Starting phenix.real_space_refine on Fri Aug 9 23:03:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbt_38228/08_2024/8xbt_38228.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbt_38228/08_2024/8xbt_38228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbt_38228/08_2024/8xbt_38228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbt_38228/08_2024/8xbt_38228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbt_38228/08_2024/8xbt_38228.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbt_38228/08_2024/8xbt_38228.cif" } resolution = 4.12 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 106 5.16 5 C 16431 2.51 5 N 5045 2.21 5 O 5885 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 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 215": "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 254": "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 "L PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 247": "NH1" <-> "NH2" Residue "M ARG 250": "NH1" <-> "NH2" Residue "M ARG 254": "NH1" <-> "NH2" Residue "M ARG 299": "NH1" <-> "NH2" Residue "M ARG 306": "NH1" <-> "NH2" Residue "M ARG 310": "NH1" <-> "NH2" Residue "N ARG 130": "NH1" <-> "NH2" Residue "N ARG 150": "NH1" <-> "NH2" Residue "N PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 27": "NH1" <-> "NH2" Residue "O PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 27": "NH1" <-> "NH2" Residue "P ARG 130": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "P PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 GLU 50": "OE1" <-> "OE2" 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 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" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27776 Number of models: 1 Model: "" Number of chains: 18 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: 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "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 Time building chain proxies: 14.44, per 1000 atoms: 0.52 Number of scatterers: 27776 At special positions: 0 Unit cell: (183.38, 149.46, 131.44, 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 106 16.00 P 309 15.00 O 5885 8.00 N 5045 7.00 C 16431 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: 13.44 Conformation dependent library (CDL) restraints added in 3.9 seconds 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 18 sheets defined 58.1% alpha, 14.3% beta 150 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 10.46 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: 3.739A 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 24 through 26 No H-bonds generated for 'chain 'K' and resid 24 through 26' Processing helix chain 'K' and resid 27 through 32 Processing helix chain 'K' and resid 34 through 44 Processing helix chain 'K' and resid 49 through 54 Processing helix chain 'K' and resid 56 through 62 removed outlier: 4.287A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 79 Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.521A 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 179 Processing helix chain 'K' and resid 181 through 188 removed outlier: 4.003A pdb=" N ASP K 187 " --> pdb=" O SER K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 211 removed outlier: 4.221A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 231 removed outlier: 4.051A pdb=" N LEU K 227 " --> pdb=" O SER K 223 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR K 228 " --> pdb=" O ALA K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 259 removed outlier: 3.687A pdb=" N ARG K 241 " --> pdb=" O GLU K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 296 Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 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 179 removed outlier: 3.870A pdb=" N LEU L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 213 removed outlier: 4.009A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 232 removed outlier: 4.191A pdb=" N TYR L 228 " --> pdb=" O ALA L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 236 No H-bonds generated for 'chain 'L' and resid 234 through 236' Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 289 through 293 Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 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 179 removed outlier: 3.572A pdb=" N LEU M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG M 177 " --> pdb=" O ALA M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 211 removed outlier: 4.178A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 232 Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 237 through 260 removed outlier: 4.284A pdb=" N GLN M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET M 243 " --> pdb=" O SER M 239 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS M 244 " --> pdb=" O ALA M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 296 Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 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 179 removed outlier: 3.785A pdb=" N ARG N 177 " --> pdb=" O ALA N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 211 removed outlier: 3.665A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 232 removed outlier: 3.568A pdb=" N LEU N 227 " --> pdb=" O SER N 223 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 236 No H-bonds generated for 'chain 'N' and resid 234 through 236' Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 291 through 296 removed outlier: 4.639A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 32 removed outlier: 4.197A pdb=" N GLU O 29 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN O 30 " --> pdb=" O ARG O 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS O 31 " --> pdb=" O LEU O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 45 Processing helix chain 'O' and resid 48 through 54 removed outlier: 3.520A pdb=" N VAL O 52 " --> pdb=" O THR O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 62 removed outlier: 3.880A pdb=" N LEU O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 82 Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 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 176 Processing helix chain 'O' and resid 177 through 179 No H-bonds generated for 'chain 'O' and resid 177 through 179' Processing helix chain 'O' and resid 181 through 188 removed outlier: 3.589A pdb=" N ASP O 187 " --> pdb=" O SER O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 196 through 212 removed outlier: 3.543A pdb=" N MET O 210 " --> pdb=" O GLN O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 232 removed outlier: 4.353A pdb=" N LEU O 227 " --> pdb=" O SER O 223 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR O 228 " --> pdb=" O ALA O 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 234 through 236 No H-bonds generated for 'chain 'O' and resid 234 through 236' Processing helix chain 'O' and resid 237 through 260 Processing helix chain 'O' and resid 291 through 295 removed outlier: 4.869A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 291 through 295' Processing helix chain 'P' and resid 24 through 31 Processing helix chain 'P' and resid 34 through 45 removed outlier: 4.085A pdb=" N LEU P 41 " --> pdb=" O ASP P 37 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU P 42 " --> pdb=" O VAL P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 54 removed outlier: 3.844A pdb=" N VAL P 52 " --> pdb=" O THR P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 63 removed outlier: 3.611A pdb=" N LEU P 60 " --> pdb=" O PRO P 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 82 Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 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 removed outlier: 3.645A pdb=" N LEU P 171 " --> pdb=" O ARG P 167 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG P 177 " --> pdb=" O ALA P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 188 removed outlier: 3.791A pdb=" N ASP P 187 " --> pdb=" O SER P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 211 removed outlier: 3.748A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 232 Processing helix chain 'P' and resid 234 through 236 No H-bonds generated for 'chain 'P' and resid 234 through 236' Processing helix chain 'P' and resid 237 through 260 Processing helix chain 'P' and resid 290 through 296 removed outlier: 4.039A pdb=" N HIS P 294 " --> pdb=" O ASN P 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 113 Processing helix chain 'Q' and resid 132 through 144 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 removed outlier: 3.728A pdb=" N ARG Q 177 " --> pdb=" O ALA Q 173 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR Q 178 " --> pdb=" O VAL Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 188 Processing helix chain 'Q' and resid 196 through 211 removed outlier: 3.573A pdb=" N ALA Q 209 " --> pdb=" O TYR Q 205 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 223 through 232 removed outlier: 3.897A pdb=" N LEU Q 227 " --> pdb=" O SER Q 223 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR Q 228 " --> pdb=" O ALA Q 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 260 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 3.915A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 32 removed outlier: 3.578A pdb=" N ARG R 27 " --> pdb=" O PRO R 24 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU R 29 " --> pdb=" O SER R 26 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN R 30 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 45 Processing helix chain 'R' and resid 48 through 52 Processing helix chain 'R' and resid 56 through 62 removed outlier: 3.794A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 82 Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.511A pdb=" N ILE R 136 " --> pdb=" O GLY R 132 " (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 179 removed outlier: 3.590A pdb=" N LEU R 171 " --> pdb=" O ARG R 167 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG R 177 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR R 178 " --> pdb=" O VAL R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 188 Processing helix chain 'R' and resid 196 through 211 Processing helix chain 'R' and resid 225 through 232 Processing helix chain 'R' and resid 234 through 236 No H-bonds generated for 'chain 'R' and resid 234 through 236' Processing helix chain 'R' and resid 237 through 260 Processing helix chain 'R' and resid 291 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.076A 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: 6.826A 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: 6.824A 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: 3.671A pdb=" N ALA K 192 " --> pdb=" O TYR K 159 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP K 316 " --> pdb=" O ARG K 299 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR K 301 " --> pdb=" O ILE K 314 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE K 314 " --> pdb=" O TYR K 301 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 323 " --> pdb=" O ILE K 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 189 through 193 removed outlier: 3.854A pdb=" N ALA L 192 " --> pdb=" O TYR L 159 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP L 161 " --> pdb=" O ALA L 192 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LYS L 156 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE L 220 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N MET L 158 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASP L 222 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE L 160 " --> pdb=" O ASP L 222 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER L 121 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE L 265 " --> pdb=" O SER L 121 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR L 123 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASN L 267 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N MET L 125 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE L 122 " --> pdb=" O THR L 298 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N LEU L 300 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU L 124 " --> pdb=" O LEU L 300 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU L 302 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE L 126 " --> pdb=" O LEU L 302 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE L 311 " --> pdb=" O ARG L 303 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY L 333 " --> pdb=" O ASN L 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 189 through 193 removed outlier: 5.139A pdb=" N LYS M 156 " --> pdb=" O TYR M 216 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER M 121 " --> pdb=" O VAL M 263 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE M 265 " --> pdb=" O SER M 121 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR M 123 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ASN M 267 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET M 125 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR M 298 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE M 327 " --> pdb=" O ARG M 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 189 through 193 removed outlier: 5.522A pdb=" N LYS N 156 " --> pdb=" O TYR N 216 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR N 315 " --> pdb=" O ARG N 299 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY N 333 " --> pdb=" O ASN N 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 189 through 193 removed outlier: 3.640A pdb=" N ALA O 192 " --> pdb=" O TYR O 159 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER O 121 " --> pdb=" O VAL O 263 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE O 265 " --> pdb=" O SER O 121 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR O 123 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN O 267 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET O 125 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE O 122 " --> pdb=" O SER O 296 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR O 298 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG O 299 " --> pdb=" O TYR O 315 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE O 311 " --> pdb=" O ARG O 303 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 189 through 193 removed outlier: 6.992A pdb=" N ALA P 157 " --> pdb=" O ALA P 190 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ALA P 192 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR P 159 " --> pdb=" O ALA P 192 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR P 298 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N TYR P 301 " --> pdb=" O ILE P 314 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE P 314 " --> pdb=" O TYR P 301 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG P 303 " --> pdb=" O CYS P 312 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N CYS P 312 " --> pdb=" O ARG P 303 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 189 through 193 removed outlier: 5.231A pdb=" N LYS Q 156 " --> pdb=" O TYR Q 216 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR Q 298 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU Q 124 " --> pdb=" O THR Q 298 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP Q 316 " --> pdb=" O ARG Q 299 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR Q 301 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE Q 314 " --> pdb=" O TYR Q 301 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG Q 303 " --> pdb=" O CYS Q 312 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N CYS Q 312 " --> pdb=" O ARG Q 303 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA Q 323 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 189 through 193 removed outlier: 5.407A pdb=" N LYS R 156 " --> pdb=" O TYR R 216 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N GLN R 268 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG R 299 " --> pdb=" O TYR R 315 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE R 311 " --> pdb=" O ARG R 303 " (cutoff:3.500A) 1199 hydrogen bonds defined for protein. 3453 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 756 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 11.27 Time building geometry restraints manager: 14.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5468 1.33 - 1.45: 7911 1.45 - 1.57: 14656 1.57 - 1.70: 616 1.70 - 1.82: 172 Bond restraints: 28823 Sorted by residual: bond pdb=" N ARG N 150 " pdb=" CA ARG N 150 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.10e-02 8.26e+03 1.17e+01 bond pdb=" N TYR P 178 " pdb=" CA TYR P 178 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" N GLU N 322 " pdb=" CA GLU N 322 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" N GLY M 305 " pdb=" CA GLY M 305 " ideal model delta sigma weight residual 1.442 1.467 -0.026 7.70e-03 1.69e+04 1.10e+01 bond pdb=" CZ ARG L 150 " pdb=" NH1 ARG L 150 " ideal model delta sigma weight residual 1.323 1.277 0.046 1.40e-02 5.10e+03 1.10e+01 ... (remaining 28818 not shown) Histogram of bond angle deviations from ideal: 94.98 - 102.66: 577 102.66 - 110.34: 8848 110.34 - 118.03: 13348 118.03 - 125.71: 16118 125.71 - 133.39: 1313 Bond angle restraints: 40204 Sorted by residual: angle pdb=" CA PHE Q 195 " pdb=" CB PHE Q 195 " pdb=" CG PHE Q 195 " ideal model delta sigma weight residual 113.80 121.20 -7.40 1.00e+00 1.00e+00 5.47e+01 angle pdb=" CA PHE R 129 " pdb=" CB PHE R 129 " pdb=" CG PHE R 129 " ideal model delta sigma weight residual 113.80 120.92 -7.12 1.00e+00 1.00e+00 5.07e+01 angle pdb=" C ASN Q 196 " pdb=" N THR Q 197 " pdb=" CA THR Q 197 " ideal model delta sigma weight residual 120.28 129.09 -8.81 1.34e+00 5.57e-01 4.33e+01 angle pdb=" CA PHE K 46 " pdb=" CB PHE K 46 " pdb=" CG PHE K 46 " ideal model delta sigma weight residual 113.80 120.26 -6.46 1.00e+00 1.00e+00 4.18e+01 angle pdb=" CA PHE O 129 " pdb=" CB PHE O 129 " pdb=" CG PHE O 129 " ideal model delta sigma weight residual 113.80 119.96 -6.16 1.00e+00 1.00e+00 3.80e+01 ... (remaining 40199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.41: 13386 20.41 - 40.82: 1780 40.82 - 61.24: 1351 61.24 - 81.65: 91 81.65 - 102.06: 12 Dihedral angle restraints: 16620 sinusoidal: 8702 harmonic: 7918 Sorted by residual: dihedral pdb=" CD ARG Q 310 " pdb=" NE ARG Q 310 " pdb=" CZ ARG Q 310 " pdb=" NH1 ARG Q 310 " ideal model delta sinusoidal sigma weight residual 0.00 -90.30 90.30 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CD ARG R 310 " pdb=" NE ARG R 310 " pdb=" CZ ARG R 310 " pdb=" NH1 ARG R 310 " ideal model delta sinusoidal sigma weight residual 0.00 86.20 -86.20 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CD ARG K 254 " pdb=" NE ARG K 254 " pdb=" CZ ARG K 254 " pdb=" NH1 ARG K 254 " ideal model delta sinusoidal sigma weight residual 0.00 85.48 -85.48 1 1.00e+01 1.00e-02 8.84e+01 ... (remaining 16617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 4193 0.135 - 0.269: 357 0.269 - 0.404: 33 0.404 - 0.538: 4 0.538 - 0.673: 10 Chirality restraints: 4597 Sorted by residual: chirality pdb=" CA SER P 317 " pdb=" N SER P 317 " pdb=" C SER P 317 " pdb=" CB SER P 317 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" P DC J 4 " pdb=" OP1 DC J 4 " pdb=" OP2 DC J 4 " pdb=" O5' DC J 4 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DC I 151 " pdb=" OP1 DC I 151 " pdb=" OP2 DC I 151 " pdb=" O5' DC I 151 " both_signs ideal model delta sigma weight residual True 2.35 -3.00 -0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 4594 not shown) Planarity restraints: 4092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 254 " -1.097 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG K 254 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG K 254 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 254 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG K 254 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 310 " -1.092 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG Q 310 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG Q 310 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 310 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 310 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 310 " -1.090 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG R 310 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG R 310 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG R 310 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG R 310 " -0.016 2.00e-02 2.50e+03 ... (remaining 4089 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 14 1.83 - 2.60: 220 2.60 - 3.37: 35959 3.37 - 4.13: 76884 4.13 - 4.90: 125378 Nonbonded interactions: 238455 Sorted by model distance: nonbonded pdb=" O GLY O 305 " pdb=" NH1 ARG O 310 " model vdw 1.066 3.120 nonbonded pdb=" O THR R 165 " pdb=" NH1 ARG R 170 " model vdw 1.281 3.120 nonbonded pdb=" OP1 DA I 153 " pdb=" CB ARG P 235 " model vdw 1.336 3.440 nonbonded pdb=" O THR R 165 " pdb=" CZ ARG R 170 " model vdw 1.424 3.270 nonbonded pdb=" ND1 HIS M 138 " pdb=" NH2 ARG M 170 " model vdw 1.427 3.200 ... (remaining 238450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain '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 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'Q' } 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 83.040 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.180 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.050 28823 Z= 0.696 Angle : 1.499 15.251 40204 Z= 0.979 Chirality : 0.083 0.673 4597 Planarity : 0.037 0.492 4092 Dihedral : 23.156 102.062 11550 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.05 % Allowed : 4.51 % Favored : 93.43 % Cbeta Deviations : 0.20 % 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: 2714 helix: -0.67 (0.12), residues: 1396 sheet: 0.03 (0.31), residues: 269 loop : -1.09 (0.17), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.004 HIS R 244 PHE 0.106 0.013 PHE N 126 TYR 0.118 0.014 TYR N 228 ARG 0.010 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 271 time to evaluate : 2.847 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: A 51 ILE cc_start: 0.9652 (mt) cc_final: 0.9418 (mm) REVERT: A 105 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9116 (mm-30) REVERT: A 119 ILE cc_start: 0.9407 (pt) cc_final: 0.9103 (pt) REVERT: B 88 TYR cc_start: 0.9147 (m-10) cc_final: 0.8817 (m-80) REVERT: B 92 ARG cc_start: 0.9374 (ptm-80) cc_final: 0.8967 (ttp80) REVERT: C 38 ASN cc_start: 0.9139 (m-40) cc_final: 0.8625 (m-40) REVERT: C 56 GLU cc_start: 0.9324 (tt0) cc_final: 0.8446 (tt0) REVERT: C 64 GLU cc_start: 0.9192 (tp30) cc_final: 0.8638 (tp30) REVERT: D 80 LEU cc_start: 0.9729 (mt) cc_final: 0.9522 (tp) REVERT: D 99 ARG cc_start: 0.9240 (mtt90) cc_final: 0.8954 (ttm110) REVERT: E 53 ARG cc_start: 0.9469 (ttt180) cc_final: 0.9137 (ttp80) REVERT: E 94 GLU cc_start: 0.9687 (mm-30) cc_final: 0.8980 (mm-30) REVERT: E 96 CYS cc_start: 0.9400 (m) cc_final: 0.9194 (p) REVERT: E 106 ASP cc_start: 0.9285 (m-30) cc_final: 0.8572 (p0) REVERT: E 120 MET cc_start: 0.8717 (mtt) cc_final: 0.8217 (mtp) REVERT: F 44 LYS cc_start: 0.9089 (tttt) cc_final: 0.8768 (ttmt) REVERT: F 59 LYS cc_start: 0.9695 (tttm) cc_final: 0.9226 (tppp) REVERT: F 63 GLU cc_start: 0.9538 (mt-10) cc_final: 0.9066 (mt-10) REVERT: F 84 MET cc_start: 0.9186 (mmm) cc_final: 0.8843 (mmm) REVERT: G 25 PHE cc_start: 0.8825 (m-80) cc_final: 0.8543 (m-10) REVERT: G 56 GLU cc_start: 0.9314 (tt0) cc_final: 0.8907 (tt0) REVERT: K 243 MET cc_start: 0.1410 (mmt) cc_final: 0.1188 (mmm) REVERT: K 251 MET cc_start: 0.6914 (mtp) cc_final: 0.6354 (mmm) REVERT: M 196 ASN cc_start: 0.7574 (p0) cc_final: 0.7306 (t0) REVERT: N 210 MET cc_start: 0.1465 (tmm) cc_final: 0.1139 (tmm) REVERT: N 243 MET cc_start: 0.0676 (mmt) cc_final: 0.0445 (mmt) REVERT: P 125 MET cc_start: 0.5208 (pmm) cc_final: 0.4898 (pmm) REVERT: P 158 MET cc_start: 0.2224 (mmm) cc_final: 0.1916 (ttt) REVERT: P 210 MET cc_start: 0.0524 (tmm) cc_final: 0.0214 (tmm) REVERT: Q 210 MET cc_start: -0.1192 (tmm) cc_final: -0.1683 (tmm) REVERT: Q 235 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7706 (tpm170) REVERT: R 125 MET cc_start: 0.5649 (pmm) cc_final: 0.5398 (ptt) REVERT: R 233 SER cc_start: -0.1615 (OUTLIER) cc_final: -0.1917 (t) REVERT: R 243 MET cc_start: 0.5393 (mmt) cc_final: 0.5157 (ptt) outliers start: 46 outliers final: 15 residues processed: 312 average time/residue: 0.4512 time to fit residues: 212.0886 Evaluate side-chains 151 residues out of total 2239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 254 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 175 optimal weight: 40.0000 chunk 273 optimal weight: 30.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 84 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** K 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 GLN O 114 GLN P 206 GLN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 206 GLN ** R 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 114 GLN R 244 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 28823 Z= 0.370 Angle : 0.727 17.468 40204 Z= 0.406 Chirality : 0.042 0.169 4597 Planarity : 0.006 0.164 4092 Dihedral : 26.630 91.069 6442 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % 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: 0.14 (0.15), residues: 2714 helix: 0.69 (0.13), residues: 1436 sheet: -0.15 (0.28), residues: 345 loop : -0.59 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS E 113 PHE 0.026 0.002 PHE M 126 TYR 0.023 0.002 TYR M 301 ARG 0.009 0.001 ARG N 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9411 (pt) cc_final: 0.9164 (pt) REVERT: A 120 MET cc_start: 0.9176 (mmm) cc_final: 0.8855 (mmm) REVERT: B 44 LYS cc_start: 0.9579 (tttt) cc_final: 0.9233 (ttmm) REVERT: B 66 ILE cc_start: 0.9732 (mm) cc_final: 0.9426 (tt) REVERT: B 88 TYR cc_start: 0.8990 (m-10) cc_final: 0.8749 (m-10) REVERT: C 64 GLU cc_start: 0.9041 (tp30) cc_final: 0.8534 (tp30) REVERT: D 99 ARG cc_start: 0.9262 (mtt90) cc_final: 0.9037 (ttm110) REVERT: E 50 GLU cc_start: 0.9359 (tp30) cc_final: 0.9111 (tp30) REVERT: E 105 GLU cc_start: 0.9271 (tm-30) cc_final: 0.9070 (tm-30) REVERT: E 106 ASP cc_start: 0.8943 (m-30) cc_final: 0.8265 (m-30) REVERT: E 120 MET cc_start: 0.8221 (mtt) cc_final: 0.7967 (mtp) REVERT: F 44 LYS cc_start: 0.9165 (tttt) cc_final: 0.8776 (ttmm) REVERT: F 63 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9036 (tp30) REVERT: F 68 ASP cc_start: 0.9491 (m-30) cc_final: 0.9290 (m-30) REVERT: G 56 GLU cc_start: 0.9264 (tt0) cc_final: 0.8711 (tt0) REVERT: K 125 MET cc_start: 0.6029 (pmm) cc_final: 0.5576 (pmm) REVERT: M 251 MET cc_start: -0.5541 (ttt) cc_final: -0.6419 (mmp) REVERT: P 158 MET cc_start: 0.2905 (mmm) cc_final: 0.2680 (ttt) REVERT: P 210 MET cc_start: 0.1209 (tmm) cc_final: 0.0872 (tmm) REVERT: Q 235 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7105 (tpt170) REVERT: Q 326 MET cc_start: 0.6949 (tpp) cc_final: 0.6597 (pmm) REVERT: R 125 MET cc_start: 0.5587 (pmm) cc_final: 0.5228 (ptt) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.4509 time to fit residues: 105.6720 Evaluate side-chains 111 residues out of total 2239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 227 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 273 optimal weight: 40.0000 chunk 295 optimal weight: 40.0000 chunk 243 optimal weight: 30.0000 chunk 271 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 219 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 135 GLN P 196 ASN P 244 HIS R 34 ASN R 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 28823 Z= 0.347 Angle : 0.680 16.331 40204 Z= 0.380 Chirality : 0.041 0.150 4597 Planarity : 0.005 0.067 4092 Dihedral : 26.531 91.612 6442 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.04 % Allowed : 2.99 % Favored : 96.96 % 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: 0.13 (0.16), residues: 2714 helix: 0.71 (0.13), residues: 1444 sheet: -0.46 (0.28), residues: 344 loop : -0.50 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS M 138 PHE 0.018 0.002 PHE K 327 TYR 0.030 0.002 TYR P 216 ARG 0.007 0.001 ARG N 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9394 (pt) cc_final: 0.9087 (pt) REVERT: A 120 MET cc_start: 0.9132 (mmm) cc_final: 0.8789 (mmm) REVERT: B 66 ILE cc_start: 0.9729 (mm) cc_final: 0.9398 (tt) REVERT: B 88 TYR cc_start: 0.8996 (m-10) cc_final: 0.8739 (m-80) REVERT: C 64 GLU cc_start: 0.9037 (tp30) cc_final: 0.8627 (tp30) REVERT: D 99 ARG cc_start: 0.9253 (mtt90) cc_final: 0.9032 (ttp-170) REVERT: E 50 GLU cc_start: 0.9457 (tp30) cc_final: 0.9227 (tp30) REVERT: E 105 GLU cc_start: 0.9361 (tm-30) cc_final: 0.9021 (tm-30) REVERT: E 120 MET cc_start: 0.8410 (mtt) cc_final: 0.7929 (mtt) REVERT: F 44 LYS cc_start: 0.9163 (tttt) cc_final: 0.8872 (ttmm) REVERT: F 84 MET cc_start: 0.9478 (mmp) cc_final: 0.8975 (mmm) REVERT: M 251 MET cc_start: -0.5541 (ttt) cc_final: -0.6452 (mmp) REVERT: O 125 MET cc_start: 0.5488 (ptt) cc_final: 0.5226 (ttp) REVERT: O 210 MET cc_start: -0.0643 (ptt) cc_final: -0.1025 (ptt) REVERT: Q 326 MET cc_start: 0.7010 (tpp) cc_final: 0.6555 (pmm) REVERT: R 125 MET cc_start: 0.6129 (pmm) cc_final: 0.5762 (ptt) REVERT: R 211 MET cc_start: 0.3645 (ttm) cc_final: 0.2907 (ttm) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.4186 time to fit residues: 85.7882 Evaluate side-chains 101 residues out of total 2239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 270 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 183 optimal weight: 50.0000 chunk 274 optimal weight: 5.9990 chunk 290 optimal weight: 30.0000 chunk 143 optimal weight: 8.9990 chunk 260 optimal weight: 50.0000 chunk 78 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN L 138 HIS ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 47 HIS ** O 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 28823 Z= 0.300 Angle : 0.637 16.820 40204 Z= 0.356 Chirality : 0.040 0.146 4597 Planarity : 0.005 0.100 4092 Dihedral : 26.517 93.094 6442 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.63 % 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: 0.25 (0.16), residues: 2714 helix: 0.87 (0.13), residues: 1451 sheet: -0.57 (0.27), residues: 361 loop : -0.50 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS F 75 PHE 0.020 0.002 PHE M 126 TYR 0.016 0.002 TYR F 51 ARG 0.007 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5428 Ramachandran restraints generated. 2714 Oldfield, 0 Emsley, 2714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ILE cc_start: 0.9414 (pt) cc_final: 0.9114 (pt) REVERT: A 120 MET cc_start: 0.9162 (mmm) cc_final: 0.8824 (mmm) REVERT: B 66 ILE cc_start: 0.9714 (mm) cc_final: 0.9379 (tt) REVERT: C 64 GLU cc_start: 0.9073 (tp30) cc_final: 0.8685 (tp30) REVERT: D 59 MET cc_start: 0.9455 (tpp) cc_final: 0.9250 (tpp) REVERT: D 79 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8865 (ttp-110) REVERT: D 99 ARG cc_start: 0.9229 (mtt90) cc_final: 0.8773 (ttm110) REVERT: E 50 GLU cc_start: 0.9502 (tp30) cc_final: 0.9247 (tp30) REVERT: E 56 LYS cc_start: 0.9498 (tppp) cc_final: 0.9272 (tppp) REVERT: E 97 GLU cc_start: 0.8899 (pp20) cc_final: 0.8671 (pp20) REVERT: E 105 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9001 (tm-30) REVERT: E 120 MET cc_start: 0.8369 (mtt) cc_final: 0.7846 (mtt) REVERT: F 84 MET cc_start: 0.9370 (mmp) cc_final: 0.9047 (mmm) REVERT: H 61 ILE cc_start: 0.9743 (OUTLIER) cc_final: 0.9494 (tp) REVERT: H 71 GLU cc_start: 0.9328 (tm-30) cc_final: 0.9117 (tm-30) REVERT: M 211 MET cc_start: 0.3149 (ttt) cc_final: 0.2401 (tpp) REVERT: M 251 MET cc_start: -0.5700 (ttt) cc_final: -0.6552 (mmp) REVERT: O 125 MET cc_start: 0.5402 (ptt) cc_final: 0.5085 (ttp) REVERT: O 210 MET cc_start: 0.0178 (ptt) cc_final: -0.0076 (ptt) REVERT: P 211 MET cc_start: -0.2428 (ptt) cc_final: -0.2762 (ptt) REVERT: P 243 MET cc_start: 0.5528 (mmp) cc_final: 0.5205 (tmm) REVERT: Q 235 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6100 (tpt170) REVERT: Q 326 MET cc_start: 0.6944 (tpp) cc_final: 0.6370 (pmm) REVERT: R 125 MET cc_start: 0.6042 (pmm) cc_final: 0.5805 (ptt) REVERT: R 211 MET cc_start: 0.3621 (ttm) cc_final: 0.3060 (ttm) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.3921 time to fit residues: 80.0514 Evaluate side-chains 105 residues out of total 2239 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 242 optimal weight: 50.0000 chunk 165 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 216 optimal weight: 30.0000 chunk 120 optimal weight: 30.0000 chunk 248 optimal weight: 30.0000 chunk 201 optimal weight: 50.0000 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 50.0000 chunk 261 optimal weight: 50.0000 chunk 73 optimal weight: 10.0000 overall best weight: 14.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: