O 169 " --> pdb=" O GLU O 165 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU O 178 " --> pdb=" O LEU O 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 61 removed outlier: 3.661A pdb=" N LYS P 53 " --> pdb=" O GLY P 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET P 56 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR P 58 " --> pdb=" O GLY P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 84 removed outlier: 3.756A pdb=" N PHE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 110 removed outlier: 4.585A pdb=" N ASP P 110 " --> pdb=" O ALA P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 113 No H-bonds generated for 'chain 'P' and resid 111 through 113' Processing helix chain 'P' and resid 162 through 178 removed outlier: 3.708A pdb=" N LYS P 168 " --> pdb=" O GLU P 164 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL P 169 " --> pdb=" O GLU P 165 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU P 178 " --> pdb=" O LEU P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 189 removed outlier: 4.450A pdb=" N ARG P 188 " --> pdb=" O SER P 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 5 through 6 removed outlier: 4.258A pdb=" N PHE I 64 " --> pdb=" O TYR I 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 72 through 73 Processing sheet with id=AA3, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.607A pdb=" N ASP I 129 " --> pdb=" O THR I 147 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 145 " --> pdb=" O VAL I 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 204 through 205 removed outlier: 3.726A pdb=" N PHE I 294 " --> pdb=" O THR I 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 303 through 307 removed outlier: 4.465A pdb=" N ALA J 304 " --> pdb=" O PHE J 246 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE J 246 " --> pdb=" O ALA J 304 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA J 340 " --> pdb=" O ASP J 247 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR J 338 " --> pdb=" O SER J 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 303 through 307 removed outlier: 4.465A pdb=" N ALA J 304 " --> pdb=" O PHE J 246 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE J 246 " --> pdb=" O ALA J 304 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE J 241 " --> pdb=" O PHE J 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 434 through 436 removed outlier: 4.315A pdb=" N HIS J 434 " --> pdb=" O VAL J 454 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 568 through 570 removed outlier: 3.745A pdb=" N SER J 568 " --> pdb=" O ILE J 580 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE J 580 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL J 514 " --> pdb=" O ALA J 579 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY J 581 " --> pdb=" O ALA J 512 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA J 512 " --> pdb=" O GLY J 581 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU J 511 " --> pdb=" O PHE J 614 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE J 614 " --> pdb=" O LEU J 511 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 517 through 518 Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 97 removed outlier: 7.781A pdb=" N LYS C 5 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR C 202 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS C 7 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA C 200 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER C 9 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU C 198 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 119 through 122 Processing sheet with id=AB3, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AB4, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AB5, first strand: chain 'E' and resid 119 through 122 Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.071A pdb=" N THR E 125 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 133 " --> pdb=" O THR E 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 96 through 97 removed outlier: 3.503A pdb=" N ILE N 152 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 148 through 149 removed outlier: 3.518A pdb=" N PHE N 149 " --> pdb=" O ALA N 10 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA N 10 " --> pdb=" O PHE N 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 119 through 122 Processing sheet with id=AC1, first strand: chain 'N' and resid 125 through 126 removed outlier: 3.517A pdb=" N THR N 125 " --> pdb=" O ALA N 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 148 through 154 Processing sheet with id=AC3, first strand: chain 'O' and resid 148 through 154 Processing sheet with id=AC4, first strand: chain 'O' and resid 118 through 122 Processing sheet with id=AC5, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AC6, first strand: chain 'P' and resid 96 through 97 Processing sheet with id=AC7, first strand: chain 'P' and resid 119 through 122 removed outlier: 3.531A pdb=" N LYS P 121 " --> pdb=" O ILE P 138 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 125 through 126 removed outlier: 4.356A pdb=" N THR P 125 " --> pdb=" O ALA P 133 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA P 133 " --> pdb=" O THR P 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 380 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 8.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5978 1.33 - 1.45: 3663 1.45 - 1.57: 11494 1.57 - 1.69: 137 1.69 - 1.81: 66 Bond restraints: 21338 Sorted by residual: bond pdb=" C4 ATP J 801 " pdb=" C5 ATP J 801 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C5 ATP J 801 " pdb=" C6 ATP J 801 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C8 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.29e+01 bond pdb=" C5 ATP J 801 " pdb=" N7 ATP J 801 " ideal model delta sigma weight residual 1.387 1.345 0.042 1.00e-02 1.00e+04 1.74e+01 bond pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.51e+01 ... (remaining 21333 not shown) Histogram of bond angle deviations from ideal: 100.87 - 107.91: 822 107.91 - 114.95: 12724 114.95 - 121.99: 11005 121.99 - 129.03: 4386 129.03 - 136.07: 103 Bond angle restraints: 29040 Sorted by residual: angle pdb=" PB ATP J 801 " pdb=" O3B ATP J 801 " pdb=" PG ATP J 801 " ideal model delta sigma weight residual 139.87 120.91 18.96 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PA ATP J 801 " pdb=" O3A ATP J 801 " pdb=" PB ATP J 801 " ideal model delta sigma weight residual 136.83 120.59 16.24 1.00e+00 1.00e+00 2.64e+02 angle pdb=" C5 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N3 ATP J 801 " ideal model delta sigma weight residual 126.80 118.63 8.17 1.00e+00 1.00e+00 6.67e+01 angle pdb=" N3 ATP J 801 " pdb=" C4 ATP J 801 " pdb=" N9 ATP J 801 " ideal model delta sigma weight residual 127.04 135.06 -8.02 1.15e+00 7.59e-01 4.88e+01 angle pdb=" N VAL O 63 " pdb=" CA VAL O 63 " pdb=" C VAL O 63 " ideal model delta sigma weight residual 113.71 108.94 4.77 9.50e-01 1.11e+00 2.52e+01 ... (remaining 29035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 12728 35.48 - 70.97: 213 70.97 - 106.45: 17 106.45 - 141.94: 0 141.94 - 177.42: 13 Dihedral angle restraints: 12971 sinusoidal: 5914 harmonic: 7057 Sorted by residual: dihedral pdb=" O4' U U 21 " pdb=" C1' U U 21 " pdb=" N1 U U 21 " pdb=" C2 U U 21 " ideal model delta sinusoidal sigma weight residual 200.00 50.16 149.84 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" O4' C H 17 " pdb=" C1' C H 17 " pdb=" N1 C H 17 " pdb=" C2 C H 17 " ideal model delta sinusoidal sigma weight residual 200.00 54.59 145.41 1 1.50e+01 4.44e-03 7.78e+01 dihedral pdb=" O4' U U 14 " pdb=" C1' U U 14 " pdb=" N1 U U 14 " pdb=" C2 U U 14 " ideal model delta sinusoidal sigma weight residual 200.00 54.64 145.36 1 1.50e+01 4.44e-03 7.78e+01 ... (remaining 12968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2099 0.028 - 0.056: 881 0.056 - 0.084: 153 0.084 - 0.112: 106 0.112 - 0.140: 24 Chirality restraints: 3263 Sorted by residual: chirality pdb=" CB ILE J 755 " pdb=" CA ILE J 755 " pdb=" CG1 ILE J 755 " pdb=" CG2 ILE J 755 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE N 32 " pdb=" N ILE N 32 " pdb=" C ILE N 32 " pdb=" CB ILE N 32 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" C1' C H 40 " pdb=" O4' C H 40 " pdb=" C2' C H 40 " pdb=" N1 C H 40 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 3260 not shown) Planarity restraints: 3491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE I 196 " -0.015 5.00e-02 4.00e+02 2.30e-02 8.44e-01 pdb=" N PRO I 197 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO I 197 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 197 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 71 " -0.014 5.00e-02 4.00e+02 2.09e-02 6.99e-01 pdb=" N PRO E 72 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO E 72 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 72 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE O 44 " 0.014 5.00e-02 4.00e+02 2.09e-02 6.96e-01 pdb=" N PRO O 45 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO O 45 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO O 45 " 0.012 5.00e-02 4.00e+02 ... (remaining 3488 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6116 2.81 - 3.33: 17470 3.33 - 3.86: 31472 3.86 - 4.38: 35916 4.38 - 4.90: 61996 Nonbonded interactions: 152970 Sorted by model distance: nonbonded pdb=" O HIS I 233 " pdb=" OG SER I 264 " model vdw 2.290 3.040 nonbonded pdb=" OE2 GLU N 123 " pdb=" OH TYR N 190 " model vdw 2.313 3.040 nonbonded pdb=" O2' G U 20 " pdb=" O2 U U 21 " model vdw 2.315 3.040 nonbonded pdb=" O2' A U 23 " pdb=" OD1 ASN N 134 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR I 130 " pdb=" O VAL I 145 " model vdw 2.322 3.040 ... (remaining 152965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.170 Set scattering table: 0.180 Process input model: 58.770 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4507 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 : 0.002 0.083 21338 Z= 0.101 Angle : 0.430 18.961 29040 Z= 0.290 Chirality : 0.035 0.140 3263 Planarity : 0.002 0.023 3491 Dihedral : 13.139 177.424 8427 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 1.54 % Allowed : 14.97 % Favored : 83.49 % Rotamer: Outliers : 0.29 % Allowed : 5.67 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -5.22 (0.12), residues: 2398 helix: -4.63 (0.08), residues: 528 sheet: -2.72 (0.24), residues: 339 loop : -3.39 (0.12), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP J 733 HIS 0.001 0.000 HIS I 233 PHE 0.004 0.000 PHE J 246 TYR 0.005 0.000 TYR J 473 ARG 0.001 0.000 ARG I 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 737 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 TYR cc_start: 0.2704 (t80) cc_final: 0.2452 (t80) REVERT: J 251 ILE cc_start: 0.7504 (mt) cc_final: 0.7259 (mt) outliers start: 6 outliers final: 0 residues processed: 741 average time/residue: 0.3639 time to fit residues: 393.3225 Evaluate side-chains 320 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 116 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 221 optimal weight: 7.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN I 12 ASN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 ASN I 284 HIS J 78 ASN J 129 ASN ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN J 389 ASN J 412 HIS J 489 GLN J 502 ASN J 534 ASN ** J 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN J 675 GLN J 700 ASN J 725 GLN M 27 ASN C 85 ASN C 105 ASN C 144 ASN E 85 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN N 11 GLN N 213 ASN O 105 ASN O 159 ASN O 213 ASN P 105 ASN ** P 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 213 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21338 Z= 0.293 Angle : 0.745 12.401 29040 Z= 0.380 Chirality : 0.045 0.232 3263 Planarity : 0.005 0.048 3491 Dihedral : 15.100 177.173 3681 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.47 % Favored : 89.45 % Rotamer: Outliers : 3.80 % Allowed : 14.38 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.30 (0.14), residues: 2398 helix: -3.22 (0.15), residues: 582 sheet: -2.46 (0.26), residues: 333 loop : -2.92 (0.13), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP J 38 HIS 0.010 0.002 HIS J 482 PHE 0.031 0.002 PHE C 102 TYR 0.028 0.002 TYR J 468 ARG 0.008 0.001 ARG J 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 374 time to evaluate : 2.198 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: I 8 MET cc_start: 0.6752 (ptt) cc_final: 0.6478 (ptt) REVERT: J 243 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7871 (tt) REVERT: J 336 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6636 (ptt180) REVERT: C 92 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5760 (mmtt) REVERT: P 103 LEU cc_start: 0.5020 (tt) cc_final: 0.4290 (tt) outliers start: 79 outliers final: 40 residues processed: 429 average time/residue: 0.3216 time to fit residues: 213.0638 Evaluate side-chains 299 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 256 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 54 TYR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 541 SER Chi-restraints excluded: chain J residue 549 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 197 optimal weight: 0.3980 chunk 220 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 HIS ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN J 532 GLN J 536 GLN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 584 GLN J 602 ASN E 11 GLN E 159 ASN O 159 ASN P 65 ASN P 85 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.6632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21338 Z= 0.217 Angle : 0.623 9.091 29040 Z= 0.315 Chirality : 0.042 0.210 3263 Planarity : 0.004 0.046 3491 Dihedral : 15.194 179.045 3681 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 4.04 % Allowed : 16.49 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.73 (0.15), residues: 2398 helix: -2.32 (0.17), residues: 644 sheet: -1.92 (0.28), residues: 304 loop : -2.80 (0.14), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 38 HIS 0.008 0.001 HIS J 434 PHE 0.020 0.002 PHE P 98 TYR 0.018 0.002 TYR N 181 ARG 0.006 0.001 ARG J 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 291 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 8 MET cc_start: 0.7058 (ptt) cc_final: 0.6702 (ptt) REVERT: J 266 GLN cc_start: 0.7461 (pp30) cc_final: 0.7161 (pp30) REVERT: J 336 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6759 (ptt180) REVERT: J 589 PHE cc_start: 0.4394 (t80) cc_final: 0.4147 (t80) REVERT: J 623 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6090 (tmm) REVERT: E 81 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6412 (pmt100) REVERT: N 198 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7297 (tp) REVERT: O 119 GLU cc_start: 0.6001 (pm20) cc_final: 0.5670 (pm20) REVERT: P 76 SER cc_start: 0.7188 (OUTLIER) cc_final: 0.6903 (m) outliers start: 84 outliers final: 49 residues processed: 356 average time/residue: 0.3277 time to fit residues: 180.2020 Evaluate side-chains 275 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 221 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 42 CYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 155 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 371 MET Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 532 GLN Chi-restraints excluded: chain J residue 541 SER Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 222 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN ** J 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 602 ASN J 626 GLN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.8015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21338 Z= 0.263 Angle : 0.664 10.642 29040 Z= 0.339 Chirality : 0.043 0.185 3263 Planarity : 0.004 0.047 3491 Dihedral : 15.477 178.376 3681 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.18 % Allowed : 17.07 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.42 (0.15), residues: 2398 helix: -1.91 (0.18), residues: 689 sheet: -1.63 (0.28), residues: 309 loop : -2.72 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 343 HIS 0.010 0.002 HIS J 434 PHE 0.021 0.002 PHE P 98 TYR 0.020 0.002 TYR J 649 ARG 0.011 0.001 ARG J 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 267 time to evaluate : 2.435 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: A 106 TYR cc_start: 0.5184 (t80) cc_final: 0.4979 (t80) REVERT: I 8 MET cc_start: 0.7530 (ptt) cc_final: 0.7324 (ptt) REVERT: J 283 ASP cc_start: 0.4568 (t0) cc_final: 0.4094 (t0) REVERT: J 336 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6909 (ptt-90) REVERT: J 623 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.5838 (tmm) REVERT: E 81 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6267 (pmt100) REVERT: O 119 GLU cc_start: 0.6255 (pm20) cc_final: 0.5843 (pm20) outliers start: 87 outliers final: 54 residues processed: 333 average time/residue: 0.3071 time to fit residues: 162.9799 Evaluate side-chains 268 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 211 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 206 LYS Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 541 SER Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 592 GLU Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 648 ASP Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 169 VAL Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 12 ILE Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 202 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.4980 chunk 211 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 12 ASN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 471 ASN ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.8223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21338 Z= 0.180 Angle : 0.588 10.262 29040 Z= 0.296 Chirality : 0.041 0.235 3263 Planarity : 0.003 0.045 3491 Dihedral : 15.419 178.667 3681 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 3.80 % Allowed : 19.33 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.10 (0.15), residues: 2398 helix: -1.55 (0.18), residues: 702 sheet: -1.52 (0.28), residues: 313 loop : -2.54 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 101 HIS 0.006 0.001 HIS J 434 PHE 0.021 0.001 PHE O 102 TYR 0.031 0.002 TYR I 289 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 234 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 8 MET cc_start: 0.7444 (ptt) cc_final: 0.7208 (ptt) REVERT: J 336 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6659 (ptt180) REVERT: J 623 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.5810 (tmm) REVERT: E 81 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6084 (pmt100) REVERT: N 151 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7352 (tp) REVERT: P 179 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6704 (mt) outliers start: 79 outliers final: 48 residues processed: 300 average time/residue: 0.3092 time to fit residues: 146.5604 Evaluate side-chains 264 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 211 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 206 LYS Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 225 LEU Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 311 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 485 VAL Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 749 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 148 ASP Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 203 VAL Chi-restraints excluded: chain O residue 207 TYR Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 179 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 236 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 GLN ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 494 HIS C 124 ASN ** N 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 134 ASN O 137 GLN ** P 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.9693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 21338 Z= 0.392 Angle : 0.776 10.277 29040 Z= 0.398 Chirality : 0.048 0.260 3263 Planarity : 0.005 0.048 3491 Dihedral : 16.032 175.483 3681 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 4.42 % Allowed : 19.57 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.14 (0.16), residues: 2398 helix: -1.71 (0.18), residues: 732 sheet: -1.76 (0.30), residues: 286 loop : -2.44 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP J 343 HIS 0.010 0.002 HIS J 434 PHE 0.027 0.003 PHE A 103 TYR 0.025 0.002 TYR J 298 ARG 0.006 0.001 ARG J 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 236 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 235 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8302 (tt) REVERT: J 623 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.5648 (tmm) REVERT: E 81 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6240 (pmt100) REVERT: E 102 PHE cc_start: 0.3273 (OUTLIER) cc_final: 0.2948 (p90) REVERT: O 81 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7350 (pmt100) REVERT: P 179 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6981 (mt) outliers start: 92 outliers final: 56 residues processed: 314 average time/residue: 0.3385 time to fit residues: 164.2939 Evaluate side-chains 255 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 193 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 206 LYS Chi-restraints excluded: chain I residue 235 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 327 GLN Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 482 HIS Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 514 VAL Chi-restraints excluded: chain J residue 541 SER Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 206 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 chunk 198 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 0.0970 chunk 108 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 HIS C 124 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.9608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21338 Z= 0.157 Angle : 0.609 9.930 29040 Z= 0.305 Chirality : 0.041 0.160 3263 Planarity : 0.003 0.046 3491 Dihedral : 15.741 179.889 3681 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.17 % Allowed : 21.44 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.81 (0.16), residues: 2398 helix: -1.33 (0.18), residues: 733 sheet: -1.57 (0.28), residues: 334 loop : -2.30 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 101 HIS 0.004 0.001 HIS J 434 PHE 0.026 0.001 PHE A 103 TYR 0.023 0.001 TYR J 298 ARG 0.003 0.000 ARG N 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 223 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLN cc_start: 0.3758 (mm-40) cc_final: 0.3435 (mm-40) REVERT: B 100 LEU cc_start: 0.5112 (tt) cc_final: 0.4729 (tt) REVERT: J 336 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6929 (ptt180) REVERT: J 623 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5569 (tmm) REVERT: E 81 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6006 (pmt100) REVERT: N 130 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.7022 (m) REVERT: O 119 GLU cc_start: 0.6941 (pp20) cc_final: 0.6635 (pt0) REVERT: P 179 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6921 (mt) outliers start: 66 outliers final: 36 residues processed: 275 average time/residue: 0.3526 time to fit residues: 151.6519 Evaluate side-chains 240 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 592 GLU Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 12 ASN ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 HIS ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 1.0180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21338 Z= 0.333 Angle : 0.715 10.078 29040 Z= 0.364 Chirality : 0.046 0.231 3263 Planarity : 0.004 0.046 3491 Dihedral : 15.943 176.239 3681 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 3.27 % Allowed : 21.63 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.71 (0.16), residues: 2398 helix: -1.28 (0.18), residues: 733 sheet: -1.44 (0.32), residues: 268 loop : -2.23 (0.15), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 343 HIS 0.006 0.001 HIS J 68 PHE 0.024 0.002 PHE A 103 TYR 0.019 0.002 TYR O 181 ARG 0.005 0.001 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 218 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 149 TYR cc_start: 0.5507 (OUTLIER) cc_final: 0.5202 (m-80) REVERT: J 623 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5536 (tmm) REVERT: E 81 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6148 (pmt100) REVERT: P 209 VAL cc_start: 0.5216 (t) cc_final: 0.4972 (m) outliers start: 68 outliers final: 50 residues processed: 276 average time/residue: 0.3113 time to fit residues: 135.3276 Evaluate side-chains 252 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 149 TYR Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 508 ILE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 592 GLU Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 647 SER Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 70 GLU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 179 LEU Chi-restraints excluded: chain P residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 205 optimal weight: 0.2980 chunk 219 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 0.0270 chunk 198 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 218 optimal weight: 0.6980 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN E 124 ASN E 134 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 1.0068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21338 Z= 0.159 Angle : 0.626 12.411 29040 Z= 0.311 Chirality : 0.041 0.173 3263 Planarity : 0.003 0.063 3491 Dihedral : 15.792 179.370 3681 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 2.93 % Allowed : 22.55 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.48 (0.16), residues: 2398 helix: -0.97 (0.19), residues: 713 sheet: -1.54 (0.28), residues: 333 loop : -2.09 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 101 HIS 0.011 0.001 HIS J 482 PHE 0.025 0.001 PHE J 546 TYR 0.022 0.001 TYR J 298 ARG 0.005 0.000 ARG O 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 218 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 336 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7155 (ptt-90) REVERT: J 623 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5501 (tmm) REVERT: E 81 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.5903 (pmt100) REVERT: P 179 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6984 (mt) outliers start: 61 outliers final: 42 residues processed: 270 average time/residue: 0.3440 time to fit residues: 143.8957 Evaluate side-chains 246 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 200 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 237 THR Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 592 GLU Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0020 chunk 231 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 0.0070 chunk 118 optimal weight: 0.4980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** N 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 1.0046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21338 Z= 0.154 Angle : 0.615 11.698 29040 Z= 0.303 Chirality : 0.041 0.164 3263 Planarity : 0.003 0.057 3491 Dihedral : 15.646 178.730 3681 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.21 % Allowed : 23.17 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.34 (0.17), residues: 2398 helix: -0.82 (0.19), residues: 725 sheet: -1.30 (0.28), residues: 318 loop : -2.09 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 101 HIS 0.009 0.001 HIS J 482 PHE 0.025 0.001 PHE O 167 TYR 0.024 0.001 TYR A 106 ARG 0.005 0.000 ARG O 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4796 Ramachandran restraints generated. 2398 Oldfield, 0 Emsley, 2398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 213 MET cc_start: 0.7633 (tmm) cc_final: 0.7005 (ttt) REVERT: I 215 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8194 (pp) REVERT: J 336 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6916 (ptt180) REVERT: J 623 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5509 (tmm) REVERT: E 81 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.5879 (pmt100) REVERT: P 179 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6970 (mt) outliers start: 46 outliers final: 35 residues processed: 265 average time/residue: 0.3358 time to fit residues: 138.3581 Evaluate side-chains 250 residues out of total 2080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 145 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 233 SER Chi-restraints excluded: chain J residue 247 ASP Chi-restraints excluded: chain J residue 260 THR Chi-restraints excluded: chain J residue 336 ARG Chi-restraints excluded: chain J residue 343 TRP Chi-restraints excluded: chain J residue 373 SER Chi-restraints excluded: chain J residue 384 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 464 PHE Chi-restraints excluded: chain J residue 513 VAL Chi-restraints excluded: chain J residue 554 PHE Chi-restraints excluded: chain J residue 623 MET Chi-restraints excluded: chain J residue 657 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 206 ASN Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain P residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: