Starting phenix.real_space_refine on Thu Jul 25 19:56:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnd_36442/07_2024/8jnd_36442.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnd_36442/07_2024/8jnd_36442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnd_36442/07_2024/8jnd_36442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnd_36442/07_2024/8jnd_36442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnd_36442/07_2024/8jnd_36442.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jnd_36442/07_2024/8jnd_36442.cif" } resolution = 3.66 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 119 5.16 5 C 18079 2.51 5 N 5506 2.21 5 O 6391 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 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 "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 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 27": "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 27": "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 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 27": "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" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30404 Number of models: 1 Model: "" Number of chains: 19 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: 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: 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: 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: 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: "S" 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: 18.51, per 1000 atoms: 0.61 Number of scatterers: 30404 At special positions: 0 Unit cell: (180.2, 153.7, 138.86, 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 119 16.00 P 309 15.00 O 6391 8.00 N 5506 7.00 C 18079 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: 16.39 Conformation dependent library (CDL) restraints added in 4.7 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5702 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 19 sheets defined 57.7% alpha, 14.1% beta 156 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 12.90 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 25 through 31 removed outlier: 3.775A pdb=" N GLU K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN K 30 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS K 31 " --> pdb=" O ARG K 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 31' Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 63 removed outlier: 4.313A pdb=" N LEU K 60 " --> pdb=" O PRO K 56 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 82 removed outlier: 3.584A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 3.550A 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: 3.739A 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: 3.909A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER K 214 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 231 Processing helix chain 'K' and resid 237 through 260 removed outlier: 3.519A pdb=" N ARG K 241 " --> pdb=" O GLU K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 296 removed outlier: 4.329A pdb=" N HIS K 294 " --> pdb=" O ASN K 290 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.644A 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: 4.023A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL L 212 " --> pdb=" O SER L 208 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER L 214 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 231 removed outlier: 3.523A 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 295 removed outlier: 4.074A pdb=" N HIS L 294 " --> pdb=" O ASN L 290 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 290 through 295' Processing helix chain 'M' and resid 106 through 113 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.629A 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: 4.018A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER M 214 " --> pdb=" O MET M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 231 Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 290 through 296 removed outlier: 4.330A pdb=" N HIS M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA M 295 " --> pdb=" O ILE M 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 31 removed outlier: 3.766A pdb=" N GLU N 29 " --> pdb=" O ILE N 25 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN N 30 " --> pdb=" O SER N 26 " (cutoff:3.500A) removed outlier: 3.577A 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 56 through 63 removed outlier: 4.259A pdb=" N LEU N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE N 63 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 82 removed outlier: 3.545A pdb=" N LYS N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.533A 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: 3.642A 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 removed outlier: 3.538A pdb=" N LEU N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 4.032A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA N 209 " --> pdb=" O TYR N 205 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER N 214 " --> pdb=" O MET N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 231 Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 290 through 296 removed outlier: 4.207A pdb=" N HIS N 294 " --> pdb=" O ASN N 290 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA N 295 " --> pdb=" O ILE N 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 31 removed outlier: 3.765A pdb=" N GLU O 29 " --> pdb=" O ILE O 25 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN O 30 " --> pdb=" O SER O 26 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 25 through 31' Processing helix chain 'O' and resid 34 through 45 Processing helix chain 'O' and resid 48 through 54 Processing helix chain 'O' and resid 56 through 63 removed outlier: 4.279A pdb=" N LEU O 60 " --> pdb=" O PRO O 56 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE O 63 " --> pdb=" O GLU O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 82 removed outlier: 3.619A pdb=" N LYS O 80 " --> pdb=" O ALA O 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU O 81 " --> pdb=" O GLU O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 113 Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.674A 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: 3.934A pdb=" N LEU O 204 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR O 205 " --> pdb=" O THR O 201 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN O 206 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA O 209 " --> pdb=" O TYR O 205 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL O 212 " --> pdb=" O SER O 208 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU O 213 " --> pdb=" O ALA O 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER O 214 " --> pdb=" O MET O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 231 removed outlier: 3.533A 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 291 through 296 removed outlier: 3.880A pdb=" N ALA O 295 " --> pdb=" O ILE O 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 31 removed outlier: 3.850A pdb=" N GLU P 29 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN P 30 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS P 31 " --> pdb=" O ARG P 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 25 through 31' Processing helix chain 'P' and resid 34 through 45 Processing helix chain 'P' and resid 48 through 54 Processing helix chain 'P' and resid 56 through 62 removed outlier: 4.225A pdb=" N LEU P 60 " --> pdb=" O PRO P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 82 removed outlier: 3.714A pdb=" N LYS P 80 " --> pdb=" O ALA P 76 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU P 81 " --> pdb=" O GLU P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 113 Processing helix chain 'P' and resid 132 through 144 removed outlier: 3.738A 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: 3.951A pdb=" N LEU P 204 " --> pdb=" O GLN P 200 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR P 205 " --> pdb=" O THR P 201 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN P 206 " --> pdb=" O GLN P 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA P 209 " --> pdb=" O TYR P 205 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU P 213 " --> pdb=" O ALA P 209 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER P 214 " --> pdb=" O MET P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 231 Processing helix chain 'P' and resid 237 through 260 Processing helix chain 'P' and resid 291 through 296 removed outlier: 4.114A pdb=" N ALA P 295 " --> pdb=" O ILE P 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 31 removed outlier: 3.778A pdb=" N GLU Q 29 " --> pdb=" O ILE Q 25 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN Q 30 " --> pdb=" O SER Q 26 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS Q 31 " --> pdb=" O ARG Q 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 25 through 31' Processing helix chain 'Q' and resid 34 through 45 Processing helix chain 'Q' and resid 48 through 54 Processing helix chain 'Q' and resid 56 through 62 removed outlier: 4.241A pdb=" N LEU Q 60 " --> pdb=" O PRO Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 82 removed outlier: 3.523A pdb=" N LYS Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.669A 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: 3.974A pdb=" N LEU Q 204 " --> pdb=" O GLN Q 200 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR Q 205 " --> pdb=" O THR Q 201 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN Q 206 " --> pdb=" O GLN Q 202 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA Q 209 " --> pdb=" O TYR Q 205 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL Q 212 " --> pdb=" O SER Q 208 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU Q 213 " --> pdb=" O ALA Q 209 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER Q 214 " --> pdb=" O MET Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 225 through 231 Processing helix chain 'Q' and resid 237 through 260 Processing helix chain 'Q' and resid 290 through 296 removed outlier: 4.296A pdb=" N HIS Q 294 " --> pdb=" O ASN Q 290 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA Q 295 " --> pdb=" O ILE Q 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 113 Processing helix chain 'R' and resid 132 through 144 removed outlier: 3.686A 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: 3.955A pdb=" N LEU R 204 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR R 205 " --> pdb=" O THR R 201 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN R 206 " --> pdb=" O GLN R 202 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA R 209 " --> pdb=" O TYR R 205 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL R 212 " --> pdb=" O SER R 208 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 231 removed outlier: 3.513A 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: 4.233A pdb=" N HIS R 294 " --> pdb=" O ASN R 290 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 31 removed outlier: 3.799A pdb=" N GLU S 29 " --> pdb=" O ILE S 25 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN S 30 " --> pdb=" O SER S 26 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS S 31 " --> pdb=" O ARG S 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 25 through 31' Processing helix chain 'S' and resid 34 through 45 Processing helix chain 'S' and resid 48 through 54 Processing helix chain 'S' and resid 56 through 63 removed outlier: 4.164A pdb=" N LEU S 60 " --> pdb=" O PRO S 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE S 63 " --> pdb=" O GLU S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 82 removed outlier: 3.598A pdb=" N LYS S 80 " --> pdb=" O ALA S 76 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 113 Processing helix chain 'S' and resid 132 through 144 removed outlier: 3.687A 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: 4.015A pdb=" N LEU S 204 " --> pdb=" O GLN S 200 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR S 205 " --> pdb=" O THR S 201 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN S 206 " --> pdb=" O GLN S 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU S 213 " --> pdb=" O ALA S 209 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER S 214 " --> pdb=" O MET S 210 " (cutoff:3.500A) Processing helix chain 'S' and resid 225 through 231 Processing helix chain 'S' and resid 237 through 260 Processing helix chain 'S' and resid 290 through 296 removed outlier: 4.365A pdb=" N HIS S 294 " --> pdb=" O ASN S 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA S 295 " --> pdb=" O ILE S 291 " (cutoff:3.500A) 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: 6.827A 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: 7.243A 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: 4.996A pdb=" N LYS K 156 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN K 268 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE K 265 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET K 125 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN K 267 " --> pdb=" O MET K 125 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.676A 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: 5.068A pdb=" N LYS L 156 " --> pdb=" O TYR L 216 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLN L 268 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE L 265 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET L 125 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN L 267 " --> pdb=" O MET L 125 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE L 122 " --> pdb=" O THR L 297 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG L 299 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU L 124 " --> pdb=" O ARG L 299 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N TYR L 301 " --> pdb=" O GLU L 124 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE L 126 " --> pdb=" O TYR L 301 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG L 303 " --> pdb=" O PHE L 126 " (cutoff:3.500A) removed outlier: 6.659A 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: 5.020A pdb=" N LYS M 156 " --> pdb=" O TYR M 216 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU M 218 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA M 217 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL M 264 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU M 219 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR M 266 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL M 221 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N GLN M 268 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE M 265 " --> pdb=" O THR M 123 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET M 125 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN M 267 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 6.560A 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: 4.954A pdb=" N LYS N 156 " --> pdb=" O TYR N 216 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLN N 268 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE N 265 " --> pdb=" O THR N 123 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET N 125 " --> pdb=" O ILE N 265 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN N 267 " --> pdb=" O MET N 125 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY N 127 " --> pdb=" O ASN N 267 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE N 122 " --> pdb=" O THR N 298 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N LEU N 300 " --> pdb=" O ILE N 122 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU N 124 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU N 302 " --> pdb=" O GLU N 124 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE N 126 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N LYS N 304 " --> pdb=" O PHE N 126 " (cutoff:3.500A) removed outlier: 6.563A 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: 5.370A pdb=" N LYS O 156 " --> pdb=" O TYR O 216 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU O 218 " --> pdb=" O LYS O 156 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA O 217 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL O 264 " --> pdb=" O ALA O 217 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU O 219 " --> pdb=" O VAL O 264 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR O 266 " --> pdb=" O LEU O 219 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL O 221 " --> pdb=" O THR O 266 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLN O 268 " --> pdb=" O VAL O 221 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE O 265 " --> pdb=" O THR O 123 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET O 125 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN O 267 " --> pdb=" O MET O 125 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY O 127 " --> pdb=" O ASN O 267 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE O 122 " --> pdb=" O THR O 298 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU O 300 " --> pdb=" O ILE O 122 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU O 124 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU O 302 " --> pdb=" O GLU O 124 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE O 126 " --> pdb=" O LEU O 302 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LYS O 304 " --> pdb=" O PHE O 126 " (cutoff:3.500A) removed outlier: 6.742A 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: 3.507A pdb=" N ALA P 190 " --> pdb=" O ALA P 157 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA P 192 " --> pdb=" O TYR P 159 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS P 156 " --> pdb=" O LEU P 218 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ILE P 220 " --> pdb=" O LYS P 156 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET P 158 " --> pdb=" O ILE P 220 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASP P 222 " --> pdb=" O MET P 158 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE P 160 " --> pdb=" O ASP P 222 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA P 217 " --> pdb=" O ALA P 262 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N VAL P 264 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU P 219 " --> pdb=" O VAL P 264 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR P 266 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL P 221 " --> pdb=" O THR P 266 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLN P 268 " --> pdb=" O VAL P 221 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE P 265 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET P 125 " --> pdb=" O ILE P 265 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN P 267 " --> pdb=" O MET P 125 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY P 127 " --> pdb=" O ASN P 267 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE P 122 " --> pdb=" O THR P 298 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU P 300 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU P 124 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU P 302 " --> pdb=" O GLU P 124 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE P 126 " --> pdb=" O LEU P 302 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N LYS P 304 " --> pdb=" O PHE P 126 " (cutoff:3.500A) removed outlier: 6.552A 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: 6.642A pdb=" N LYS Q 156 " --> pdb=" O LEU Q 218 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE Q 220 " --> pdb=" O LYS Q 156 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET Q 158 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASP Q 222 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE Q 160 " --> pdb=" O ASP Q 222 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA Q 217 " --> pdb=" O ALA Q 262 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL Q 264 " --> pdb=" O ALA Q 217 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU Q 219 " --> pdb=" O VAL Q 264 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR Q 266 " --> pdb=" O LEU Q 219 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL Q 221 " --> pdb=" O THR Q 266 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N GLN Q 268 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE Q 265 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET Q 125 " --> pdb=" O ILE Q 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN Q 267 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY Q 127 " --> pdb=" O ASN Q 267 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR Q 298 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 6.525A 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: 6.653A pdb=" N LYS R 156 " --> pdb=" O LEU R 218 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ILE R 220 " --> pdb=" O LYS R 156 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N MET R 158 " --> pdb=" O ILE R 220 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP R 222 " --> pdb=" O MET R 158 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE R 160 " --> pdb=" O ASP R 222 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA R 217 " --> pdb=" O ALA R 262 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N VAL R 264 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU R 219 " --> pdb=" O VAL R 264 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N THR R 266 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL R 221 " --> pdb=" O THR R 266 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N GLN R 268 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE R 265 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET R 125 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN R 267 " --> pdb=" O MET R 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR R 298 " --> pdb=" O ILE R 122 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR R 301 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE R 314 " --> pdb=" O TYR R 301 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG R 303 " --> pdb=" O CYS R 312 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N CYS R 312 " --> pdb=" O ARG R 303 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 189 through 193 removed outlier: 5.116A pdb=" N LYS S 156 " --> pdb=" O TYR S 216 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU S 218 " --> pdb=" O LYS S 156 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA S 217 " --> pdb=" O ALA S 262 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL S 264 " --> pdb=" O ALA S 217 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU S 219 " --> pdb=" O VAL S 264 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR S 266 " --> pdb=" O LEU S 219 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL S 221 " --> pdb=" O THR S 266 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLN S 268 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE S 265 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET S 125 " --> pdb=" O ILE S 265 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN S 267 " --> pdb=" O MET S 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY S 127 " --> pdb=" O ASN S 267 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE S 122 " --> pdb=" O THR S 298 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N LEU S 300 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU S 124 " --> pdb=" O LEU S 300 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU S 302 " --> pdb=" O GLU S 124 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE S 126 " --> pdb=" O LEU S 302 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS S 304 " --> pdb=" O PHE S 126 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR S 301 " --> pdb=" O ILE S 314 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE S 314 " --> pdb=" O TYR S 301 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG S 303 " --> pdb=" O CYS S 312 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N CYS S 312 " --> pdb=" O ARG S 303 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3654 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 397 hydrogen bonds 786 hydrogen bond angles 0 basepair planarities 156 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 12.37 Time building geometry restraints manager: 17.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5963 1.33 - 1.45: 8379 1.45 - 1.57: 16333 1.57 - 1.69: 616 1.69 - 1.81: 192 Bond restraints: 31483 Sorted by residual: bond pdb=" CZ ARG P 150 " pdb=" NH2 ARG P 150 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.48e+00 bond pdb=" C GLY P 151 " pdb=" O GLY P 151 " ideal model delta sigma weight residual 1.238 1.207 0.030 1.42e-02 4.96e+03 4.60e+00 bond pdb=" P DC I 151 " pdb=" OP2 DC I 151 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.88e+00 bond pdb=" P DT J 14 " pdb=" OP1 DT J 14 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" P DA I 146 " pdb=" OP2 DA I 146 " ideal model delta sigma weight residual 1.480 1.519 -0.039 2.00e-02 2.50e+03 3.80e+00 ... (remaining 31478 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.39: 1317 104.39 - 111.49: 14887 111.49 - 118.60: 10325 118.60 - 125.70: 16196 125.70 - 132.81: 1062 Bond angle restraints: 43787 Sorted by residual: angle pdb=" C4' DA I 153 " pdb=" C3' DA I 153 " pdb=" O3' DA I 153 " ideal model delta sigma weight residual 110.00 117.49 -7.49 1.50e+00 4.44e-01 2.49e+01 angle pdb=" C ILE P 102 " pdb=" N THR P 103 " pdb=" CA THR P 103 " ideal model delta sigma weight residual 121.05 127.30 -6.25 1.43e+00 4.89e-01 1.91e+01 angle pdb=" O3' DA I 147 " pdb=" P DC I 148 " pdb=" O5' DC I 148 " ideal model delta sigma weight residual 104.00 98.14 5.86 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C3' DA I 153 " pdb=" O3' DA I 153 " pdb=" P DC I 154 " ideal model delta sigma weight residual 120.20 114.37 5.83 1.50e+00 4.44e-01 1.51e+01 angle pdb=" CA GLY P 151 " pdb=" C GLY P 151 " pdb=" N GLY P 152 " ideal model delta sigma weight residual 118.48 122.99 -4.51 1.17e+00 7.31e-01 1.49e+01 ... (remaining 43782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.41: 15239 20.41 - 40.83: 1661 40.83 - 61.24: 1271 61.24 - 81.65: 76 81.65 - 102.06: 4 Dihedral angle restraints: 18251 sinusoidal: 9349 harmonic: 8902 Sorted by residual: dihedral pdb=" CA VAL Q 334 " pdb=" C VAL Q 334 " pdb=" N GLY Q 335 " pdb=" CA GLY Q 335 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA VAL M 334 " pdb=" C VAL M 334 " pdb=" N GLY M 335 " pdb=" CA GLY M 335 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA VAL O 334 " pdb=" C VAL O 334 " pdb=" N GLY O 335 " pdb=" CA GLY O 335 " ideal model delta harmonic sigma weight residual 180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 18248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 4865 0.113 - 0.225: 136 0.225 - 0.338: 4 0.338 - 0.451: 0 0.451 - 0.564: 6 Chirality restraints: 5011 Sorted by residual: chirality pdb=" P DA I 146 " pdb=" OP1 DA I 146 " pdb=" OP2 DA I 146 " pdb=" O5' DA I 146 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.94e+00 chirality pdb=" P DT J 14 " pdb=" OP1 DT J 14 " pdb=" OP2 DT J 14 " pdb=" O5' DT J 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" P DA J 97 " pdb=" OP1 DA J 97 " pdb=" OP2 DA J 97 " pdb=" O5' DA J 97 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.76e+00 ... (remaining 5008 not shown) Planarity restraints: 4558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 142 " -0.050 2.00e-02 2.50e+03 3.04e-02 2.07e+01 pdb=" N1 DC I 142 " 0.070 2.00e-02 2.50e+03 pdb=" C2 DC I 142 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DC I 142 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC I 142 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC I 142 " -0.010 2.00e-02 2.50e+03 pdb=" N4 DC I 142 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 142 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC I 142 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 143 " 0.030 2.00e-02 2.50e+03 1.82e-02 9.94e+00 pdb=" N9 DG I 143 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DG I 143 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DG I 143 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 143 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 143 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 143 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG I 143 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 143 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 143 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG I 143 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 143 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 118 " 0.030 2.00e-02 2.50e+03 1.93e-02 8.37e+00 pdb=" N1 DC I 118 " -0.048 2.00e-02 2.50e+03 pdb=" C2 DC I 118 " 0.008 2.00e-02 2.50e+03 pdb=" O2 DC I 118 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC I 118 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 118 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 118 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 118 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DC I 118 " 0.002 2.00e-02 2.50e+03 ... (remaining 4555 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3272 2.74 - 3.28: 30952 3.28 - 3.82: 55589 3.82 - 4.36: 66620 4.36 - 4.90: 101755 Nonbonded interactions: 258188 Sorted by model distance: nonbonded pdb=" N THR Q 103 " pdb=" O GLY Q 151 " model vdw 2.205 2.520 nonbonded pdb=" NH1 ARG P 170 " pdb=" O ALA P 331 " model vdw 2.213 2.520 nonbonded pdb=" OG SER S 106 " pdb=" OD1 ASP S 336 " model vdw 2.222 2.440 nonbonded pdb=" N THR R 103 " pdb=" O GLY R 151 " model vdw 2.231 2.520 nonbonded pdb=" N THR M 103 " pdb=" O GLY M 151 " model vdw 2.238 2.520 ... (remaining 258183 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 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'R' } 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: 3.830 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: 0.000 Extract box with map and model: 1.250 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 97.170 Find NCS groups from input model: 1.080 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 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 : 0.006 0.040 31483 Z= 0.336 Angle : 0.803 12.666 43787 Z= 0.460 Chirality : 0.051 0.564 5011 Planarity : 0.006 0.064 4558 Dihedral : 21.262 102.065 12549 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.04 % Allowed : 1.31 % Favored : 98.65 % 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: -0.34 (0.14), residues: 3051 helix: -0.03 (0.12), residues: 1569 sheet: 0.77 (0.21), residues: 480 loop : -0.83 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS A 39 PHE 0.027 0.002 PHE E 78 TYR 0.025 0.002 TYR S 54 ARG 0.017 0.002 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 3.099 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: A 50 GLU cc_start: 0.9342 (mt-10) cc_final: 0.9137 (mm-30) REVERT: A 76 GLN cc_start: 0.9732 (tp40) cc_final: 0.9524 (tp-100) REVERT: A 81 ASP cc_start: 0.8637 (t0) cc_final: 0.7928 (t70) REVERT: A 119 ILE cc_start: 0.9254 (pt) cc_final: 0.8842 (pt) REVERT: B 30 THR cc_start: 0.9107 (p) cc_final: 0.8839 (t) REVERT: B 59 LYS cc_start: 0.9347 (tttm) cc_final: 0.9136 (tttp) REVERT: B 63 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8870 (mt-10) REVERT: B 84 MET cc_start: 0.9025 (mmm) cc_final: 0.8643 (mmm) REVERT: B 92 ARG cc_start: 0.9196 (ptm-80) cc_final: 0.8768 (ttp80) REVERT: C 56 GLU cc_start: 0.9124 (tt0) cc_final: 0.8522 (tt0) REVERT: D 62 MET cc_start: 0.9575 (mmm) cc_final: 0.9250 (mmp) REVERT: D 64 SER cc_start: 0.8915 (m) cc_final: 0.8456 (t) REVERT: D 94 ILE cc_start: 0.9603 (mm) cc_final: 0.9376 (tp) REVERT: E 93 GLN cc_start: 0.9289 (tt0) cc_final: 0.8921 (tp40) REVERT: E 94 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9022 (mm-30) REVERT: E 123 ASP cc_start: 0.8775 (m-30) cc_final: 0.7840 (m-30) REVERT: F 44 LYS cc_start: 0.8940 (tttt) cc_final: 0.8671 (tttt) REVERT: G 64 GLU cc_start: 0.9304 (tp30) cc_final: 0.8766 (tp30) REVERT: G 71 ARG cc_start: 0.9420 (ttm170) cc_final: 0.9184 (tmm-80) REVERT: H 62 MET cc_start: 0.9609 (mmm) cc_final: 0.9312 (mmm) REVERT: K 294 HIS cc_start: 0.4607 (t-90) cc_final: 0.4058 (t70) REVERT: L 158 MET cc_start: -0.0447 (mmm) cc_final: -0.0678 (mmm) REVERT: L 326 MET cc_start: 0.2790 (tpt) cc_final: 0.2469 (tpt) REVERT: M 125 MET cc_start: -0.1932 (pmm) cc_final: -0.2551 (ptp) REVERT: P 247 ARG cc_start: 0.9440 (ttp-170) cc_final: 0.9214 (tpp-160) REVERT: Q 149 ASP cc_start: 0.9411 (t70) cc_final: 0.9187 (p0) REVERT: Q 210 MET cc_start: 0.7215 (tmm) cc_final: 0.6450 (ptt) REVERT: Q 248 PHE cc_start: 0.9258 (t80) cc_final: 0.8919 (t80) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.4718 time to fit residues: 218.8244 Evaluate side-chains 153 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 7.9990 chunk 253 optimal weight: 50.0000 chunk 140 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 135 optimal weight: 40.0000 chunk 262 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 195 optimal weight: 50.0000 chunk 304 optimal weight: 20.0000 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 G 73 ASN K 23 GLN K 47 HIS K 206 GLN L 101 GLN M 206 GLN M 268 GLN N 23 GLN N 47 HIS O 23 GLN O 47 HIS P 23 GLN P 47 HIS P 206 GLN Q 23 GLN Q 47 HIS Q 62 ASN R 206 GLN S 206 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 31483 Z= 0.382 Angle : 0.693 15.999 43787 Z= 0.387 Chirality : 0.042 0.153 5011 Planarity : 0.005 0.051 4558 Dihedral : 25.652 93.780 6814 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.51 % Allowed : 5.33 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.15), residues: 3051 helix: 1.15 (0.13), residues: 1576 sheet: 0.79 (0.22), residues: 456 loop : -0.68 (0.18), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS B 75 PHE 0.016 0.002 PHE L 248 TYR 0.022 0.002 TYR D 37 ARG 0.009 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 158 time to evaluate : 3.054 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 81 ASP cc_start: 0.8839 (t0) cc_final: 0.8064 (t70) REVERT: B 63 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8661 (mt-10) REVERT: B 84 MET cc_start: 0.9096 (mmm) cc_final: 0.8778 (tpp) REVERT: C 56 GLU cc_start: 0.9058 (tt0) cc_final: 0.8474 (tt0) REVERT: D 62 MET cc_start: 0.9575 (mmm) cc_final: 0.9301 (mmp) REVERT: D 64 SER cc_start: 0.9072 (m) cc_final: 0.8703 (t) REVERT: D 71 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8995 (mm-30) REVERT: E 120 MET cc_start: 0.8533 (mtm) cc_final: 0.8007 (mtm) REVERT: F 63 GLU cc_start: 0.9350 (tt0) cc_final: 0.8559 (tp30) REVERT: G 64 GLU cc_start: 0.9237 (tp30) cc_final: 0.8985 (tm-30) REVERT: H 93 GLU cc_start: 0.9051 (mp0) cc_final: 0.8773 (mp0) REVERT: K 294 HIS cc_start: 0.4817 (t-90) cc_final: 0.4236 (t70) REVERT: L 211 MET cc_start: -0.1434 (mtt) cc_final: -0.1751 (mmm) REVERT: M 125 MET cc_start: -0.2353 (pmm) cc_final: -0.2940 (ptp) REVERT: M 158 MET cc_start: 0.5053 (mmm) cc_final: 0.4519 (ttt) REVERT: M 210 MET cc_start: 0.1012 (ppp) cc_final: 0.0326 (ppp) REVERT: O 158 MET cc_start: 0.6048 (tpp) cc_final: 0.5808 (ptm) REVERT: O 210 MET cc_start: 0.2096 (ptt) cc_final: 0.1192 (ptt) REVERT: O 243 MET cc_start: 0.8640 (mmt) cc_final: 0.7933 (tpt) REVERT: P 211 MET cc_start: -0.1957 (mmm) cc_final: -0.2345 (tpt) REVERT: P 247 ARG cc_start: 0.9487 (ttp-170) cc_final: 0.9268 (ttp80) REVERT: Q 210 MET cc_start: 0.7106 (tmm) cc_final: 0.6743 (ptt) REVERT: Q 248 PHE cc_start: 0.9236 (t80) cc_final: 0.8925 (t80) REVERT: S 210 MET cc_start: 0.3567 (ptt) cc_final: 0.3212 (ppp) REVERT: S 211 MET cc_start: -0.0268 (ttm) cc_final: -0.0923 (ttp) outliers start: 38 outliers final: 26 residues processed: 188 average time/residue: 0.3869 time to fit residues: 120.5312 Evaluate side-chains 156 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain P residue 326 MET Chi-restraints excluded: chain S residue 34 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 50.0000 chunk 94 optimal weight: 5.9990 chunk 253 optimal weight: 50.0000 chunk 207 optimal weight: 0.0060 chunk 83 optimal weight: 6.9990 chunk 304 optimal weight: 50.0000 chunk 329 optimal weight: 0.0870 chunk 271 optimal weight: 8.9990 chunk 302 optimal weight: 0.4980 chunk 103 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 overall best weight: 2.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN G 31 HIS H 84 ASN ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN M 206 GLN ** Q 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31483 Z= 0.188 Angle : 0.547 11.550 43787 Z= 0.311 Chirality : 0.038 0.146 5011 Planarity : 0.003 0.040 4558 Dihedral : 25.362 93.598 6814 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.11 % Allowed : 6.73 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.15), residues: 3051 helix: 1.73 (0.13), residues: 1580 sheet: 1.14 (0.22), residues: 477 loop : -0.51 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 75 PHE 0.012 0.001 PHE S 248 TYR 0.016 0.001 TYR D 83 ARG 0.004 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 3.191 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: A 50 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8608 (mm-30) REVERT: A 81 ASP cc_start: 0.8673 (t0) cc_final: 0.7742 (t70) REVERT: A 94 GLU cc_start: 0.9314 (OUTLIER) cc_final: 0.8986 (tp30) REVERT: B 63 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8539 (mt-10) REVERT: B 84 MET cc_start: 0.8843 (mmm) cc_final: 0.8383 (tpp) REVERT: C 56 GLU cc_start: 0.9067 (tt0) cc_final: 0.8385 (tt0) REVERT: D 62 MET cc_start: 0.9504 (mmm) cc_final: 0.9126 (mmp) REVERT: D 64 SER cc_start: 0.9014 (m) cc_final: 0.8635 (t) REVERT: D 71 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8840 (mm-30) REVERT: D 93 GLU cc_start: 0.9363 (mp0) cc_final: 0.8919 (mp0) REVERT: E 90 MET cc_start: 0.9086 (mmm) cc_final: 0.8754 (mmp) REVERT: F 84 MET cc_start: 0.9284 (tpp) cc_final: 0.8935 (mmm) REVERT: F 88 TYR cc_start: 0.9201 (m-80) cc_final: 0.8949 (m-80) REVERT: G 71 ARG cc_start: 0.9401 (ttm170) cc_final: 0.9182 (tmm-80) REVERT: H 93 GLU cc_start: 0.8991 (mp0) cc_final: 0.8668 (mp0) REVERT: H 94 ILE cc_start: 0.9578 (mm) cc_final: 0.9317 (tt) REVERT: K 294 HIS cc_start: 0.4745 (t-90) cc_final: 0.4250 (t70) REVERT: M 125 MET cc_start: -0.1847 (pmm) cc_final: -0.2349 (ptp) REVERT: M 158 MET cc_start: 0.4888 (mmm) cc_final: 0.4332 (ttt) REVERT: M 210 MET cc_start: 0.0666 (ppp) cc_final: 0.0084 (ppp) REVERT: O 158 MET cc_start: 0.6066 (tpp) cc_final: 0.5738 (ptp) REVERT: O 210 MET cc_start: 0.2218 (ptt) cc_final: 0.1133 (ppp) REVERT: P 211 MET cc_start: -0.2060 (mmm) cc_final: -0.2390 (tpt) REVERT: P 251 MET cc_start: 0.6949 (tpt) cc_final: 0.6597 (tpt) REVERT: Q 213 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: Q 248 PHE cc_start: 0.9250 (t80) cc_final: 0.8899 (t80) REVERT: S 210 MET cc_start: 0.3404 (ptt) cc_final: 0.2940 (ppp) REVERT: S 211 MET cc_start: -0.0243 (ttm) cc_final: -0.1606 (tpt) REVERT: S 243 MET cc_start: 0.8167 (mmm) cc_final: 0.7471 (tpt) outliers start: 28 outliers final: 17 residues processed: 172 average time/residue: 0.3774 time to fit residues: 110.9411 Evaluate side-chains 148 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain P residue 149 ASP Chi-restraints excluded: chain Q residue 213 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 50.0000 chunk 229 optimal weight: 0.0670 chunk 158 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 204 optimal weight: 0.8980 chunk 305 optimal weight: 20.0000 chunk 323 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 overall best weight: 3.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 206 GLN N 23 GLN Q 114 GLN Q 206 GLN ** Q 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 268 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31483 Z= 0.220 Angle : 0.545 11.922 43787 Z= 0.310 Chirality : 0.038 0.144 5011 Planarity : 0.003 0.042 4558 Dihedral : 25.212 95.913 6814 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.51 % Allowed : 7.60 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.43 (0.15), residues: 3051 helix: 1.78 (0.13), residues: 1589 sheet: 1.42 (0.23), residues: 441 loop : -0.58 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.016 0.001 PHE P 248 TYR 0.033 0.001 TYR D 83 ARG 0.003 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 3.130 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 81 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.7795 (t70) REVERT: A 94 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8934 (tp30) REVERT: A 120 MET cc_start: 0.8290 (mmm) cc_final: 0.7608 (mmm) REVERT: B 92 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8584 (ttp80) REVERT: D 62 MET cc_start: 0.9540 (mmm) cc_final: 0.9228 (mmp) REVERT: D 64 SER cc_start: 0.9022 (m) cc_final: 0.8676 (t) REVERT: D 71 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8836 (mm-30) REVERT: D 93 GLU cc_start: 0.9275 (mp0) cc_final: 0.8904 (mp0) REVERT: E 90 MET cc_start: 0.9015 (mmm) cc_final: 0.8722 (mmp) REVERT: E 93 GLN cc_start: 0.8804 (tp40) cc_final: 0.8453 (tp40) REVERT: E 120 MET cc_start: 0.8681 (mtm) cc_final: 0.8414 (mtm) REVERT: F 63 GLU cc_start: 0.9271 (tt0) cc_final: 0.8422 (tp30) REVERT: F 84 MET cc_start: 0.9329 (tpp) cc_final: 0.8984 (mmm) REVERT: H 76 GLU cc_start: 0.8885 (tp30) cc_final: 0.8648 (mm-30) REVERT: H 94 ILE cc_start: 0.9572 (mm) cc_final: 0.9309 (tt) REVERT: K 243 MET cc_start: 0.8794 (ptm) cc_final: 0.8249 (mmp) REVERT: K 294 HIS cc_start: 0.4809 (t-90) cc_final: 0.4271 (t70) REVERT: M 125 MET cc_start: -0.1686 (pmm) cc_final: -0.2168 (ptp) REVERT: M 158 MET cc_start: 0.4401 (mmm) cc_final: 0.4041 (ttt) REVERT: M 210 MET cc_start: 0.0379 (ppp) cc_final: -0.0270 (ppp) REVERT: N 211 MET cc_start: 0.4931 (OUTLIER) cc_final: 0.2640 (mmt) REVERT: O 210 MET cc_start: 0.2035 (ptt) cc_final: 0.1056 (ppp) REVERT: O 243 MET cc_start: 0.8651 (mmt) cc_final: 0.7743 (tpt) REVERT: P 211 MET cc_start: -0.1799 (mmm) cc_final: -0.2123 (tpt) REVERT: Q 211 MET cc_start: 0.0603 (ttm) cc_final: -0.0892 (ttp) REVERT: Q 213 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: Q 248 PHE cc_start: 0.9256 (t80) cc_final: 0.8912 (t80) REVERT: R 211 MET cc_start: 0.2839 (mmm) cc_final: 0.2531 (mmm) REVERT: S 37 ASP cc_start: 0.3651 (OUTLIER) cc_final: 0.2976 (m-30) REVERT: S 211 MET cc_start: 0.0208 (ttm) cc_final: -0.0752 (ttp) REVERT: S 243 MET cc_start: 0.8309 (mmm) cc_final: 0.7651 (tpt) outliers start: 38 outliers final: 23 residues processed: 167 average time/residue: 0.3768 time to fit residues: 106.3941 Evaluate side-chains 154 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain P residue 149 ASP Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 50.0000 chunk 183 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 241 optimal weight: 50.0000 chunk 133 optimal weight: 6.9990 chunk 276 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 50.0000 chunk 290 optimal weight: 50.0000 chunk 81 optimal weight: 8.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN N 23 GLN O 268 GLN P 244 HIS Q 268 GLN R 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 31483 Z= 0.430 Angle : 0.725 17.979 43787 Z= 0.401 Chirality : 0.044 0.150 5011 Planarity : 0.005 0.090 4558 Dihedral : 25.597 101.891 6814 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 2.27 % Allowed : 8.56 % Favored : 89.17 % 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 (0.15), residues: 3051 helix: 1.20 (0.13), residues: 1542 sheet: 1.31 (0.24), residues: 429 loop : -0.60 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 75 PHE 0.021 0.002 PHE E 84 TYR 0.030 0.002 TYR D 83 ARG 0.008 0.001 ARG F 17 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 122 time to evaluate : 3.048 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: 0.9316 (mm-30) cc_final: 0.8696 (tp30) REVERT: A 63 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8697 (mmm160) REVERT: A 80 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.8170 (t) REVERT: A 119 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8894 (pp) REVERT: A 120 MET cc_start: 0.8472 (mmm) cc_final: 0.7938 (mmm) REVERT: B 92 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8878 (ttp80) REVERT: D 64 SER cc_start: 0.9141 (m) cc_final: 0.8762 (t) REVERT: D 71 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9077 (mm-30) REVERT: D 93 GLU cc_start: 0.9246 (mp0) cc_final: 0.8865 (mp0) REVERT: E 81 ASP cc_start: 0.9137 (m-30) cc_final: 0.8928 (p0) REVERT: E 120 MET cc_start: 0.8681 (mtm) cc_final: 0.8354 (mtm) REVERT: F 63 GLU cc_start: 0.9409 (tt0) cc_final: 0.8975 (tm-30) REVERT: F 84 MET cc_start: 0.9469 (tpp) cc_final: 0.9011 (mmm) REVERT: H 59 MET cc_start: 0.9570 (tpp) cc_final: 0.9225 (tpp) REVERT: H 93 GLU cc_start: 0.9024 (mp0) cc_final: 0.8460 (mp0) REVERT: H 94 ILE cc_start: 0.9646 (mm) cc_final: 0.9416 (tt) REVERT: K 243 MET cc_start: 0.8858 (ptm) cc_final: 0.8333 (mmp) REVERT: K 294 HIS cc_start: 0.4513 (t-90) cc_final: 0.4080 (t70) REVERT: M 125 MET cc_start: -0.1028 (pmm) cc_final: -0.1368 (ptp) REVERT: M 158 MET cc_start: 0.4086 (mmm) cc_final: 0.3730 (ttt) REVERT: M 210 MET cc_start: 0.0034 (ppp) cc_final: -0.0545 (ppp) REVERT: O 210 MET cc_start: 0.1529 (ptt) cc_final: 0.1094 (ppp) REVERT: O 211 MET cc_start: 0.0421 (tpt) cc_final: -0.0103 (tpt) REVERT: P 205 TYR cc_start: 0.8917 (t80) cc_final: 0.8454 (t80) REVERT: P 211 MET cc_start: -0.1236 (mmm) cc_final: -0.1664 (tpt) REVERT: Q 211 MET cc_start: 0.2549 (ttm) cc_final: 0.0805 (ttm) REVERT: Q 213 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: Q 248 PHE cc_start: 0.9248 (t80) cc_final: 0.8936 (t80) REVERT: R 195 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6747 (m-10) REVERT: R 235 ARG cc_start: 0.4949 (mmt180) cc_final: 0.3868 (mmp80) REVERT: S 37 ASP cc_start: 0.4195 (OUTLIER) cc_final: 0.3833 (m-30) REVERT: S 158 MET cc_start: 0.4950 (mmm) cc_final: 0.4535 (mmt) REVERT: S 211 MET cc_start: -0.0387 (ttm) cc_final: -0.0934 (ttp) REVERT: S 243 MET cc_start: 0.8391 (mmm) cc_final: 0.7772 (tpt) outliers start: 57 outliers final: 40 residues processed: 169 average time/residue: 0.3720 time to fit residues: 106.2166 Evaluate side-chains 165 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 118 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain L residue 243 MET Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain P residue 149 ASP Chi-restraints excluded: chain Q residue 46 PHE Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 30.0000 chunk 291 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 190 optimal weight: 50.0000 chunk 79 optimal weight: 4.9990 chunk 324 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 170 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 244 HIS Q 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 31483 Z= 0.283 Angle : 0.607 13.665 43787 Z= 0.339 Chirality : 0.039 0.163 5011 Planarity : 0.004 0.047 4558 Dihedral : 25.591 102.878 6814 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.19 % Allowed : 8.52 % Favored : 89.29 % 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: 1.19 (0.15), residues: 3051 helix: 1.56 (0.13), residues: 1539 sheet: 1.37 (0.25), residues: 429 loop : -0.53 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.015 0.001 PHE P 248 TYR 0.023 0.001 TYR D 83 ARG 0.004 0.000 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 131 time to evaluate : 2.997 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: 0.9295 (mm-30) cc_final: 0.8823 (tp30) REVERT: A 94 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.9025 (tp30) REVERT: A 119 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9025 (pp) REVERT: A 120 MET cc_start: 0.8445 (mmm) cc_final: 0.7884 (mmm) REVERT: B 88 TYR cc_start: 0.8872 (m-80) cc_final: 0.8449 (m-80) REVERT: B 92 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8921 (ttp80) REVERT: D 64 SER cc_start: 0.9074 (m) cc_final: 0.8690 (t) REVERT: D 71 GLU cc_start: 0.9249 (mm-30) cc_final: 0.9023 (mm-30) REVERT: D 93 GLU cc_start: 0.9287 (mp0) cc_final: 0.8928 (mp0) REVERT: E 39 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7817 (t70) REVERT: E 120 MET cc_start: 0.8604 (mtm) cc_final: 0.8188 (mtm) REVERT: F 63 GLU cc_start: 0.9364 (tt0) cc_final: 0.8865 (tm-30) REVERT: F 84 MET cc_start: 0.9378 (tpp) cc_final: 0.8893 (mmm) REVERT: H 93 GLU cc_start: 0.9032 (mp0) cc_final: 0.8414 (mp0) REVERT: H 105 GLU cc_start: 0.9133 (mp0) cc_final: 0.8804 (pm20) REVERT: K 243 MET cc_start: 0.8818 (ptm) cc_final: 0.8283 (mmp) REVERT: K 294 HIS cc_start: 0.4736 (t70) cc_final: 0.4088 (t70) REVERT: K 326 MET cc_start: 0.7278 (mmp) cc_final: 0.6401 (tpt) REVERT: M 125 MET cc_start: -0.0906 (pmm) cc_final: -0.1304 (ptp) REVERT: M 158 MET cc_start: 0.3989 (mmm) cc_final: 0.3624 (ttt) REVERT: M 210 MET cc_start: -0.0777 (ppp) cc_final: -0.1370 (ppp) REVERT: N 211 MET cc_start: 0.5030 (OUTLIER) cc_final: 0.4578 (tpt) REVERT: O 211 MET cc_start: 0.0362 (tpt) cc_final: 0.0004 (tpt) REVERT: P 211 MET cc_start: -0.0719 (mmm) cc_final: -0.1076 (tpt) REVERT: Q 211 MET cc_start: 0.2531 (ttm) cc_final: 0.0779 (ttm) REVERT: Q 213 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7775 (pm20) REVERT: Q 248 PHE cc_start: 0.9272 (t80) cc_final: 0.8948 (t80) REVERT: R 235 ARG cc_start: 0.4905 (mmt180) cc_final: 0.3811 (mmp80) REVERT: S 158 MET cc_start: 0.4899 (mmm) cc_final: 0.4593 (mmm) REVERT: S 210 MET cc_start: 0.4335 (ppp) cc_final: 0.3934 (ppp) REVERT: S 211 MET cc_start: -0.0362 (ttm) cc_final: -0.1110 (ttp) REVERT: S 243 MET cc_start: 0.8537 (mmm) cc_final: 0.7965 (tpt) REVERT: S 252 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7949 (mm) outliers start: 55 outliers final: 35 residues processed: 177 average time/residue: 0.3650 time to fit residues: 110.0928 Evaluate side-chains 164 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 122 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 39 HIS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 149 ASP Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 37 ASP Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 30.0000 chunk 36 optimal weight: 0.9980 chunk 184 optimal weight: 50.0000 chunk 236 optimal weight: 6.9990 chunk 183 optimal weight: 30.0000 chunk 272 optimal weight: 40.0000 chunk 180 optimal weight: 30.0000 chunk 322 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 196 optimal weight: 50.0000 chunk 149 optimal weight: 40.0000 overall best weight: 13.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 GLN ** P 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 268 GLN Q 62 ASN ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.141 31483 Z= 0.649 Angle : 0.888 20.099 43787 Z= 0.487 Chirality : 0.050 0.227 5011 Planarity : 0.006 0.097 4558 Dihedral : 26.066 107.938 6814 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 31.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.99 % Allowed : 8.64 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.30 % 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: -0.03 (0.14), residues: 3051 helix: 0.26 (0.12), residues: 1563 sheet: 1.13 (0.25), residues: 423 loop : -0.76 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 49 PHE 0.026 0.003 PHE E 84 TYR 0.034 0.003 TYR H 83 ARG 0.011 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 117 time to evaluate : 3.270 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: 0.9500 (mm-30) cc_final: 0.8931 (tp30) REVERT: B 63 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8621 (tm-30) REVERT: B 92 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8893 (ttp80) REVERT: D 64 SER cc_start: 0.9258 (m) cc_final: 0.8880 (t) REVERT: D 93 GLU cc_start: 0.9281 (mp0) cc_final: 0.8964 (mp0) REVERT: E 81 ASP cc_start: 0.9155 (m-30) cc_final: 0.8927 (p0) REVERT: E 120 MET cc_start: 0.8758 (mtm) cc_final: 0.8431 (mtm) REVERT: F 63 GLU cc_start: 0.9461 (tt0) cc_final: 0.9018 (tm-30) REVERT: H 93 GLU cc_start: 0.9162 (mp0) cc_final: 0.8753 (mp0) REVERT: K 243 MET cc_start: 0.8897 (ptm) cc_final: 0.8388 (mmp) REVERT: K 294 HIS cc_start: 0.4407 (t70) cc_final: 0.3823 (t70) REVERT: M 125 MET cc_start: -0.0190 (pmm) cc_final: -0.0515 (ptp) REVERT: M 158 MET cc_start: 0.3904 (mmm) cc_final: 0.3596 (ttt) REVERT: M 210 MET cc_start: -0.0745 (ppp) cc_final: -0.1155 (ppp) REVERT: N 211 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.4608 (tpt) REVERT: N 235 ARG cc_start: -0.1953 (mmt180) cc_final: -0.2247 (mpt180) REVERT: P 211 MET cc_start: 0.0889 (mmm) cc_final: 0.0362 (tpt) REVERT: Q 211 MET cc_start: 0.4588 (ttm) cc_final: 0.2901 (ttm) REVERT: Q 213 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: Q 248 PHE cc_start: 0.9172 (t80) cc_final: 0.8854 (t80) REVERT: R 195 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6451 (m-10) REVERT: S 158 MET cc_start: 0.5570 (mmm) cc_final: 0.5038 (mmm) REVERT: S 210 MET cc_start: 0.4355 (ppp) cc_final: 0.4011 (ppp) REVERT: S 211 MET cc_start: -0.0478 (ttm) cc_final: -0.1175 (ttm) REVERT: S 243 MET cc_start: 0.8651 (mmm) cc_final: 0.8159 (tpt) REVERT: S 252 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.8039 (mm) outliers start: 75 outliers final: 52 residues processed: 182 average time/residue: 0.3684 time to fit residues: 115.3182 Evaluate side-chains 167 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 110 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain M residue 187 ASP Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain P residue 34 ASN Chi-restraints excluded: chain P residue 149 ASP Chi-restraints excluded: chain Q residue 46 PHE Chi-restraints excluded: chain Q residue 213 GLU Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain R residue 309 THR Chi-restraints excluded: chain S residue 34 ASN Chi-restraints excluded: chain S residue 252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 30.0000 chunk 128 optimal weight: 0.0470 chunk 192 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 330 ASN ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31483 Z= 0.191 Angle : 0.603 15.599 43787 Z= 0.334 Chirality : 0.039 0.165 5011 Planarity : 0.003 0.052 4558 Dihedral : 25.970 106.743 6814 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 1.07 % Allowed : 10.79 % Favored : 88.14 % 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 (0.15), residues: 3051 helix: 1.26 (0.13), residues: 1584 sheet: 1.15 (0.24), residues: 450 loop : -0.75 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 113 PHE 0.013 0.001 PHE O 259 TYR 0.045 0.001 TYR D 83 ARG 0.004 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8805 (tp30) REVERT: A 94 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.8986 (tp30) REVERT: B 92 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8687 (ttp80) REVERT: D 64 SER cc_start: 0.9142 (m) cc_final: 0.8746 (t) REVERT: D 93 GLU cc_start: 0.9173 (mp0) cc_final: 0.8800 (mp0) REVERT: E 120 MET cc_start: 0.8593 (mtm) cc_final: 0.8368 (mtm) REVERT: F 63 GLU cc_start: 0.9314 (tt0) cc_final: 0.8765 (tm-30) REVERT: F 92 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8696 (ttp80) REVERT: H 93 GLU cc_start: 0.9076 (mp0) cc_final: 0.8401 (mp0) REVERT: H 105 GLU cc_start: 0.9067 (mp0) cc_final: 0.8755 (pm20) REVERT: K 243 MET cc_start: 0.8838 (ptm) cc_final: 0.8307 (mmp) REVERT: K 294 HIS cc_start: 0.4587 (t70) cc_final: 0.4068 (t70) REVERT: M 125 MET cc_start: -0.0951 (pmm) cc_final: -0.1329 (ptp) REVERT: M 210 MET cc_start: -0.0887 (ppp) cc_final: -0.1439 (ttt) REVERT: N 211 MET cc_start: 0.5020 (OUTLIER) cc_final: 0.3098 (mmp) REVERT: P 211 MET cc_start: 0.0990 (mmm) cc_final: 0.0637 (tpp) REVERT: Q 125 MET cc_start: 0.8437 (ptt) cc_final: 0.8232 (tmm) REVERT: Q 210 MET cc_start: 0.5638 (ptt) cc_final: 0.4663 (ppp) REVERT: Q 211 MET cc_start: 0.3672 (ttm) cc_final: 0.1995 (ttm) REVERT: Q 248 PHE cc_start: 0.9215 (t80) cc_final: 0.8905 (t80) REVERT: S 158 MET cc_start: 0.5587 (mmm) cc_final: 0.5278 (mmm) REVERT: S 210 MET cc_start: 0.4473 (ppp) cc_final: 0.4257 (ppp) REVERT: S 211 MET cc_start: -0.0719 (ttm) cc_final: -0.1299 (ttm) REVERT: S 243 MET cc_start: 0.8692 (mmm) cc_final: 0.8198 (tpt) REVERT: S 326 MET cc_start: 0.6775 (tpt) cc_final: 0.6459 (pmm) outliers start: 27 outliers final: 19 residues processed: 156 average time/residue: 0.4038 time to fit residues: 104.5214 Evaluate side-chains 146 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain P residue 149 ASP Chi-restraints excluded: chain P residue 205 TYR Chi-restraints excluded: chain S residue 34 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 10.0000 chunk 309 optimal weight: 50.0000 chunk 282 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 181 optimal weight: 50.0000 chunk 131 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 284 optimal weight: 30.0000 chunk 299 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 31483 Z= 0.323 Angle : 0.660 15.696 43787 Z= 0.361 Chirality : 0.040 0.170 5011 Planarity : 0.004 0.066 4558 Dihedral : 25.842 107.220 6814 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.59 % Allowed : 10.59 % Favored : 87.82 % 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 (0.15), residues: 3051 helix: 1.19 (0.13), residues: 1587 sheet: 1.16 (0.25), residues: 420 loop : -0.87 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 113 PHE 0.015 0.002 PHE O 259 TYR 0.044 0.002 TYR D 83 ARG 0.007 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9371 (mm-30) cc_final: 0.8631 (tp30) REVERT: A 94 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8993 (tp30) REVERT: B 92 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8882 (ttp80) REVERT: D 64 SER cc_start: 0.9155 (m) cc_final: 0.8777 (t) REVERT: D 93 GLU cc_start: 0.9220 (mp0) cc_final: 0.8872 (mp0) REVERT: E 120 MET cc_start: 0.8653 (mtm) cc_final: 0.8388 (mtm) REVERT: F 63 GLU cc_start: 0.9376 (tt0) cc_final: 0.8918 (tm-30) REVERT: H 93 GLU cc_start: 0.9089 (mp0) cc_final: 0.8492 (mp0) REVERT: H 105 GLU cc_start: 0.9098 (mp0) cc_final: 0.8780 (pm20) REVERT: K 294 HIS cc_start: 0.4654 (t70) cc_final: 0.4075 (t70) REVERT: M 125 MET cc_start: -0.0748 (pmm) cc_final: -0.1130 (ptp) REVERT: M 210 MET cc_start: -0.1255 (ppp) cc_final: -0.1473 (ttt) REVERT: N 211 MET cc_start: 0.5184 (OUTLIER) cc_final: 0.3322 (mmm) REVERT: O 243 MET cc_start: 0.8797 (mmt) cc_final: 0.7871 (tpt) REVERT: P 211 MET cc_start: 0.0981 (mmm) cc_final: 0.0580 (tpt) REVERT: Q 125 MET cc_start: 0.8460 (ptt) cc_final: 0.8252 (tmm) REVERT: Q 248 PHE cc_start: 0.9252 (t80) cc_final: 0.8941 (t80) REVERT: R 195 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6375 (m-10) REVERT: S 243 MET cc_start: 0.8727 (mmm) cc_final: 0.8213 (tpt) REVERT: S 326 MET cc_start: 0.6804 (tpt) cc_final: 0.6462 (pmm) outliers start: 40 outliers final: 33 residues processed: 149 average time/residue: 0.3758 time to fit residues: 95.4096 Evaluate side-chains 153 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain K residue 248 PHE Chi-restraints excluded: chain L residue 248 PHE Chi-restraints excluded: chain N residue 187 ASP Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain P residue 149 ASP Chi-restraints excluded: chain P residue 205 TYR Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain R residue 195 PHE Chi-restraints excluded: chain S residue 34 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 20.0000 chunk 318 optimal weight: 7.9990 chunk 194 optimal weight: 30.0000 chunk 150 optimal weight: 50.0000 chunk 221 optimal weight: 3.9990 chunk 333 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 265 optimal weight: 50.0000 chunk 27 optimal weight: 4.9990 chunk 205 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31483 Z= 0.227 Angle : 0.611 14.969 43787 Z= 0.335 Chirality : 0.039 0.176 5011 Planarity : 0.003 0.050 4558 Dihedral : 25.753 106.872 6814 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.15 % Allowed : 11.15 % Favored : 87.70 % 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: 1.05 (0.15), residues: 3051 helix: 1.43 (0.13), residues: 1587 sheet: 1.18 (0.24), residues: 444 loop : -0.65 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 113 PHE 0.015 0.001 PHE O 259 TYR 0.055 0.002 TYR D 83 ARG 0.006 0.000 ARG F 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9344 (mm-30) cc_final: 0.8855 (tp30) REVERT: A 94 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8933 (tp30) REVERT: B 92 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8883 (ttp80) REVERT: D 64 SER cc_start: 0.9144 (m) cc_final: 0.8737 (t) REVERT: D 93 GLU cc_start: 0.9187 (mp0) cc_final: 0.8843 (mp0) REVERT: E 120 MET cc_start: 0.8581 (mtm) cc_final: 0.8336 (mtm) REVERT: F 63 GLU cc_start: 0.9314 (tt0) cc_final: 0.8762 (tm-30) REVERT: H 93 GLU cc_start: 0.9090 (mp0) cc_final: 0.8432 (mp0) REVERT: H 105 GLU cc_start: 0.9082 (mp0) cc_final: 0.8791 (pm20) REVERT: K 294 HIS cc_start: 0.4735 (t70) cc_final: 0.4186 (t70) REVERT: M 125 MET cc_start: -0.0708 (pmm) cc_final: -0.1108 (ptp) REVERT: M 243 MET cc_start: 0.3580 (ptt) cc_final: 0.3304 (mtt) REVERT: N 210 MET cc_start: 0.3065 (ppp) cc_final: 0.2220 (mmm) REVERT: N 211 MET cc_start: 0.4748 (OUTLIER) cc_final: 0.3068 (mmp) REVERT: O 243 MET cc_start: 0.8808 (mmt) cc_final: 0.7862 (tpt) REVERT: P 211 MET cc_start: 0.1019 (mmm) cc_final: 0.0605 (tpp) REVERT: Q 125 MET cc_start: 0.8466 (ptt) cc_final: 0.8266 (tmm) REVERT: Q 248 PHE cc_start: 0.9233 (t80) cc_final: 0.8918 (t80) REVERT: S 158 MET cc_start: 0.4111 (mmm) cc_final: 0.3489 (mmt) REVERT: S 211 MET cc_start: -0.1044 (ttm) cc_final: -0.1297 (ttp) REVERT: S 243 MET cc_start: 0.8765 (mmm) cc_final: 0.8271 (tpt) REVERT: S 326 MET cc_start: 0.6794 (tpt) cc_final: 0.6470 (pmm) outliers start: 29 outliers final: 22 residues processed: 145 average time/residue: 0.3737 time to fit residues: 92.3866 Evaluate side-chains 144 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain K residue 34 ASN Chi-restraints excluded: chain N residue 211 MET Chi-restraints excluded: chain P residue 149 ASP Chi-restraints excluded: chain P residue 205 TYR Chi-restraints excluded: chain R residue 158 MET Chi-restraints excluded: chain S residue 34 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 30.0000 chunk 283 optimal weight: 40.0000 chunk 81 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 chunk 273 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN Q 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.077929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.045663 restraints weight = 222626.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.047019 restraints weight = 78445.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.047665 restraints weight = 42924.972| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31483 Z= 0.193 Angle : 0.585 14.669 43787 Z= 0.320 Chirality : 0.038 0.189 5011 Planarity : 0.003 0.050 4558 Dihedral : 25.504 105.894 6814 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.07 % Allowed : 11.35 % Favored : 87.58 % 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: 1.36 (0.15), residues: 3051 helix: 1.67 (0.13), residues: 1583 sheet: 1.28 (0.24), residues: 462 loop : -0.50 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.014 0.001 PHE O 259 TYR 0.051 0.001 TYR F 88 ARG 0.006 0.000 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5463.85 seconds wall clock time: 99 minutes 32.77 seconds (5972.77 seconds total)