Starting phenix.real_space_refine on Sun Apr 14 20:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbu_38229/04_2024/8xbu_38229.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbu_38229/04_2024/8xbu_38229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbu_38229/04_2024/8xbu_38229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbu_38229/04_2024/8xbu_38229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbu_38229/04_2024/8xbu_38229.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbu_38229/04_2024/8xbu_38229.pdb" } resolution = 4.24 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= 0.000 sd= 0.001 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 309 5.49 5 S 131 5.16 5 C 19432 2.51 5 N 5887 2.21 5 O 6808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 42": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "K ARG 27": "NH1" <-> "NH2" Residue "K ARG 130": "NH1" <-> "NH2" Residue "K ARG 150": "NH1" <-> "NH2" Residue "K ARG 167": "NH1" <-> "NH2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 193": "NH1" <-> "NH2" Residue "K ARG 215": "NH1" <-> "NH2" Residue "K ARG 229": "NH1" <-> "NH2" Residue "K ARG 235": "NH1" <-> "NH2" Residue "K ARG 241": "NH1" <-> "NH2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "K ARG 250": "NH1" <-> "NH2" Residue "K ARG 254": "NH1" <-> "NH2" Residue "K ARG 299": "NH1" <-> "NH2" Residue "K ARG 303": "NH1" <-> "NH2" Residue "K ARG 306": "NH1" <-> "NH2" Residue "K ARG 310": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "L ARG 150": "NH1" <-> "NH2" Residue "L ARG 167": "NH1" <-> "NH2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "L ARG 177": "NH1" <-> "NH2" Residue "L ARG 193": "NH1" <-> "NH2" Residue "L ARG 229": "NH1" <-> "NH2" Residue "L ARG 235": "NH1" <-> "NH2" Residue "L ARG 241": "NH1" <-> "NH2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "L ARG 250": "NH1" <-> "NH2" Residue "L ARG 299": "NH1" <-> "NH2" Residue "L ARG 303": "NH1" <-> "NH2" Residue "L ARG 306": "NH1" <-> "NH2" Residue "L ARG 310": "NH1" <-> "NH2" Residue "M ARG 27": "NH1" <-> "NH2" Residue "M ARG 130": "NH1" <-> "NH2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M ARG 167": "NH1" <-> "NH2" Residue "M ARG 170": "NH1" <-> "NH2" Residue "M ARG 177": "NH1" <-> "NH2" Residue "M ARG 193": "NH1" <-> "NH2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M ARG 229": "NH1" <-> "NH2" Residue "M ARG 235": "NH1" <-> "NH2" Residue "M ARG 241": "NH1" <-> "NH2" Residue "M ARG 250": "NH1" <-> "NH2" Residue "M ARG 299": "NH1" <-> "NH2" Residue "M ARG 303": "NH1" <-> "NH2" Residue "M ARG 306": "NH1" <-> "NH2" Residue "M ARG 310": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "N ARG 150": "NH1" <-> "NH2" Residue "N ARG 167": "NH1" <-> "NH2" Residue "N ARG 170": "NH1" <-> "NH2" Residue "N ARG 177": "NH1" <-> "NH2" Residue "N ARG 193": "NH1" <-> "NH2" Residue "N ARG 215": "NH1" <-> "NH2" Residue "N ARG 229": "NH1" <-> "NH2" Residue "N ARG 235": "NH1" <-> "NH2" Residue "N ARG 241": "NH1" <-> "NH2" Residue "N ARG 247": "NH1" <-> "NH2" Residue "N ARG 250": "NH1" <-> "NH2" Residue "N ARG 254": "NH1" <-> "NH2" Residue "N ARG 299": "NH1" <-> "NH2" Residue "N ARG 303": "NH1" <-> "NH2" Residue "N ARG 306": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "O ARG 130": "NH1" <-> "NH2" Residue "O ARG 150": "NH1" <-> "NH2" Residue "O ARG 167": "NH1" <-> "NH2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O ARG 177": "NH1" <-> "NH2" Residue "O ARG 193": "NH1" <-> "NH2" Residue "O ARG 215": "NH1" <-> "NH2" Residue "O ARG 229": "NH1" <-> "NH2" Residue "O ARG 235": "NH1" <-> "NH2" Residue "O ARG 241": "NH1" <-> "NH2" Residue "O ARG 247": "NH1" <-> "NH2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O ARG 254": "NH1" <-> "NH2" Residue "O ARG 299": "NH1" <-> "NH2" Residue "O ARG 303": "NH1" <-> "NH2" Residue "O ARG 306": "NH1" <-> "NH2" Residue "O ARG 310": "NH1" <-> "NH2" Residue "P ARG 130": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "P ARG 167": "NH1" <-> "NH2" Residue "P ARG 170": "NH1" <-> "NH2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "P ARG 193": "NH1" <-> "NH2" Residue "P ARG 215": "NH1" <-> "NH2" Residue "P ARG 229": "NH1" <-> "NH2" Residue "P ARG 235": "NH1" <-> "NH2" Residue "P ARG 241": "NH1" <-> "NH2" Residue "P ARG 247": "NH1" <-> "NH2" Residue "P ARG 250": "NH1" <-> "NH2" Residue "P ARG 254": "NH1" <-> "NH2" Residue "P ARG 299": "NH1" <-> "NH2" Residue "P ARG 303": "NH1" <-> "NH2" Residue "P ARG 306": "NH1" <-> "NH2" Residue "P ARG 310": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ARG 130": "NH1" <-> "NH2" Residue "Q ARG 150": "NH1" <-> "NH2" Residue "Q ARG 167": "NH1" <-> "NH2" Residue "Q ARG 170": "NH1" <-> "NH2" Residue "Q ARG 177": "NH1" <-> "NH2" Residue "Q ARG 193": "NH1" <-> "NH2" Residue "Q ARG 215": "NH1" <-> "NH2" Residue "Q ARG 229": "NH1" <-> "NH2" Residue "Q ARG 235": "NH1" <-> "NH2" Residue "Q ARG 241": "NH1" <-> "NH2" Residue "Q ARG 247": "NH1" <-> "NH2" Residue "Q ARG 250": "NH1" <-> "NH2" Residue "Q ARG 254": "NH1" <-> "NH2" Residue "Q ARG 299": "NH1" <-> "NH2" Residue "Q ARG 303": "NH1" <-> "NH2" Residue "Q ARG 306": "NH1" <-> "NH2" Residue "Q ARG 310": "NH1" <-> "NH2" Residue "R ARG 27": "NH1" <-> "NH2" Residue "R ARG 130": "NH1" <-> "NH2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R ARG 167": "NH1" <-> "NH2" Residue "R ARG 170": "NH1" <-> "NH2" Residue "R ARG 177": "NH1" <-> "NH2" Residue "R ARG 193": "NH1" <-> "NH2" Residue "R ARG 215": "NH1" <-> "NH2" Residue "R ARG 229": "NH1" <-> "NH2" Residue "R ARG 235": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R ARG 247": "NH1" <-> "NH2" Residue "R ARG 250": "NH1" <-> "NH2" Residue "R ARG 254": "NH1" <-> "NH2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 303": "NH1" <-> "NH2" Residue "R ARG 306": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "S ARG 130": "NH1" <-> "NH2" Residue "S ARG 150": "NH1" <-> "NH2" Residue "S ARG 167": "NH1" <-> "NH2" Residue "S ARG 170": "NH1" <-> "NH2" Residue "S ARG 177": "NH1" <-> "NH2" Residue "S ARG 193": "NH1" <-> "NH2" Residue "S ARG 215": "NH1" <-> "NH2" Residue "S ARG 229": "NH1" <-> "NH2" Residue "S ARG 235": "NH1" <-> "NH2" Residue "S ARG 241": "NH1" <-> "NH2" Residue "S ARG 247": "NH1" <-> "NH2" Residue "S ARG 250": "NH1" <-> "NH2" Residue "S ARG 254": "NH1" <-> "NH2" Residue "S ARG 299": "NH1" <-> "NH2" Residue "S ARG 303": "NH1" <-> "NH2" Residue "S ARG 306": "NH1" <-> "NH2" Residue "S ARG 310": "NH1" <-> "NH2" Residue "T ARG 27": "NH1" <-> "NH2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 150": "NH1" <-> "NH2" Residue "T ARG 167": "NH1" <-> "NH2" Residue "T ARG 170": "NH1" <-> "NH2" Residue "T ARG 177": "NH1" <-> "NH2" Residue "T ARG 193": "NH1" <-> "NH2" Residue "T ARG 215": "NH1" <-> "NH2" Residue "T ARG 229": "NH1" <-> "NH2" Residue "T ARG 235": "NH1" <-> "NH2" Residue "T ARG 241": "NH1" <-> "NH2" Residue "T ARG 247": "NH1" <-> "NH2" Residue "T ARG 250": "NH1" <-> "NH2" Residue "T ARG 254": "NH1" <-> "NH2" Residue "T ARG 299": "NH1" <-> "NH2" Residue "T ARG 303": "NH1" <-> "NH2" Residue "T ARG 306": "NH1" <-> "NH2" Residue "T ARG 310": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 32567 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 714 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3189 Classifications: {'DNA': 156} Link IDs: {'rna3p': 155} Chain: "J" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3143 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "L" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "M" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "N" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "O" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "P" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "Q" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Chain: "S" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1698 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 1 Chain: "T" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2163 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 2 Time building chain proxies: 16.90, per 1000 atoms: 0.52 Number of scatterers: 32567 At special positions: 0 Unit cell: (171.72, 156.88, 167.48, 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 131 16.00 P 309 15.00 O 6808 8.00 N 5887 7.00 C 19432 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: 16.36 Conformation dependent library (CDL) restraints added in 4.7 seconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6218 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 20 sheets defined 57.2% alpha, 14.2% beta 151 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 14.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.698A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.595A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.579A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.738A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.486A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 25 through 30 removed outlier: 3.751A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 30' Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.784A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.765A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 178 Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS K 294 " --> pdb=" O ASN K 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 30 removed outlier: 3.813A pdb=" N GLU L 29 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN L 30 " --> pdb=" O SER L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 30' Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 57 through 63 removed outlier: 3.783A pdb=" N ILE L 63 " --> pdb=" O GLU L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS L 80 " --> pdb=" O ALA L 76 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 146 No H-bonds generated for 'chain 'L' and resid 145 through 146' Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 178 Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS L 294 " --> pdb=" O ASN L 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 30 removed outlier: 3.813A pdb=" N GLU M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN M 30 " --> pdb=" O SER M 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 25 through 30' Processing helix chain 'M' and resid 34 through 45 Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 57 through 63 removed outlier: 3.783A pdb=" N ILE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU M 81 " --> pdb=" O GLU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 178 Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER M 214 " --> pdb=" O MET M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 removed outlier: 3.590A pdb=" N ARG M 229 " --> pdb=" O THR M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 31 removed outlier: 3.749A pdb=" N GLU N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN N 30 " --> pdb=" O SER N 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS N 31 " --> pdb=" O ARG N 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 25 through 31' Processing helix chain 'N' and resid 34 through 45 Processing helix chain 'N' and resid 48 through 54 Processing helix chain 'N' and resid 57 through 63 removed outlier: 3.784A pdb=" N ILE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 removed outlier: 3.815A pdb=" N VAL N 142 " --> pdb=" O HIS N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 146 No H-bonds generated for 'chain 'N' and resid 145 through 146' Processing helix chain 'N' and resid 147 through 151 Processing helix chain 'N' and resid 167 through 178 Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 231 removed outlier: 3.587A pdb=" N ARG N 229 " --> pdb=" O THR N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 290 through 296 removed outlier: 4.219A pdb=" N HIS N 294 " --> pdb=" O ASN N 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL O 142 " --> pdb=" O HIS O 138 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 146 No H-bonds generated for 'chain 'O' and resid 145 through 146' Processing helix chain 'O' and resid 147 through 151 Processing helix chain 'O' and resid 167 through 178 Processing helix chain 'O' and resid 181 through 188 Processing helix chain 'O' and resid 196 through 214 removed outlier: 4.099A pdb=" N LEU O 204 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR O 205 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN O 206 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA O 209 " --> pdb=" O TYR O 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL O 212 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU O 213 " --> pdb=" O ALA O 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER O 214 " --> pdb=" O MET O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG O 229 " --> pdb=" O THR O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS O 294 " --> pdb=" O ASN O 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 removed outlier: 3.815A pdb=" N VAL P 142 " --> pdb=" O HIS P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 146 No H-bonds generated for 'chain 'P' and resid 145 through 146' Processing helix chain 'P' and resid 147 through 151 Processing helix chain 'P' and resid 167 through 178 Processing helix chain 'P' and resid 181 through 188 Processing helix chain 'P' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR P 205 " --> pdb=" O THR P 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN P 206 " --> pdb=" O GLN P 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA P 209 " --> pdb=" O TYR P 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU P 213 " --> pdb=" O ALA P 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER P 214 " --> pdb=" O MET P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG P 229 " --> pdb=" O THR P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 260 Processing helix chain 'P' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA P 295 " --> pdb=" O ILE P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN Q 30 " --> pdb=" O SER Q 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 30' Processing helix chain 'Q' and resid 34 through 45 Processing helix chain 'Q' and resid 48 through 54 Processing helix chain 'Q' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE Q 63 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Q 81 " --> pdb=" O GLU Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'Q' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL Q 142 " --> pdb=" O HIS Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 146 No H-bonds generated for 'chain 'Q' and resid 145 through 146' Processing helix chain 'Q' and resid 147 through 151 Processing helix chain 'Q' and resid 167 through 178 Processing helix chain 'Q' and resid 181 through 188 Processing helix chain 'Q' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU Q 204 " --> pdb=" O GLN Q 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR Q 205 " --> pdb=" O THR Q 201 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN Q 206 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA Q 209 " --> pdb=" O TYR Q 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL Q 212 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU Q 213 " --> pdb=" O ALA Q 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER Q 214 " --> pdb=" O MET Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG Q 229 " --> pdb=" O THR Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 260 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN R 30 " --> pdb=" O SER R 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 25 through 30' Processing helix chain 'R' and resid 34 through 45 Processing helix chain 'R' and resid 48 through 54 Processing helix chain 'R' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE R 63 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 82 removed outlier: 3.767A pdb=" N LYS R 80 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL R 142 " --> pdb=" O HIS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 146 No H-bonds generated for 'chain 'R' and resid 145 through 146' Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 167 through 178 Processing helix chain 'R' and resid 181 through 188 Processing helix chain 'R' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU R 204 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN R 206 " --> pdb=" O GLN R 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA R 209 " --> pdb=" O TYR R 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG R 229 " --> pdb=" O THR R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 260 Processing helix chain 'R' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS R 294 " --> pdb=" O ASN R 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 113 Processing helix chain 'S' and resid 132 through 144 removed outlier: 3.813A pdb=" N VAL S 142 " --> pdb=" O HIS S 138 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 146 No H-bonds generated for 'chain 'S' and resid 145 through 146' Processing helix chain 'S' and resid 147 through 151 Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 181 through 188 Processing helix chain 'S' and resid 196 through 214 removed outlier: 4.100A pdb=" N LEU S 204 " --> pdb=" O GLN S 200 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR S 205 " --> pdb=" O THR S 201 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN S 206 " --> pdb=" O GLN S 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA S 209 " --> pdb=" O TYR S 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU S 213 " --> pdb=" O ALA S 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER S 214 " --> pdb=" O MET S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 231 removed outlier: 3.588A pdb=" N ARG S 229 " --> pdb=" O THR S 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 260 Processing helix chain 'S' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS S 294 " --> pdb=" O ASN S 290 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA S 295 " --> pdb=" O ILE S 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.750A pdb=" N GLU T 29 " --> pdb=" O ILE T 25 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN T 30 " --> pdb=" O SER T 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 25 through 30' Processing helix chain 'T' and resid 34 through 45 Processing helix chain 'T' and resid 48 through 54 Processing helix chain 'T' and resid 57 through 63 removed outlier: 3.785A pdb=" N ILE T 63 " --> pdb=" O GLU T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 82 removed outlier: 3.766A pdb=" N LYS T 80 " --> pdb=" O ALA T 76 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU T 81 " --> pdb=" O GLU T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 113 Processing helix chain 'T' and resid 132 through 144 removed outlier: 3.814A pdb=" N VAL T 142 " --> pdb=" O HIS T 138 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 146 No H-bonds generated for 'chain 'T' and resid 145 through 146' Processing helix chain 'T' and resid 147 through 151 Processing helix chain 'T' and resid 167 through 178 Processing helix chain 'T' and resid 181 through 188 Processing helix chain 'T' and resid 196 through 214 removed outlier: 4.101A pdb=" N LEU T 204 " --> pdb=" O GLN T 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR T 205 " --> pdb=" O THR T 201 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA T 209 " --> pdb=" O TYR T 205 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL T 212 " --> pdb=" O SER T 208 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU T 213 " --> pdb=" O ALA T 209 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER T 214 " --> pdb=" O MET T 210 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 231 removed outlier: 3.589A pdb=" N ARG T 229 " --> pdb=" O THR T 225 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 260 Processing helix chain 'T' and resid 290 through 296 removed outlier: 4.218A pdb=" N HIS T 294 " --> pdb=" O ASN T 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA T 295 " --> pdb=" O ILE T 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.075A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.827A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.244A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.825A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA K 190 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR K 159 " --> pdb=" O ALA K 190 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA K 192 " --> pdb=" O TYR K 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS K 156 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE K 220 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA L 190 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 159 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA L 192 " --> pdb=" O TYR L 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS L 156 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE L 220 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET L 158 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP L 222 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE L 160 " --> pdb=" O ASP L 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS L 304 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA M 190 " --> pdb=" O ALA M 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR M 159 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA M 192 " --> pdb=" O TYR M 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS M 156 " --> pdb=" O LEU M 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE M 220 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET M 158 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP M 222 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE M 160 " --> pdb=" O ASP M 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA N 190 " --> pdb=" O ALA N 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR N 159 " --> pdb=" O ALA N 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA N 192 " --> pdb=" O TYR N 159 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LYS N 156 " --> pdb=" O LEU N 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE N 220 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET N 158 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP N 222 " --> pdb=" O MET N 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE N 160 " --> pdb=" O ASP N 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN N 268 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE N 265 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET N 125 " --> pdb=" O ILE N 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN N 267 " --> pdb=" O MET N 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY N 127 " --> pdb=" O ASN N 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA O 190 " --> pdb=" O ALA O 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR O 159 " --> pdb=" O ALA O 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA O 192 " --> pdb=" O TYR O 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS O 156 " --> pdb=" O LEU O 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE O 220 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET O 158 " --> pdb=" O ILE O 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP O 222 " --> pdb=" O MET O 158 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE O 160 " --> pdb=" O ASP O 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA O 217 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL O 264 " --> pdb=" O ALA O 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU O 219 " --> pdb=" O VAL O 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR O 266 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL O 221 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN O 268 " --> pdb=" O VAL O 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE O 265 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET O 125 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN O 267 " --> pdb=" O MET O 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY O 127 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE O 122 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU O 300 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU O 124 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU O 302 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE O 126 " --> pdb=" O LEU O 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS O 304 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG O 299 " --> pdb=" O TYR O 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA P 190 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR P 159 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA P 192 " --> pdb=" O TYR P 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA P 217 " --> pdb=" O ALA P 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL P 264 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU P 219 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR P 266 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL P 221 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLN P 268 " --> pdb=" O VAL P 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE P 265 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET P 125 " --> pdb=" O ILE P 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN P 267 " --> pdb=" O MET P 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY P 127 " --> pdb=" O ASN P 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE P 122 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU P 300 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU P 124 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU P 302 " --> pdb=" O GLU P 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE P 126 " --> pdb=" O LEU P 302 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS P 304 " --> pdb=" O PHE P 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG P 299 " --> pdb=" O TYR P 315 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 189 through 193 removed outlier: 3.592A pdb=" N ALA Q 190 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR Q 159 " --> pdb=" O ALA Q 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA Q 192 " --> pdb=" O TYR Q 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS Q 156 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE Q 220 " --> pdb=" O LYS Q 156 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N MET Q 158 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP Q 222 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE Q 160 " --> pdb=" O ASP Q 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N GLN Q 268 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE Q 265 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET Q 125 " --> pdb=" O ILE Q 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN Q 267 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY Q 127 " --> pdb=" O ASN Q 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE Q 122 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU Q 300 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU Q 124 " --> pdb=" O LEU Q 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU Q 302 " --> pdb=" O GLU Q 124 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE Q 126 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS Q 304 " --> pdb=" O PHE Q 126 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG Q 299 " --> pdb=" O TYR Q 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 189 through 193 removed outlier: 3.591A pdb=" N ALA R 190 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR R 159 " --> pdb=" O ALA R 190 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA R 192 " --> pdb=" O TYR R 159 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS R 156 " --> pdb=" O LEU R 218 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ILE R 220 " --> pdb=" O LYS R 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET R 158 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP R 222 " --> pdb=" O MET R 158 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE R 160 " --> pdb=" O ASP R 222 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN R 268 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET R 125 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN R 267 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY R 127 " --> pdb=" O ASN R 267 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE R 122 " --> pdb=" O THR R 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU R 300 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU R 124 " --> pdb=" O LEU R 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU R 302 " --> pdb=" O GLU R 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE R 126 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS R 304 " --> pdb=" O PHE R 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG R 299 " --> pdb=" O TYR R 315 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA S 190 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR S 159 " --> pdb=" O ALA S 190 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA S 192 " --> pdb=" O TYR S 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS S 156 " --> pdb=" O LEU S 218 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE S 220 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N MET S 158 " --> pdb=" O ILE S 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP S 222 " --> pdb=" O MET S 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE S 160 " --> pdb=" O ASP S 222 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA S 217 " --> pdb=" O ALA S 262 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL S 264 " --> pdb=" O ALA S 217 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU S 219 " --> pdb=" O VAL S 264 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR S 266 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL S 221 " --> pdb=" O THR S 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN S 268 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE S 265 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET S 125 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN S 267 " --> pdb=" O MET S 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY S 127 " --> pdb=" O ASN S 267 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE S 122 " --> pdb=" O THR S 298 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LEU S 300 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU S 124 " --> pdb=" O LEU S 300 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU S 302 " --> pdb=" O GLU S 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE S 126 " --> pdb=" O LEU S 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS S 304 " --> pdb=" O PHE S 126 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ARG S 299 " --> pdb=" O TYR S 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 189 through 193 removed outlier: 3.590A pdb=" N ALA T 190 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR T 159 " --> pdb=" O ALA T 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA T 192 " --> pdb=" O TYR T 159 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS T 156 " --> pdb=" O LEU T 218 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE T 220 " --> pdb=" O LYS T 156 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET T 158 " --> pdb=" O ILE T 220 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP T 222 " --> pdb=" O MET T 158 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE T 160 " --> pdb=" O ASP T 222 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA T 217 " --> pdb=" O ALA T 262 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL T 264 " --> pdb=" O ALA T 217 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU T 219 " --> pdb=" O VAL T 264 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR T 266 " --> pdb=" O LEU T 219 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL T 221 " --> pdb=" O THR T 266 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N GLN T 268 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE T 265 " --> pdb=" O THR T 123 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET T 125 " --> pdb=" O ILE T 265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN T 267 " --> pdb=" O MET T 125 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY T 127 " --> pdb=" O ASN T 267 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE T 122 " --> pdb=" O THR T 298 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N LEU T 300 " --> pdb=" O ILE T 122 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU T 124 " --> pdb=" O LEU T 300 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU T 302 " --> pdb=" O GLU T 124 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N PHE T 126 " --> pdb=" O LEU T 302 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N LYS T 304 " --> pdb=" O PHE T 126 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG T 299 " --> pdb=" O TYR T 315 " (cutoff:3.500A) 1279 hydrogen bonds defined for protein. 3750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 762 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 13.29 Time building geometry restraints manager: 17.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 3848 1.24 - 1.39: 9182 1.39 - 1.53: 17107 1.53 - 1.67: 3325 1.67 - 1.81: 211 Bond restraints: 33673 Sorted by residual: bond pdb=" CA ARG Q 167 " pdb=" CB ARG Q 167 " ideal model delta sigma weight residual 1.529 1.363 0.166 1.26e-02 6.30e+03 1.73e+02 bond pdb=" C PRO P 318 " pdb=" O PRO P 318 " ideal model delta sigma weight residual 1.238 1.102 0.136 1.24e-02 6.50e+03 1.20e+02 bond pdb=" CE1 HIS L 47 " pdb=" NE2 HIS L 47 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.77e+01 bond pdb=" CE1 HIS M 47 " pdb=" NE2 HIS M 47 " ideal model delta sigma weight residual 1.321 1.234 0.087 1.00e-02 1.00e+04 7.66e+01 bond pdb=" CD2 HIS L 47 " pdb=" NE2 HIS L 47 " ideal model delta sigma weight residual 1.374 1.287 0.087 1.10e-02 8.26e+03 6.27e+01 ... (remaining 33668 not shown) Histogram of bond angle deviations from ideal: 91.49 - 101.28: 260 101.28 - 111.08: 15095 111.08 - 120.87: 21460 120.87 - 130.67: 9782 130.67 - 140.46: 141 Bond angle restraints: 46738 Sorted by residual: angle pdb=" O PRO P 318 " pdb=" C PRO P 318 " pdb=" N CYS P 319 " ideal model delta sigma weight residual 122.22 140.46 -18.24 1.29e+00 6.01e-01 2.00e+02 angle pdb=" CA PRO P 318 " pdb=" C PRO P 318 " pdb=" O PRO P 318 " ideal model delta sigma weight residual 119.55 100.16 19.39 1.52e+00 4.33e-01 1.63e+02 angle pdb=" CA ARG Q 167 " pdb=" CB ARG Q 167 " pdb=" CG ARG Q 167 " ideal model delta sigma weight residual 114.10 127.96 -13.86 2.00e+00 2.50e-01 4.80e+01 angle pdb=" C VAL L 52 " pdb=" N ALA L 53 " pdb=" CA ALA L 53 " ideal model delta sigma weight residual 120.65 129.68 -9.03 1.32e+00 5.74e-01 4.68e+01 angle pdb=" C VAL M 52 " pdb=" N ALA M 53 " pdb=" CA ALA M 53 " ideal model delta sigma weight residual 120.65 129.65 -9.00 1.32e+00 5.74e-01 4.65e+01 ... (remaining 46733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.42: 16468 20.42 - 40.83: 1739 40.83 - 61.25: 1288 61.25 - 81.66: 82 81.66 - 102.08: 8 Dihedral angle restraints: 19585 sinusoidal: 9877 harmonic: 9708 Sorted by residual: dihedral pdb=" CD ARG L 215 " pdb=" NE ARG L 215 " pdb=" CZ ARG L 215 " pdb=" NH1 ARG L 215 " ideal model delta sinusoidal sigma weight residual 0.00 87.74 -87.74 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CD ARG M 247 " pdb=" NE ARG M 247 " pdb=" CZ ARG M 247 " pdb=" NH1 ARG M 247 " ideal model delta sinusoidal sigma weight residual 0.00 -82.75 82.75 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CD ARG M 27 " pdb=" NE ARG M 27 " pdb=" CZ ARG M 27 " pdb=" NH1 ARG M 27 " ideal model delta sinusoidal sigma weight residual 0.00 59.42 -59.42 1 1.00e+01 1.00e-02 4.72e+01 ... (remaining 19582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 5208 0.141 - 0.282: 55 0.282 - 0.422: 8 0.422 - 0.563: 48 0.563 - 0.704: 32 Chirality restraints: 5351 Sorted by residual: chirality pdb=" CG LEU M 249 " pdb=" CB LEU M 249 " pdb=" CD1 LEU M 249 " pdb=" CD2 LEU M 249 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB ILE M 122 " pdb=" CA ILE M 122 " pdb=" CG1 ILE M 122 " pdb=" CG2 ILE M 122 " both_signs ideal model delta sigma weight residual False 2.64 1.95 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CG LEU L 255 " pdb=" CB LEU L 255 " pdb=" CD1 LEU L 255 " pdb=" CD2 LEU L 255 " both_signs ideal model delta sigma weight residual False -2.59 -1.90 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 5348 not shown) Planarity restraints: 4942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 215 " 1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG L 215 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG L 215 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG L 215 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG L 215 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 247 " -1.084 9.50e-02 1.11e+02 4.86e-01 1.42e+02 pdb=" NE ARG M 247 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ARG M 247 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG M 247 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG M 247 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 27 " -0.949 9.50e-02 1.11e+02 4.25e-01 1.09e+02 pdb=" NE ARG M 27 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG M 27 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG M 27 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG M 27 " -0.025 2.00e-02 2.50e+03 ... (remaining 4939 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.87: 43 1.87 - 2.63: 650 2.63 - 3.39: 44980 3.39 - 4.14: 86970 4.14 - 4.90: 144465 Nonbonded interactions: 277108 Sorted by model distance: nonbonded pdb=" OG1 THR L 48 " pdb=" OE2 GLU L 258 " model vdw 1.118 2.440 nonbonded pdb=" O PRO P 318 " pdb=" CB ARG Q 167 " model vdw 1.260 3.440 nonbonded pdb=" CA PHE R 46 " pdb=" NH2 ARG R 254 " model vdw 1.297 3.550 nonbonded pdb=" OE2 GLU R 322 " pdb=" O ILE S 329 " model vdw 1.303 3.040 nonbonded pdb=" CB PRO P 318 " pdb=" O PHE Q 166 " model vdw 1.312 3.440 ... (remaining 277103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.420 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 98.650 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.380 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.174 33673 Z= 0.568 Angle : 0.952 19.386 46738 Z= 0.576 Chirality : 0.086 0.704 5351 Planarity : 0.015 0.496 4942 Dihedral : 20.920 102.079 13367 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.15 % Allowed : 1.06 % Favored : 98.79 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 3328 helix: -0.01 (0.12), residues: 1618 sheet: 0.79 (0.20), residues: 530 loop : -0.25 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 39 PHE 0.026 0.002 PHE E 78 TYR 0.023 0.003 TYR H 37 ARG 0.013 0.002 ARG M 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 472 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8356 (mm-30) REVERT: B 49 LEU cc_start: 0.9705 (mt) cc_final: 0.8921 (mp) REVERT: B 74 GLU cc_start: 0.9139 (tt0) cc_final: 0.8632 (tm-30) REVERT: B 92 ARG cc_start: 0.9182 (ptm-80) cc_final: 0.8867 (ttp80) REVERT: C 25 PHE cc_start: 0.8795 (m-80) cc_final: 0.8303 (m-10) REVERT: C 90 ASP cc_start: 0.9085 (t70) cc_final: 0.8786 (t0) REVERT: C 102 ILE cc_start: 0.9276 (mm) cc_final: 0.9058 (tp) REVERT: D 43 LYS cc_start: 0.9317 (mttt) cc_final: 0.9104 (mmmm) REVERT: E 93 GLN cc_start: 0.9425 (tt0) cc_final: 0.8690 (tp40) REVERT: E 97 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8494 (mm-30) REVERT: E 130 ILE cc_start: 0.9284 (mt) cc_final: 0.8988 (mt) REVERT: F 35 ARG cc_start: 0.9252 (ttp-110) cc_final: 0.9020 (ttm110) REVERT: F 43 VAL cc_start: 0.9523 (t) cc_final: 0.9245 (p) REVERT: F 44 LYS cc_start: 0.8819 (tttt) cc_final: 0.8425 (tppt) REVERT: F 65 VAL cc_start: 0.9667 (t) cc_final: 0.9417 (p) REVERT: G 55 LEU cc_start: 0.9651 (mt) cc_final: 0.9420 (mt) REVERT: G 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8466 (tt0) REVERT: K 198 ASP cc_start: 0.8690 (t70) cc_final: 0.8306 (m-30) REVERT: K 318 PRO cc_start: 0.5211 (Cg_exo) cc_final: 0.4671 (Cg_endo) REVERT: L 58 LYS cc_start: 0.8462 (tppt) cc_final: 0.8208 (tptp) REVERT: L 125 MET cc_start: 0.8158 (pmm) cc_final: 0.7639 (pmm) REVERT: L 158 MET cc_start: 0.6854 (mmm) cc_final: 0.6530 (mmm) REVERT: L 210 MET cc_start: 0.7650 (tmm) cc_final: 0.7386 (tmm) REVERT: L 244 HIS cc_start: 0.8948 (t70) cc_final: 0.8450 (t-90) REVERT: M 60 LEU cc_start: 0.9520 (mt) cc_final: 0.9292 (tp) REVERT: M 248 PHE cc_start: 0.9589 (t80) cc_final: 0.9188 (t80) REVERT: N 129 PHE cc_start: 0.8086 (p90) cc_final: 0.7746 (p90) REVERT: N 290 ASN cc_start: 0.7675 (m-40) cc_final: 0.7129 (p0) REVERT: N 326 MET cc_start: 0.8738 (tpt) cc_final: 0.8271 (tpp) REVERT: O 195 PHE cc_start: 0.4616 (m-10) cc_final: 0.4163 (t80) REVERT: O 251 MET cc_start: -0.1556 (mtp) cc_final: -0.1836 (ttm) REVERT: P 326 MET cc_start: 0.1786 (tpt) cc_final: 0.0543 (mtp) REVERT: R 30 GLN cc_start: -0.2648 (mp10) cc_final: -0.2951 (mm110) REVERT: R 72 ASP cc_start: 0.6994 (m-30) cc_final: 0.6787 (t70) REVERT: S 210 MET cc_start: 0.1480 (tmm) cc_final: 0.0549 (tpp) REVERT: S 211 MET cc_start: 0.1390 (ttm) cc_final: 0.0855 (mtt) REVERT: S 243 MET cc_start: 0.2258 (mmt) cc_final: 0.1747 (tmm) REVERT: T 63 ILE cc_start: -0.0783 (mt) cc_final: -0.1091 (mm) REVERT: T 210 MET cc_start: 0.2232 (tmm) cc_final: 0.1191 (ttt) REVERT: T 251 MET cc_start: -0.0819 (mtp) cc_final: -0.1358 (mmm) outliers start: 4 outliers final: 0 residues processed: 473 average time/residue: 0.4963 time to fit residues: 359.7170 Evaluate side-chains 223 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 20.0000 chunk 275 optimal weight: 30.0000 chunk 152 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 329 optimal weight: 40.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 84 ASN E 68 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN K 23 GLN K 47 HIS L 47 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN N 242 GLN ** N 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 294 HIS ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 47 HIS ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 294 HIS T 23 GLN T 268 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33673 Z= 0.311 Angle : 0.656 16.742 46738 Z= 0.370 Chirality : 0.041 0.176 5351 Planarity : 0.005 0.075 4942 Dihedral : 25.234 89.788 7123 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.18 % Allowed : 2.01 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3328 helix: 1.06 (0.12), residues: 1712 sheet: 0.63 (0.20), residues: 529 loop : -0.63 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS B 75 PHE 0.025 0.002 PHE K 195 TYR 0.038 0.002 TYR Q 54 ARG 0.009 0.001 ARG M 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 266 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9040 (tp30) cc_final: 0.8687 (tp30) REVERT: B 49 LEU cc_start: 0.9332 (mt) cc_final: 0.8917 (mm) REVERT: B 60 VAL cc_start: 0.9737 (t) cc_final: 0.9279 (p) REVERT: B 63 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8815 (mt-10) REVERT: B 85 ASP cc_start: 0.8464 (m-30) cc_final: 0.8251 (m-30) REVERT: C 38 ASN cc_start: 0.8447 (t0) cc_final: 0.8158 (t0) REVERT: C 90 ASP cc_start: 0.9109 (t70) cc_final: 0.8879 (t0) REVERT: D 93 GLU cc_start: 0.9060 (mp0) cc_final: 0.8649 (mp0) REVERT: E 68 GLN cc_start: 0.9370 (tt0) cc_final: 0.9163 (pp30) REVERT: E 93 GLN cc_start: 0.9172 (tt0) cc_final: 0.8796 (tp40) REVERT: E 94 GLU cc_start: 0.9132 (tp30) cc_final: 0.8799 (tp30) REVERT: E 105 GLU cc_start: 0.8192 (pp20) cc_final: 0.7826 (pp20) REVERT: E 106 ASP cc_start: 0.8628 (m-30) cc_final: 0.8383 (m-30) REVERT: E 119 ILE cc_start: 0.9336 (pt) cc_final: 0.8934 (pt) REVERT: F 44 LYS cc_start: 0.8937 (tttt) cc_final: 0.8726 (tppt) REVERT: F 79 LYS cc_start: 0.9418 (mppt) cc_final: 0.9084 (mmtm) REVERT: H 64 SER cc_start: 0.9335 (m) cc_final: 0.9102 (p) REVERT: K 158 MET cc_start: 0.6400 (tpp) cc_final: 0.6187 (tpp) REVERT: K 198 ASP cc_start: 0.8674 (t70) cc_final: 0.8167 (m-30) REVERT: K 211 MET cc_start: 0.6068 (tpt) cc_final: 0.5824 (tpt) REVERT: K 232 TYR cc_start: 0.8235 (m-10) cc_final: 0.7992 (m-10) REVERT: L 125 MET cc_start: 0.8294 (pmm) cc_final: 0.7907 (pmm) REVERT: L 158 MET cc_start: 0.6494 (mmm) cc_final: 0.6255 (mmm) REVERT: M 251 MET cc_start: 0.9531 (tpt) cc_final: 0.9190 (tpp) REVERT: N 52 VAL cc_start: -0.1867 (m) cc_final: -0.2409 (t) REVERT: N 290 ASN cc_start: 0.7280 (m-40) cc_final: 0.6926 (p0) REVERT: N 326 MET cc_start: 0.8554 (tpt) cc_final: 0.8204 (tpp) REVERT: O 176 GLU cc_start: 0.8555 (pp20) cc_final: 0.8322 (pt0) REVERT: O 211 MET cc_start: 0.3061 (ttm) cc_final: 0.2848 (ttm) REVERT: O 251 MET cc_start: -0.1791 (mtp) cc_final: -0.2048 (ttm) REVERT: P 210 MET cc_start: 0.1229 (ppp) cc_final: 0.0634 (ppp) REVERT: P 309 THR cc_start: 0.4434 (OUTLIER) cc_final: 0.4139 (t) REVERT: P 326 MET cc_start: 0.1372 (tpt) cc_final: 0.0818 (mtt) REVERT: R 72 ASP cc_start: 0.6880 (m-30) cc_final: 0.6556 (t70) REVERT: R 211 MET cc_start: 0.5545 (tpp) cc_final: 0.5344 (tpp) REVERT: S 210 MET cc_start: 0.1321 (tmm) cc_final: 0.0760 (tpp) REVERT: S 211 MET cc_start: 0.2114 (ttm) cc_final: 0.1556 (mtt) REVERT: S 243 MET cc_start: 0.2447 (mmt) cc_final: 0.1883 (tmm) REVERT: T 158 MET cc_start: -0.1853 (mtm) cc_final: -0.2246 (mtm) REVERT: T 210 MET cc_start: 0.0639 (tmm) cc_final: 0.0296 (ttt) REVERT: T 251 MET cc_start: -0.1685 (mtp) cc_final: -0.2288 (mmm) outliers start: 5 outliers final: 2 residues processed: 271 average time/residue: 0.4513 time to fit residues: 197.3459 Evaluate side-chains 189 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 3.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 274 optimal weight: 0.5980 chunk 224 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 330 optimal weight: 5.9990 chunk 356 optimal weight: 8.9990 chunk 294 optimal weight: 0.0770 chunk 327 optimal weight: 4.9990 chunk 112 optimal weight: 30.0000 chunk 264 optimal weight: 1.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 242 GLN L 244 HIS L 268 GLN N 202 GLN P 114 GLN ** P 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 268 GLN Q 47 HIS R 23 GLN ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 23 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33673 Z= 0.155 Angle : 0.518 10.952 46738 Z= 0.297 Chirality : 0.038 0.169 5351 Planarity : 0.003 0.054 4942 Dihedral : 24.802 91.555 7123 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.07 % Allowed : 1.24 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3328 helix: 1.64 (0.13), residues: 1742 sheet: 1.02 (0.22), residues: 506 loop : -0.56 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS P 294 PHE 0.019 0.001 PHE A 104 TYR 0.031 0.001 TYR F 88 ARG 0.007 0.000 ARG L 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9080 (tp30) cc_final: 0.8868 (tp30) REVERT: A 106 ASP cc_start: 0.8951 (t70) cc_final: 0.8390 (t70) REVERT: B 49 LEU cc_start: 0.9233 (mt) cc_final: 0.7869 (mm) REVERT: B 60 VAL cc_start: 0.9695 (t) cc_final: 0.9210 (p) REVERT: B 63 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8648 (mt-10) REVERT: C 38 ASN cc_start: 0.8329 (t0) cc_final: 0.7920 (t0) REVERT: C 90 ASP cc_start: 0.9089 (t70) cc_final: 0.8841 (t0) REVERT: D 93 GLU cc_start: 0.8942 (mp0) cc_final: 0.8631 (mp0) REVERT: E 57 SER cc_start: 0.9324 (m) cc_final: 0.8793 (p) REVERT: E 93 GLN cc_start: 0.9043 (tt0) cc_final: 0.8836 (tp40) REVERT: E 94 GLU cc_start: 0.8978 (tp30) cc_final: 0.8691 (tp30) REVERT: E 105 GLU cc_start: 0.8307 (pp20) cc_final: 0.8059 (pp20) REVERT: E 106 ASP cc_start: 0.8603 (m-30) cc_final: 0.8363 (m-30) REVERT: E 119 ILE cc_start: 0.9389 (pt) cc_final: 0.9137 (pt) REVERT: E 120 MET cc_start: 0.9042 (mmp) cc_final: 0.8195 (mmm) REVERT: F 35 ARG cc_start: 0.9332 (ttp-110) cc_final: 0.8983 (ttm110) REVERT: F 68 ASP cc_start: 0.9096 (m-30) cc_final: 0.8896 (m-30) REVERT: F 79 LYS cc_start: 0.9295 (mppt) cc_final: 0.8958 (mmtm) REVERT: G 56 GLU cc_start: 0.8879 (tt0) cc_final: 0.8194 (mt-10) REVERT: H 61 ILE cc_start: 0.9673 (OUTLIER) cc_final: 0.9436 (tp) REVERT: H 64 SER cc_start: 0.9300 (m) cc_final: 0.9079 (p) REVERT: K 68 GLU cc_start: 0.9690 (pm20) cc_final: 0.9446 (mp0) REVERT: K 198 ASP cc_start: 0.8574 (t70) cc_final: 0.8200 (m-30) REVERT: K 211 MET cc_start: 0.6239 (tpt) cc_final: 0.5650 (mmm) REVERT: K 232 TYR cc_start: 0.8106 (m-10) cc_final: 0.7872 (m-10) REVERT: L 125 MET cc_start: 0.8792 (pmm) cc_final: 0.8540 (pmm) REVERT: M 248 PHE cc_start: 0.9526 (t80) cc_final: 0.9214 (t80) REVERT: M 251 MET cc_start: 0.9526 (tpt) cc_final: 0.9185 (tpp) REVERT: N 52 VAL cc_start: -0.1318 (m) cc_final: -0.2602 (t) REVERT: N 290 ASN cc_start: 0.7453 (m-40) cc_final: 0.7143 (p0) REVERT: N 326 MET cc_start: 0.8121 (tpt) cc_final: 0.7885 (tpp) REVERT: O 176 GLU cc_start: 0.8517 (pp20) cc_final: 0.8279 (pt0) REVERT: O 251 MET cc_start: -0.1885 (mtp) cc_final: -0.2194 (ttm) REVERT: P 158 MET cc_start: -0.1589 (ptp) cc_final: -0.1835 (ptp) REVERT: P 326 MET cc_start: -0.0105 (tpt) cc_final: -0.0402 (mtt) REVERT: R 72 ASP cc_start: 0.6944 (m-30) cc_final: 0.6642 (t70) REVERT: R 251 MET cc_start: 0.7106 (mtm) cc_final: 0.6878 (ptp) REVERT: S 210 MET cc_start: 0.0989 (tmm) cc_final: 0.0719 (tmm) REVERT: S 211 MET cc_start: 0.1995 (ttm) cc_final: 0.1444 (mtt) REVERT: S 243 MET cc_start: 0.2412 (mmt) cc_final: 0.1884 (tmm) REVERT: T 251 MET cc_start: -0.1941 (mtp) cc_final: -0.2315 (mmm) outliers start: 2 outliers final: 0 residues processed: 266 average time/residue: 0.4561 time to fit residues: 197.3415 Evaluate side-chains 187 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 331 optimal weight: 50.0000 chunk 350 optimal weight: 8.9990 chunk 173 optimal weight: 30.0000 chunk 314 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN M 206 GLN ** N 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 244 HIS ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 23 GLN T 244 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33673 Z= 0.264 Angle : 0.569 14.831 46738 Z= 0.322 Chirality : 0.039 0.149 5351 Planarity : 0.004 0.059 4942 Dihedral : 24.819 91.909 7123 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.14), residues: 3328 helix: 1.55 (0.13), residues: 1728 sheet: 1.24 (0.23), residues: 495 loop : -0.51 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS N 244 PHE 0.015 0.001 PHE E 104 TYR 0.029 0.002 TYR F 88 ARG 0.010 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 3.107 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 50 GLU cc_start: 0.9155 (tp30) cc_final: 0.8635 (tp30) REVERT: B 49 LEU cc_start: 0.9188 (mt) cc_final: 0.8363 (mm) REVERT: B 60 VAL cc_start: 0.9704 (t) cc_final: 0.9216 (p) REVERT: C 38 ASN cc_start: 0.8459 (t0) cc_final: 0.8098 (t0) REVERT: C 72 ASP cc_start: 0.8490 (m-30) cc_final: 0.8253 (m-30) REVERT: C 90 ASP cc_start: 0.9115 (t70) cc_final: 0.8870 (t0) REVERT: D 93 GLU cc_start: 0.9004 (mp0) cc_final: 0.8632 (mp0) REVERT: E 93 GLN cc_start: 0.9160 (tt0) cc_final: 0.8880 (tp40) REVERT: E 106 ASP cc_start: 0.8721 (m-30) cc_final: 0.8426 (m-30) REVERT: E 119 ILE cc_start: 0.9490 (pt) cc_final: 0.9059 (pt) REVERT: E 120 MET cc_start: 0.9112 (mmp) cc_final: 0.8337 (mmm) REVERT: H 59 MET cc_start: 0.9185 (tpp) cc_final: 0.8964 (tpp) REVERT: H 64 SER cc_start: 0.9367 (m) cc_final: 0.9112 (p) REVERT: K 68 GLU cc_start: 0.9644 (pm20) cc_final: 0.9392 (mp0) REVERT: K 198 ASP cc_start: 0.8734 (t70) cc_final: 0.8352 (m-30) REVERT: K 211 MET cc_start: 0.6341 (tpt) cc_final: 0.5917 (mmm) REVERT: K 232 TYR cc_start: 0.8240 (m-10) cc_final: 0.7969 (m-10) REVERT: L 243 MET cc_start: 0.9604 (mmp) cc_final: 0.9283 (tpt) REVERT: L 251 MET cc_start: 0.9528 (ttp) cc_final: 0.9274 (ptt) REVERT: M 251 MET cc_start: 0.9526 (tpt) cc_final: 0.9178 (tpp) REVERT: N 290 ASN cc_start: 0.7304 (m-40) cc_final: 0.6924 (p0) REVERT: O 176 GLU cc_start: 0.8535 (pp20) cc_final: 0.8290 (pt0) REVERT: O 251 MET cc_start: -0.1892 (mtp) cc_final: -0.2128 (ttm) REVERT: P 158 MET cc_start: -0.1567 (ptp) cc_final: -0.1955 (ptp) REVERT: Q 338 LYS cc_start: 0.5115 (mmtt) cc_final: 0.4276 (mptt) REVERT: R 72 ASP cc_start: 0.7110 (m-30) cc_final: 0.6848 (t70) REVERT: S 210 MET cc_start: 0.0777 (tmm) cc_final: 0.0478 (tmm) REVERT: S 211 MET cc_start: 0.1990 (ttm) cc_final: 0.1398 (mtt) REVERT: S 243 MET cc_start: 0.2244 (mmt) cc_final: 0.1633 (tmm) REVERT: T 251 MET cc_start: -0.1689 (mtp) cc_final: -0.2765 (mmm) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.4576 time to fit residues: 170.1875 Evaluate side-chains 166 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 299 optimal weight: 50.0000 chunk 242 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 179 optimal weight: 8.9990 chunk 314 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 23 GLN ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 206 GLN T 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33673 Z= 0.266 Angle : 0.589 13.451 46738 Z= 0.331 Chirality : 0.040 0.197 5351 Planarity : 0.004 0.054 4942 Dihedral : 24.946 95.062 7123 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.14), residues: 3328 helix: 1.45 (0.13), residues: 1745 sheet: 1.25 (0.23), residues: 491 loop : -0.52 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 75 PHE 0.015 0.002 PHE A 104 TYR 0.033 0.002 TYR F 88 ARG 0.009 0.001 ARG M 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9111 (tp30) cc_final: 0.8657 (tp30) REVERT: B 49 LEU cc_start: 0.9174 (mt) cc_final: 0.8065 (mm) REVERT: B 85 ASP cc_start: 0.8706 (m-30) cc_final: 0.8434 (m-30) REVERT: C 38 ASN cc_start: 0.8508 (t0) cc_final: 0.8193 (t0) REVERT: C 72 ASP cc_start: 0.8525 (m-30) cc_final: 0.8315 (m-30) REVERT: C 90 ASP cc_start: 0.9112 (t70) cc_final: 0.8841 (t0) REVERT: D 59 MET cc_start: 0.9262 (tpp) cc_final: 0.9030 (tpp) REVERT: E 93 GLN cc_start: 0.9085 (tt0) cc_final: 0.8838 (tp40) REVERT: E 119 ILE cc_start: 0.9430 (pt) cc_final: 0.8950 (pt) REVERT: E 120 MET cc_start: 0.9092 (mmp) cc_final: 0.8332 (mmm) REVERT: H 59 MET cc_start: 0.9166 (tpp) cc_final: 0.8861 (tpp) REVERT: H 64 SER cc_start: 0.9398 (m) cc_final: 0.9162 (p) REVERT: K 198 ASP cc_start: 0.8874 (t70) cc_final: 0.8489 (m-30) REVERT: K 211 MET cc_start: 0.6401 (tpt) cc_final: 0.5624 (mmm) REVERT: K 232 TYR cc_start: 0.8314 (m-10) cc_final: 0.8071 (m-10) REVERT: L 158 MET cc_start: 0.7571 (mmm) cc_final: 0.7154 (mmt) REVERT: L 210 MET cc_start: 0.7467 (ppp) cc_final: 0.7145 (ppp) REVERT: L 243 MET cc_start: 0.9625 (mmp) cc_final: 0.9335 (tpt) REVERT: L 251 MET cc_start: 0.9423 (ttp) cc_final: 0.9193 (ptt) REVERT: M 251 MET cc_start: 0.9530 (tpt) cc_final: 0.9206 (tpp) REVERT: N 290 ASN cc_start: 0.7312 (m-40) cc_final: 0.6974 (p0) REVERT: N 326 MET cc_start: 0.7869 (tpt) cc_final: 0.7600 (tpp) REVERT: P 125 MET cc_start: 0.4202 (pmm) cc_final: 0.3899 (pmm) REVERT: Q 338 LYS cc_start: 0.4525 (mmtt) cc_final: 0.3524 (mptt) REVERT: Q 339 ASP cc_start: 0.6095 (p0) cc_final: 0.5842 (p0) REVERT: R 72 ASP cc_start: 0.7150 (m-30) cc_final: 0.6889 (t70) REVERT: R 251 MET cc_start: 0.7939 (mpp) cc_final: 0.7524 (tpt) REVERT: S 125 MET cc_start: -0.2728 (ttp) cc_final: -0.3101 (mtt) REVERT: S 210 MET cc_start: 0.0762 (tmm) cc_final: 0.0455 (tmm) REVERT: S 211 MET cc_start: 0.2260 (ttm) cc_final: 0.1647 (mtt) REVERT: S 243 MET cc_start: 0.2124 (mmt) cc_final: 0.1528 (tmm) REVERT: T 251 MET cc_start: -0.1496 (mtp) cc_final: -0.2598 (mmm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.4430 time to fit residues: 152.2121 Evaluate side-chains 162 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 10.0000 chunk 315 optimal weight: 50.0000 chunk 69 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 291 optimal weight: 40.0000 chunk 162 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS K 202 GLN K 206 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN ** O 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 23 GLN ** T 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 33673 Z= 0.319 Angle : 0.634 15.546 46738 Z= 0.354 Chirality : 0.041 0.189 5351 Planarity : 0.004 0.056 4942 Dihedral : 25.148 97.493 7123 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3328 helix: 1.20 (0.12), residues: 1736 sheet: 1.24 (0.23), residues: 478 loop : -0.66 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS F 75 PHE 0.019 0.002 PHE K 46 TYR 0.030 0.002 TYR E 54 ARG 0.010 0.001 ARG O 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 3.092 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: A 50 GLU cc_start: 0.9192 (tp30) cc_final: 0.8644 (tp30) REVERT: B 49 LEU cc_start: 0.9200 (mt) cc_final: 0.8203 (mm) REVERT: B 85 ASP cc_start: 0.8756 (m-30) cc_final: 0.8482 (m-30) REVERT: C 90 ASP cc_start: 0.9119 (t70) cc_final: 0.8870 (t0) REVERT: E 57 SER cc_start: 0.9431 (m) cc_final: 0.8992 (p) REVERT: E 119 ILE cc_start: 0.9419 (pt) cc_final: 0.9011 (pt) REVERT: E 120 MET cc_start: 0.9115 (mmp) cc_final: 0.8535 (mmm) REVERT: H 59 MET cc_start: 0.9266 (tpp) cc_final: 0.8981 (tpp) REVERT: H 64 SER cc_start: 0.9423 (m) cc_final: 0.9214 (p) REVERT: K 68 GLU cc_start: 0.9614 (mp0) cc_final: 0.9333 (mp0) REVERT: K 198 ASP cc_start: 0.8968 (t70) cc_final: 0.8584 (m-30) REVERT: K 232 TYR cc_start: 0.8287 (m-10) cc_final: 0.8013 (m-10) REVERT: L 158 MET cc_start: 0.7010 (mmm) cc_final: 0.6677 (mmt) REVERT: L 243 MET cc_start: 0.9613 (mmp) cc_final: 0.9366 (tpt) REVERT: M 251 MET cc_start: 0.9439 (tpt) cc_final: 0.9156 (tpp) REVERT: N 290 ASN cc_start: 0.7350 (m-40) cc_final: 0.7076 (p0) REVERT: N 326 MET cc_start: 0.7974 (tpt) cc_final: 0.7728 (tpp) REVERT: O 251 MET cc_start: -0.1306 (mtp) cc_final: -0.1630 (ttm) REVERT: P 125 MET cc_start: 0.5004 (pmm) cc_final: 0.4730 (pmm) REVERT: R 72 ASP cc_start: 0.7082 (m-30) cc_final: 0.6811 (t70) REVERT: R 251 MET cc_start: 0.8233 (mpp) cc_final: 0.7867 (mtp) REVERT: S 125 MET cc_start: -0.2576 (ttp) cc_final: -0.2998 (mtt) REVERT: S 211 MET cc_start: 0.2642 (ttm) cc_final: 0.2102 (mtt) REVERT: S 243 MET cc_start: 0.1894 (mmt) cc_final: 0.1196 (tmm) REVERT: T 251 MET cc_start: -0.1539 (mtp) cc_final: -0.2201 (mmm) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 0.4424 time to fit residues: 142.3913 Evaluate side-chains 157 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 198 optimal weight: 8.9990 chunk 295 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 GLN ** N 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 200 GLN ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.6462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 33673 Z= 0.273 Angle : 0.593 17.718 46738 Z= 0.334 Chirality : 0.040 0.166 5351 Planarity : 0.004 0.058 4942 Dihedral : 25.158 96.696 7123 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3328 helix: 1.28 (0.12), residues: 1737 sheet: 1.29 (0.24), residues: 470 loop : -0.65 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.031 0.002 PHE N 248 TYR 0.029 0.002 TYR E 54 ARG 0.006 0.001 ARG T 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 3.388 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 50 GLU cc_start: 0.9142 (tp30) cc_final: 0.8602 (tp30) REVERT: B 49 LEU cc_start: 0.9108 (mt) cc_final: 0.8192 (mm) REVERT: C 90 ASP cc_start: 0.9093 (t70) cc_final: 0.8792 (t0) REVERT: E 57 SER cc_start: 0.9399 (m) cc_final: 0.8816 (p) REVERT: E 93 GLN cc_start: 0.9099 (tt0) cc_final: 0.8854 (tp40) REVERT: E 119 ILE cc_start: 0.9404 (pt) cc_final: 0.9012 (pt) REVERT: E 120 MET cc_start: 0.9143 (mmp) cc_final: 0.8634 (mmm) REVERT: F 68 ASP cc_start: 0.9209 (m-30) cc_final: 0.8981 (m-30) REVERT: H 59 MET cc_start: 0.9247 (tpp) cc_final: 0.8936 (tpp) REVERT: H 64 SER cc_start: 0.9419 (m) cc_final: 0.9217 (p) REVERT: K 198 ASP cc_start: 0.8980 (t70) cc_final: 0.8596 (m-30) REVERT: K 211 MET cc_start: 0.5761 (tpt) cc_final: 0.5334 (mmm) REVERT: K 232 TYR cc_start: 0.8315 (m-10) cc_final: 0.7969 (m-10) REVERT: L 158 MET cc_start: 0.7297 (mmm) cc_final: 0.6979 (mmt) REVERT: M 251 MET cc_start: 0.9460 (tpt) cc_final: 0.9148 (tpp) REVERT: N 290 ASN cc_start: 0.7217 (m-40) cc_final: 0.6969 (p0) REVERT: N 326 MET cc_start: 0.7888 (tpt) cc_final: 0.7580 (tpp) REVERT: O 251 MET cc_start: -0.1186 (mtp) cc_final: -0.1392 (ttp) REVERT: P 125 MET cc_start: 0.5449 (pmm) cc_final: 0.5225 (pmm) REVERT: R 72 ASP cc_start: 0.6923 (m-30) cc_final: 0.6631 (t70) REVERT: R 251 MET cc_start: 0.8178 (mpp) cc_final: 0.7844 (mtp) REVERT: S 125 MET cc_start: -0.2516 (ttp) cc_final: -0.2808 (mtt) REVERT: S 211 MET cc_start: 0.2496 (ttm) cc_final: 0.1852 (mtt) REVERT: S 243 MET cc_start: 0.2276 (mmt) cc_final: 0.1629 (tmm) REVERT: T 251 MET cc_start: -0.1323 (mtp) cc_final: -0.1951 (mmm) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.4304 time to fit residues: 136.8801 Evaluate side-chains 151 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 50.0000 chunk 139 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 105 optimal weight: 0.0000 chunk 68 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 275 optimal weight: 7.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 HIS ** N 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33673 Z= 0.176 Angle : 0.530 12.119 46738 Z= 0.301 Chirality : 0.038 0.148 5351 Planarity : 0.003 0.057 4942 Dihedral : 24.992 95.594 7123 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.15), residues: 3328 helix: 1.57 (0.13), residues: 1756 sheet: 1.44 (0.24), residues: 470 loop : -0.55 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.015 0.001 PHE N 248 TYR 0.024 0.001 TYR Q 54 ARG 0.004 0.000 ARG R 254 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 LEU cc_start: 0.8887 (mt) cc_final: 0.8090 (mm) REVERT: C 38 ASN cc_start: 0.8441 (t0) cc_final: 0.8174 (t0) REVERT: C 72 ASP cc_start: 0.8419 (m-30) cc_final: 0.8206 (m-30) REVERT: C 90 ASP cc_start: 0.9008 (t70) cc_final: 0.8729 (t0) REVERT: D 95 GLN cc_start: 0.9554 (pt0) cc_final: 0.8934 (pp30) REVERT: E 57 SER cc_start: 0.9372 (m) cc_final: 0.8894 (p) REVERT: E 81 ASP cc_start: 0.8722 (m-30) cc_final: 0.8319 (t0) REVERT: E 93 GLN cc_start: 0.9007 (tt0) cc_final: 0.8611 (tp40) REVERT: E 97 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8592 (mm-30) REVERT: E 119 ILE cc_start: 0.9354 (pt) cc_final: 0.8960 (pt) REVERT: E 120 MET cc_start: 0.9140 (mmp) cc_final: 0.8631 (mmm) REVERT: H 59 MET cc_start: 0.9211 (tpp) cc_final: 0.8882 (tpp) REVERT: K 198 ASP cc_start: 0.8915 (t70) cc_final: 0.8547 (m-30) REVERT: K 211 MET cc_start: 0.5699 (tpt) cc_final: 0.5393 (mmm) REVERT: K 232 TYR cc_start: 0.8335 (m-10) cc_final: 0.7977 (m-80) REVERT: L 158 MET cc_start: 0.6957 (mmm) cc_final: 0.6664 (mmt) REVERT: M 251 MET cc_start: 0.9462 (tpt) cc_final: 0.9160 (tpp) REVERT: N 290 ASN cc_start: 0.7148 (m-40) cc_final: 0.6900 (p0) REVERT: N 326 MET cc_start: 0.7941 (tpt) cc_final: 0.7689 (tpp) REVERT: O 251 MET cc_start: -0.1165 (mtp) cc_final: -0.1371 (ttp) REVERT: P 125 MET cc_start: 0.5603 (pmm) cc_final: 0.5380 (pmm) REVERT: Q 210 MET cc_start: 0.2409 (ptp) cc_final: 0.1933 (tmm) REVERT: R 72 ASP cc_start: 0.6881 (m-30) cc_final: 0.6586 (t70) REVERT: R 251 MET cc_start: 0.8190 (mpp) cc_final: 0.7848 (mtp) REVERT: S 211 MET cc_start: 0.2223 (ttm) cc_final: 0.1543 (mtt) REVERT: S 243 MET cc_start: 0.2441 (mmt) cc_final: 0.1846 (tmm) REVERT: T 158 MET cc_start: -0.1989 (mtm) cc_final: -0.2242 (mtm) REVERT: T 251 MET cc_start: -0.1406 (mtp) cc_final: -0.2060 (mmm) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.4113 time to fit residues: 147.3148 Evaluate side-chains 158 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 50.0000 chunk 335 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 326 optimal weight: 30.0000 chunk 196 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 256 optimal weight: 50.0000 chunk 100 optimal weight: 10.0000 chunk 294 optimal weight: 40.0000 chunk 308 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 31 HIS ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 GLN ** O 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 33673 Z= 0.364 Angle : 0.672 19.222 46738 Z= 0.373 Chirality : 0.042 0.215 5351 Planarity : 0.004 0.058 4942 Dihedral : 25.296 96.263 7123 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.14), residues: 3328 helix: 1.11 (0.12), residues: 1732 sheet: 1.21 (0.24), residues: 462 loop : -0.69 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS F 75 PHE 0.020 0.002 PHE N 327 TYR 0.035 0.002 TYR F 88 ARG 0.020 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.156 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 50 GLU cc_start: 0.9226 (tp30) cc_final: 0.8643 (tp30) REVERT: B 49 LEU cc_start: 0.9165 (mt) cc_final: 0.8563 (mm) REVERT: C 38 ASN cc_start: 0.8526 (t0) cc_final: 0.8229 (t0) REVERT: D 95 GLN cc_start: 0.9591 (pt0) cc_final: 0.8978 (pp30) REVERT: E 57 SER cc_start: 0.9397 (m) cc_final: 0.8874 (p) REVERT: E 81 ASP cc_start: 0.8802 (m-30) cc_final: 0.8380 (t0) REVERT: E 93 GLN cc_start: 0.9124 (tt0) cc_final: 0.8870 (tp40) REVERT: E 119 ILE cc_start: 0.9374 (pt) cc_final: 0.8988 (pt) REVERT: E 120 MET cc_start: 0.9140 (mmp) cc_final: 0.8642 (mmm) REVERT: F 68 ASP cc_start: 0.9233 (m-30) cc_final: 0.9033 (m-30) REVERT: H 59 MET cc_start: 0.9261 (tpp) cc_final: 0.8951 (tpp) REVERT: K 198 ASP cc_start: 0.9042 (t70) cc_final: 0.8693 (m-30) REVERT: K 211 MET cc_start: 0.5878 (tpt) cc_final: 0.5411 (mmm) REVERT: K 232 TYR cc_start: 0.8442 (m-10) cc_final: 0.8100 (m-80) REVERT: M 251 MET cc_start: 0.9463 (tpt) cc_final: 0.9072 (tpp) REVERT: N 290 ASN cc_start: 0.7255 (m-40) cc_final: 0.7021 (p0) REVERT: N 326 MET cc_start: 0.8010 (tpt) cc_final: 0.7646 (mmp) REVERT: O 211 MET cc_start: 0.4562 (ttm) cc_final: 0.3529 (mtt) REVERT: O 251 MET cc_start: -0.1033 (mtp) cc_final: -0.1410 (ttm) REVERT: P 125 MET cc_start: 0.6081 (pmm) cc_final: 0.5868 (pmm) REVERT: R 72 ASP cc_start: 0.7021 (m-30) cc_final: 0.6780 (t70) REVERT: R 251 MET cc_start: 0.8276 (mpp) cc_final: 0.7698 (tpt) REVERT: S 125 MET cc_start: -0.2734 (ttp) cc_final: -0.3063 (mtt) REVERT: S 211 MET cc_start: 0.1685 (ttm) cc_final: 0.1190 (mtt) REVERT: S 243 MET cc_start: 0.2046 (mmt) cc_final: 0.1411 (tmm) REVERT: T 251 MET cc_start: -0.1369 (mtp) cc_final: -0.2021 (mmm) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.4142 time to fit residues: 131.5980 Evaluate side-chains 149 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 20.0000 chunk 344 optimal weight: 30.0000 chunk 210 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 chunk 239 optimal weight: 0.8980 chunk 361 optimal weight: 7.9990 chunk 332 optimal weight: 50.0000 chunk 287 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 222 optimal weight: 30.0000 chunk 176 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 31 HIS ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.7419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33673 Z= 0.275 Angle : 0.604 15.598 46738 Z= 0.339 Chirality : 0.040 0.174 5351 Planarity : 0.004 0.055 4942 Dihedral : 25.289 97.875 7123 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3328 helix: 1.22 (0.12), residues: 1735 sheet: 1.17 (0.25), residues: 450 loop : -0.60 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS G 31 PHE 0.020 0.002 PHE N 327 TYR 0.030 0.002 TYR F 88 ARG 0.005 0.000 ARG G 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9182 (tp30) cc_final: 0.8611 (tp30) REVERT: B 49 LEU cc_start: 0.8999 (mt) cc_final: 0.8211 (mm) REVERT: C 38 ASN cc_start: 0.8496 (t0) cc_final: 0.8230 (t0) REVERT: D 95 GLN cc_start: 0.9564 (pt0) cc_final: 0.8840 (pp30) REVERT: E 57 SER cc_start: 0.9389 (m) cc_final: 0.9017 (p) REVERT: E 81 ASP cc_start: 0.8754 (m-30) cc_final: 0.8329 (t0) REVERT: E 93 GLN cc_start: 0.9099 (tt0) cc_final: 0.8861 (tp40) REVERT: E 119 ILE cc_start: 0.9366 (pt) cc_final: 0.8930 (pt) REVERT: E 120 MET cc_start: 0.9155 (mmp) cc_final: 0.8622 (mmm) REVERT: F 63 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8699 (tm-30) REVERT: H 59 MET cc_start: 0.9226 (tpp) cc_final: 0.8941 (tpp) REVERT: K 198 ASP cc_start: 0.8961 (t70) cc_final: 0.8674 (m-30) REVERT: K 211 MET cc_start: 0.5856 (tpt) cc_final: 0.5331 (mmm) REVERT: M 251 MET cc_start: 0.9434 (tpt) cc_final: 0.9050 (tpp) REVERT: N 326 MET cc_start: 0.7989 (tpt) cc_final: 0.7598 (mmp) REVERT: O 211 MET cc_start: 0.4467 (ttm) cc_final: 0.3396 (mtt) REVERT: P 125 MET cc_start: 0.6217 (pmm) cc_final: 0.5978 (pmm) REVERT: R 72 ASP cc_start: 0.7090 (m-30) cc_final: 0.6861 (t70) REVERT: R 251 MET cc_start: 0.8290 (mpp) cc_final: 0.7718 (tpt) REVERT: S 211 MET cc_start: 0.1602 (ttm) cc_final: 0.1359 (mtt) REVERT: S 243 MET cc_start: 0.2138 (mmt) cc_final: 0.1522 (tmm) REVERT: T 158 MET cc_start: -0.0277 (mtm) cc_final: -0.0546 (mtm) REVERT: T 251 MET cc_start: -0.1411 (mtp) cc_final: -0.2079 (mmm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.4130 time to fit residues: 129.0821 Evaluate side-chains 152 residues out of total 2737 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 8.9990 chunk 306 optimal weight: 50.0000 chunk 88 optimal weight: 7.9990 chunk 265 optimal weight: 50.0000 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 296 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS E 68 GLN ** O 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.074175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046763 restraints weight = 272669.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.046981 restraints weight = 151164.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.046887 restraints weight = 98241.555| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33673 Z= 0.300 Angle : 0.630 17.580 46738 Z= 0.350 Chirality : 0.041 0.181 5351 Planarity : 0.004 0.073 4942 Dihedral : 25.308 97.328 7123 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3328 helix: 1.09 (0.12), residues: 1735 sheet: 1.04 (0.24), residues: 451 loop : -0.62 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS F 75 PHE 0.020 0.002 PHE N 327 TYR 0.024 0.002 TYR Q 54 ARG 0.006 0.001 ARG G 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.56 seconds wall clock time: 101 minutes 50.68 seconds (6110.68 seconds total)