Starting phenix.real_space_refine (version: dev) on Tue Feb 21 18:34:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/02_2023/6ncv_0438.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/02_2023/6ncv_0438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/02_2023/6ncv_0438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/02_2023/6ncv_0438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/02_2023/6ncv_0438.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/02_2023/6ncv_0438.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.020 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 Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 55": "NH1" <-> "NH2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ASP 43": "OD1" <-> "OD2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 55": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ASP 92": "OD1" <-> "OD2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ASP 43": "OD1" <-> "OD2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 55": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ASP 43": "OD1" <-> "OD2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 58": "NH1" <-> "NH2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ASP 92": "OD1" <-> "OD2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ASP 43": "OD1" <-> "OD2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G ARG 58": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ASP 92": "OD1" <-> "OD2" Residue "G ARG 104": "NH1" <-> "NH2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ASP 43": "OD1" <-> "OD2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ARG 58": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H ARG 104": "NH1" <-> "NH2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ASP 43": "OD1" <-> "OD2" Residue "I ASP 47": "OD1" <-> "OD2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I ARG 58": "NH1" <-> "NH2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I ASP 92": "OD1" <-> "OD2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J ARG 36": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J ASP 43": "OD1" <-> "OD2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 58": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J ASP 92": "OD1" <-> "OD2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K ARG 36": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ASP 43": "OD1" <-> "OD2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K ARG 58": "NH1" <-> "NH2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K ASP 92": "OD1" <-> "OD2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L ARG 36": "NH1" <-> "NH2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L ASP 43": "OD1" <-> "OD2" Residue "L ASP 47": "OD1" <-> "OD2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ARG 58": "NH1" <-> "NH2" Residue "L ARG 82": "NH1" <-> "NH2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M ARG 36": "NH1" <-> "NH2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ASP 43": "OD1" <-> "OD2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 58": "NH1" <-> "NH2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N ARG 36": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N ASP 47": "OD1" <-> "OD2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N ARG 58": "NH1" <-> "NH2" Residue "N ARG 82": "NH1" <-> "NH2" Residue "N ASP 92": "OD1" <-> "OD2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ARG 36": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ASP 43": "OD1" <-> "OD2" Residue "O ASP 47": "OD1" <-> "OD2" Residue "O ARG 49": "NH1" <-> "NH2" Residue "O ARG 55": "NH1" <-> "NH2" Residue "O ARG 58": "NH1" <-> "NH2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O ASP 92": "OD1" <-> "OD2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P ARG 36": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ASP 43": "OD1" <-> "OD2" Residue "P ASP 47": "OD1" <-> "OD2" Residue "P ARG 49": "NH1" <-> "NH2" Residue "P ARG 55": "NH1" <-> "NH2" Residue "P ARG 58": "NH1" <-> "NH2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P ASP 92": "OD1" <-> "OD2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q ARG 36": "NH1" <-> "NH2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q ASP 43": "OD1" <-> "OD2" Residue "Q ASP 47": "OD1" <-> "OD2" Residue "Q ARG 49": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 58": "NH1" <-> "NH2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "Q ASP 92": "OD1" <-> "OD2" Residue "Q ARG 104": "NH1" <-> "NH2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R ARG 36": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ASP 43": "OD1" <-> "OD2" Residue "R ASP 47": "OD1" <-> "OD2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 58": "NH1" <-> "NH2" Residue "R ARG 82": "NH1" <-> "NH2" Residue "R ASP 92": "OD1" <-> "OD2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S ARG 36": "NH1" <-> "NH2" Residue "S ARG 38": "NH1" <-> "NH2" Residue "S ASP 43": "OD1" <-> "OD2" Residue "S ASP 47": "OD1" <-> "OD2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "S ARG 58": "NH1" <-> "NH2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "S ASP 92": "OD1" <-> "OD2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "T GLU 20": "OE1" <-> "OE2" Residue "T ARG 36": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T ASP 43": "OD1" <-> "OD2" Residue "T ASP 47": "OD1" <-> "OD2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T ARG 58": "NH1" <-> "NH2" Residue "T ARG 82": "NH1" <-> "NH2" Residue "T ASP 92": "OD1" <-> "OD2" Residue "T ARG 104": "NH1" <-> "NH2" Residue "V GLU 20": "OE1" <-> "OE2" Residue "V ARG 36": "NH1" <-> "NH2" Residue "V ARG 38": "NH1" <-> "NH2" Residue "V ASP 43": "OD1" <-> "OD2" Residue "V ASP 47": "OD1" <-> "OD2" Residue "V ARG 49": "NH1" <-> "NH2" Residue "V ARG 55": "NH1" <-> "NH2" Residue "V ARG 58": "NH1" <-> "NH2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V ASP 92": "OD1" <-> "OD2" Residue "V ARG 104": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15456 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "C" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "E" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "F" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "G" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "I" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "J" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "K" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "L" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "M" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "N" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "O" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "P" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "Q" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "R" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "S" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "T" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "V" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Time building chain proxies: 8.24, per 1000 atoms: 0.53 Number of scatterers: 15456 At special positions: 0 Unit cell: (98.58, 95.4, 122.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2772 8.00 N 3087 7.00 C 9597 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: 5.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 0 sheets defined 69.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.778A pdb=" N LEU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 39 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.874A pdb=" N THR B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG C 55 " --> pdb=" O PRO C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS D 39 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.842A pdb=" N ALA D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS E 35 " --> pdb=" O GLN E 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.746A pdb=" N ARG E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.844A pdb=" N ALA E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS F 35 " --> pdb=" O GLN F 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG F 55 " --> pdb=" O PRO F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 102 removed outlier: 3.844A pdb=" N ALA F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU F 99 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS G 35 " --> pdb=" O GLN G 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG G 55 " --> pdb=" O PRO G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR G 84 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU G 99 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG G 100 " --> pdb=" O GLN G 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS H 35 " --> pdb=" O GLN H 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG H 55 " --> pdb=" O PRO H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.842A pdb=" N ALA H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 102 " --> pdb=" O GLN H 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS I 35 " --> pdb=" O GLN I 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS I 39 " --> pdb=" O LYS I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG I 55 " --> pdb=" O PRO I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA I 69 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR I 84 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU I 99 " --> pdb=" O ALA I 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU I 102 " --> pdb=" O GLN I 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS J 35 " --> pdb=" O GLN J 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS J 39 " --> pdb=" O LYS J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG J 55 " --> pdb=" O PRO J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR J 84 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU J 99 " --> pdb=" O ALA J 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG J 100 " --> pdb=" O GLN J 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU J 102 " --> pdb=" O GLN J 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS K 35 " --> pdb=" O GLN K 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS K 39 " --> pdb=" O LYS K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG K 55 " --> pdb=" O PRO K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR K 84 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU K 99 " --> pdb=" O ALA K 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG K 100 " --> pdb=" O GLN K 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS L 35 " --> pdb=" O GLN L 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS L 39 " --> pdb=" O LYS L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG L 55 " --> pdb=" O PRO L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA L 69 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR L 72 " --> pdb=" O LEU L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR L 84 " --> pdb=" O VAL L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU L 99 " --> pdb=" O ALA L 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG L 100 " --> pdb=" O GLN L 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU L 102 " --> pdb=" O GLN L 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS M 35 " --> pdb=" O GLN M 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS M 39 " --> pdb=" O LYS M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG M 55 " --> pdb=" O PRO M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA M 69 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU M 99 " --> pdb=" O ALA M 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU M 102 " --> pdb=" O GLN M 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS N 35 " --> pdb=" O GLN N 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS N 39 " --> pdb=" O LYS N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG N 55 " --> pdb=" O PRO N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA N 69 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 102 removed outlier: 3.844A pdb=" N ALA N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU N 99 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG N 100 " --> pdb=" O GLN N 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU N 102 " --> pdb=" O GLN N 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU O 22 " --> pdb=" O ALA O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS O 35 " --> pdb=" O GLN O 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS O 39 " --> pdb=" O LYS O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG O 55 " --> pdb=" O PRO O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR O 72 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR O 84 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA O 94 " --> pdb=" O ALA O 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU O 99 " --> pdb=" O ALA O 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG O 100 " --> pdb=" O GLN O 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU O 102 " --> pdb=" O GLN O 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS P 35 " --> pdb=" O GLN P 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS P 39 " --> pdb=" O LYS P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG P 55 " --> pdb=" O PRO P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA P 69 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR P 72 " --> pdb=" O LEU P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR P 84 " --> pdb=" O VAL P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA P 94 " --> pdb=" O ALA P 90 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU P 99 " --> pdb=" O ALA P 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG P 100 " --> pdb=" O GLN P 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU P 102 " --> pdb=" O GLN P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU Q 22 " --> pdb=" O ALA Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS Q 35 " --> pdb=" O GLN Q 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS Q 39 " --> pdb=" O LYS Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG Q 55 " --> pdb=" O PRO Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA Q 69 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR Q 72 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR Q 84 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG Q 100 " --> pdb=" O GLN Q 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU Q 102 " --> pdb=" O GLN Q 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS R 35 " --> pdb=" O GLN R 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 56 removed outlier: 3.744A pdb=" N ARG R 55 " --> pdb=" O PRO R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 86 removed outlier: 3.874A pdb=" N THR R 84 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU R 99 " --> pdb=" O ALA R 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG R 100 " --> pdb=" O GLN R 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 102 " --> pdb=" O GLN R 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 24 removed outlier: 3.777A pdb=" N LEU S 22 " --> pdb=" O ALA S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 40 removed outlier: 3.508A pdb=" N LYS S 35 " --> pdb=" O GLN S 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS S 39 " --> pdb=" O LYS S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG S 55 " --> pdb=" O PRO S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 72 removed outlier: 3.786A pdb=" N ALA S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR S 72 " --> pdb=" O LEU S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR S 84 " --> pdb=" O VAL S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA S 94 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU S 99 " --> pdb=" O ALA S 95 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG S 100 " --> pdb=" O GLN S 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU S 102 " --> pdb=" O GLN S 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU T 22 " --> pdb=" O ALA T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS T 35 " --> pdb=" O GLN T 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS T 39 " --> pdb=" O LYS T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG T 55 " --> pdb=" O PRO T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA T 69 " --> pdb=" O ALA T 65 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR T 72 " --> pdb=" O LEU T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 86 removed outlier: 3.873A pdb=" N THR T 84 " --> pdb=" O VAL T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 102 removed outlier: 3.844A pdb=" N ALA T 94 " --> pdb=" O ALA T 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU T 99 " --> pdb=" O ALA T 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG T 100 " --> pdb=" O GLN T 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU T 102 " --> pdb=" O GLN T 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 24 removed outlier: 3.778A pdb=" N LEU V 22 " --> pdb=" O ALA V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 40 removed outlier: 3.507A pdb=" N LYS V 35 " --> pdb=" O GLN V 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS V 39 " --> pdb=" O LYS V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 56 removed outlier: 3.745A pdb=" N ARG V 55 " --> pdb=" O PRO V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 72 removed outlier: 3.787A pdb=" N ALA V 69 " --> pdb=" O ALA V 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR V 72 " --> pdb=" O LEU V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 86 removed outlier: 3.872A pdb=" N THR V 84 " --> pdb=" O VAL V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 90 through 102 removed outlier: 3.843A pdb=" N ALA V 94 " --> pdb=" O ALA V 90 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU V 99 " --> pdb=" O ALA V 95 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG V 100 " --> pdb=" O GLN V 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU V 102 " --> pdb=" O GLN V 98 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1767 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 6.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 2688 1.29 - 1.35: 3003 1.35 - 1.42: 651 1.42 - 1.49: 2548 1.49 - 1.55: 6755 Bond restraints: 15645 Sorted by residual: bond pdb=" CB TRP G 53 " pdb=" CG TRP G 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.65e+00 bond pdb=" CB TRP B 53 " pdb=" CG TRP B 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.61e+00 bond pdb=" CB TRP M 53 " pdb=" CG TRP M 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.59e+00 bond pdb=" CB TRP Q 53 " pdb=" CG TRP Q 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.57e+00 bond pdb=" CB TRP K 53 " pdb=" CG TRP K 53 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.56e+00 ... (remaining 15640 not shown) Histogram of bond angle deviations from ideal: 102.17 - 108.53: 674 108.53 - 114.89: 8776 114.89 - 121.26: 7763 121.26 - 127.62: 3687 127.62 - 133.98: 121 Bond angle restraints: 21021 Sorted by residual: angle pdb=" CB ARG J 58 " pdb=" CG ARG J 58 " pdb=" CD ARG J 58 " ideal model delta sigma weight residual 111.30 119.16 -7.86 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CB ARG S 58 " pdb=" CG ARG S 58 " pdb=" CD ARG S 58 " ideal model delta sigma weight residual 111.30 119.16 -7.86 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CB ARG R 58 " pdb=" CG ARG R 58 " pdb=" CD ARG R 58 " ideal model delta sigma weight residual 111.30 119.15 -7.85 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CB ARG N 58 " pdb=" CG ARG N 58 " pdb=" CD ARG N 58 " ideal model delta sigma weight residual 111.30 119.14 -7.84 2.30e+00 1.89e-01 1.16e+01 angle pdb=" CB ARG C 58 " pdb=" CG ARG C 58 " pdb=" CD ARG C 58 " ideal model delta sigma weight residual 111.30 119.13 -7.83 2.30e+00 1.89e-01 1.16e+01 ... (remaining 21016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.91: 7938 13.91 - 27.82: 1281 27.82 - 41.72: 504 41.72 - 55.63: 105 55.63 - 69.54: 105 Dihedral angle restraints: 9933 sinusoidal: 4368 harmonic: 5565 Sorted by residual: dihedral pdb=" CA GLU K 27 " pdb=" C GLU K 27 " pdb=" N GLU K 28 " pdb=" CA GLU K 28 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLU C 27 " pdb=" C GLU C 27 " pdb=" N GLU C 28 " pdb=" CA GLU C 28 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLU N 27 " pdb=" C GLU N 27 " pdb=" N GLU N 28 " pdb=" CA GLU N 28 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 9930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1023 0.026 - 0.052: 622 0.052 - 0.078: 409 0.078 - 0.104: 189 0.104 - 0.130: 46 Chirality restraints: 2289 Sorted by residual: chirality pdb=" CB VAL I 93 " pdb=" CA VAL I 93 " pdb=" CG1 VAL I 93 " pdb=" CG2 VAL I 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CB VAL S 93 " pdb=" CA VAL S 93 " pdb=" CG1 VAL S 93 " pdb=" CG2 VAL S 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CB VAL P 93 " pdb=" CA VAL P 93 " pdb=" CG1 VAL P 93 " pdb=" CG2 VAL P 93 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 2286 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 75 " 0.026 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO C 76 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU O 75 " -0.026 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO O 76 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO O 76 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO O 76 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 75 " -0.026 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO E 76 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.022 5.00e-02 4.00e+02 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5434 2.90 - 3.40: 14511 3.40 - 3.90: 23366 3.90 - 4.40: 27137 4.40 - 4.90: 45253 Nonbonded interactions: 115701 Sorted by model distance: nonbonded pdb=" OG SER M 30 " pdb=" N GLN M 31 " model vdw 2.398 2.520 nonbonded pdb=" OG SER H 30 " pdb=" N GLN H 31 " model vdw 2.398 2.520 nonbonded pdb=" OG SER J 30 " pdb=" N GLN J 31 " model vdw 2.398 2.520 nonbonded pdb=" OG SER K 30 " pdb=" N GLN K 31 " model vdw 2.398 2.520 nonbonded pdb=" OG SER B 30 " pdb=" N GLN B 31 " model vdw 2.398 2.520 ... (remaining 115696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 9597 2.51 5 N 3087 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.290 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: 0.010 Extract box with map and model: 2.830 Check model and map are aligned: 0.250 Process input model: 37.900 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 : 0.008 0.066 15645 Z= 0.511 Angle : 0.941 7.862 21021 Z= 0.527 Chirality : 0.047 0.130 2289 Planarity : 0.005 0.038 2835 Dihedral : 17.275 69.540 6279 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.46 (0.10), residues: 1869 helix: -4.69 (0.06), residues: 1155 sheet: None (None), residues: 0 loop : -3.24 (0.16), residues: 714 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 570 time to evaluate : 1.947 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 outliers start: 42 outliers final: 11 residues processed: 599 average time/residue: 0.3233 time to fit residues: 268.3920 Evaluate side-chains 402 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 391 time to evaluate : 1.928 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1323 time to fit residues: 5.3999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN F 39 HIS F 103 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN K 98 GLN ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 HIS ** N 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 GLN O 96 GLN ** P 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 HIS ** R 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN S 96 GLN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS ** V 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 15645 Z= 0.311 Angle : 0.644 8.155 21021 Z= 0.332 Chirality : 0.040 0.151 2289 Planarity : 0.005 0.036 2835 Dihedral : 4.445 16.707 2205 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer Outliers : 2.22 % 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: -4.61 (0.15), residues: 1869 helix: -3.21 (0.11), residues: 1176 sheet: None (None), residues: 0 loop : -2.44 (0.19), residues: 693 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 425 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 439 average time/residue: 0.2743 time to fit residues: 175.6100 Evaluate side-chains 400 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 382 time to evaluate : 1.922 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1546 time to fit residues: 7.3818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 170 optimal weight: 0.2980 chunk 58 optimal weight: 0.0870 chunk 137 optimal weight: 0.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 70 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN C 33 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN E 96 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 HIS P 96 GLN Q 39 HIS T 33 GLN T 96 GLN ** V 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15645 Z= 0.168 Angle : 0.535 7.871 21021 Z= 0.279 Chirality : 0.035 0.134 2289 Planarity : 0.004 0.034 2835 Dihedral : 3.864 16.022 2205 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.16), residues: 1869 helix: -2.31 (0.12), residues: 1218 sheet: None (None), residues: 0 loop : -2.03 (0.22), residues: 651 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 420 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 3 residues processed: 436 average time/residue: 0.2688 time to fit residues: 170.0493 Evaluate side-chains 380 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 377 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1592 time to fit residues: 3.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 172 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 96 GLN B 96 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS F 33 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN O 96 GLN P 39 HIS ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN Q 70 GLN S 96 GLN V 39 HIS ** V 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 103 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15645 Z= 0.185 Angle : 0.528 6.429 21021 Z= 0.277 Chirality : 0.036 0.121 2289 Planarity : 0.003 0.032 2835 Dihedral : 3.635 15.888 2205 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.18), residues: 1869 helix: -1.51 (0.13), residues: 1218 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 651 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 404 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 17 residues processed: 415 average time/residue: 0.2754 time to fit residues: 167.2319 Evaluate side-chains 389 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 372 time to evaluate : 2.140 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1619 time to fit residues: 7.7495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS D 98 GLN E 96 GLN F 98 GLN I 39 HIS I 70 GLN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 GLN M 98 GLN P 70 GLN P 96 GLN R 98 GLN S 96 GLN T 98 GLN V 67 GLN V 70 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 15645 Z= 0.313 Angle : 0.600 6.073 21021 Z= 0.312 Chirality : 0.039 0.147 2289 Planarity : 0.004 0.034 2835 Dihedral : 3.855 16.378 2205 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer Outliers : 2.09 % 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: -1.84 (0.19), residues: 1869 helix: -1.12 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : -1.11 (0.27), residues: 651 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 383 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 10 residues processed: 397 average time/residue: 0.2866 time to fit residues: 167.4779 Evaluate side-chains 380 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 370 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1713 time to fit residues: 5.8840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN C 96 GLN G 67 GLN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 HIS L 96 GLN N 67 GLN O 96 GLN P 70 GLN ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 GLN T 67 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15645 Z= 0.198 Angle : 0.562 9.015 21021 Z= 0.295 Chirality : 0.036 0.127 2289 Planarity : 0.003 0.033 2835 Dihedral : 3.623 15.117 2205 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.24 % 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: -1.14 (0.20), residues: 1869 helix: -0.48 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : -1.04 (0.27), residues: 651 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 384 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 391 average time/residue: 0.2661 time to fit residues: 152.9472 Evaluate side-chains 371 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 362 time to evaluate : 2.027 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1604 time to fit residues: 5.3959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 chunk 84 optimal weight: 0.4980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 HIS E 96 GLN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS L 98 GLN ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 GLN T 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15645 Z= 0.200 Angle : 0.565 8.034 21021 Z= 0.299 Chirality : 0.036 0.120 2289 Planarity : 0.003 0.032 2835 Dihedral : 3.495 14.840 2205 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1869 helix: -0.15 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -1.33 (0.29), residues: 609 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 372 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 5 residues processed: 384 average time/residue: 0.2541 time to fit residues: 145.8792 Evaluate side-chains 362 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 357 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1561 time to fit residues: 4.1041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN D 39 HIS ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN K 98 GLN O 96 GLN P 70 GLN ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 GLN T 67 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15645 Z= 0.282 Angle : 0.618 7.585 21021 Z= 0.323 Chirality : 0.038 0.134 2289 Planarity : 0.004 0.035 2835 Dihedral : 3.656 14.776 2205 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1869 helix: -0.15 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 609 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 375 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 380 average time/residue: 0.2596 time to fit residues: 146.7043 Evaluate side-chains 377 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 366 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1609 time to fit residues: 5.6983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.2980 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 111 optimal weight: 0.0670 chunk 179 optimal weight: 4.9990 overall best weight: 1.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN D 39 HIS E 67 GLN F 39 HIS ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 GLN S 96 GLN T 39 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 15645 Z= 0.215 Angle : 0.607 9.297 21021 Z= 0.319 Chirality : 0.036 0.123 2289 Planarity : 0.003 0.035 2835 Dihedral : 3.498 14.093 2205 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.78 % 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: -0.52 (0.20), residues: 1869 helix: 0.14 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 609 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 369 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 372 average time/residue: 0.2540 time to fit residues: 141.9123 Evaluate side-chains 361 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 358 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1704 time to fit residues: 3.5484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 0.0670 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 70 GLN B 67 GLN D 39 HIS ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 GLN ** T 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 15645 Z= 0.205 Angle : 0.616 8.952 21021 Z= 0.324 Chirality : 0.035 0.119 2289 Planarity : 0.003 0.034 2835 Dihedral : 3.408 13.335 2205 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1869 helix: 0.41 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : -1.27 (0.29), residues: 609 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 373 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 374 average time/residue: 0.2594 time to fit residues: 144.6867 Evaluate side-chains 362 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 357 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2031 time to fit residues: 3.9992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN D 39 HIS F 39 HIS G 103 GLN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 GLN P 70 GLN ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 GLN T 67 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.089892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.075249 restraints weight = 34861.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.077913 restraints weight = 18396.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.079710 restraints weight = 11804.356| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 15645 Z= 0.277 Angle : 0.647 8.348 21021 Z= 0.339 Chirality : 0.038 0.126 2289 Planarity : 0.003 0.035 2835 Dihedral : 3.554 14.125 2205 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer Outliers : 0.78 % 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: -0.38 (0.21), residues: 1869 helix: 0.25 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : -1.15 (0.31), residues: 609 =============================================================================== Job complete usr+sys time: 3165.68 seconds wall clock time: 57 minutes 29.75 seconds (3449.75 seconds total)