Starting phenix.real_space_refine on Sat Mar 16 19:12:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/03_2024/6ncv_0438.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/03_2024/6ncv_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_0438/03_2024/6ncv_0438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/03_2024/6ncv_0438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/03_2024/6ncv_0438.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ncv_0438/03_2024/6ncv_0438.pdb" } resolution = 3.7 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= 0.004 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 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. 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-5265/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: 8.11, per 1000 atoms: 0.52 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: 5.09 Conformation dependent library (CDL) restraints added in 2.7 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: 1.32 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: 3.45 Time building geometry restraints manager: 5.62 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 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: 0.020 Extract box with map and model: 2.150 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 37.550 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.130 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 % Allowed : 12.33 % Favored : 84.93 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP K 53 HIS 0.002 0.001 HIS N 39 PHE 0.004 0.001 PHE K 37 TYR 0.004 0.001 TYR P 72 ARG 0.011 0.001 ARG L 58 *********************** 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 : 1.955 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: A 35 LYS cc_start: 0.9143 (tttt) cc_final: 0.8856 (tttm) REVERT: A 40 LYS cc_start: 0.9010 (tppt) cc_final: 0.8766 (mttm) REVERT: A 57 GLU cc_start: 0.8070 (tt0) cc_final: 0.7740 (tt0) REVERT: A 66 GLU cc_start: 0.8099 (tp30) cc_final: 0.7786 (tm-30) REVERT: A 86 LYS cc_start: 0.9040 (mttt) cc_final: 0.8643 (mtpp) REVERT: A 96 GLN cc_start: 0.9339 (tm-30) cc_final: 0.8993 (tm-30) REVERT: B 30 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8296 (p) REVERT: B 31 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8651 (tm-30) REVERT: B 32 GLU cc_start: 0.9000 (tp30) cc_final: 0.8768 (tp30) REVERT: B 35 LYS cc_start: 0.9470 (tttt) cc_final: 0.9160 (ttmm) REVERT: B 60 ASP cc_start: 0.8429 (t70) cc_final: 0.8221 (t70) REVERT: C 35 LYS cc_start: 0.9132 (tttt) cc_final: 0.8855 (tttp) REVERT: C 40 LYS cc_start: 0.9081 (tppt) cc_final: 0.8849 (mmtt) REVERT: C 63 ASP cc_start: 0.8725 (m-30) cc_final: 0.8494 (m-30) REVERT: D 31 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8659 (tm-30) REVERT: D 63 ASP cc_start: 0.8673 (m-30) cc_final: 0.8348 (m-30) REVERT: E 35 LYS cc_start: 0.9382 (tttt) cc_final: 0.9111 (tttt) REVERT: E 83 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8783 (mmtm) REVERT: E 96 GLN cc_start: 0.8905 (tm-30) cc_final: 0.7867 (tm-30) REVERT: F 33 GLN cc_start: 0.8373 (mt0) cc_final: 0.8057 (mt0) REVERT: F 35 LYS cc_start: 0.9173 (tttt) cc_final: 0.8840 (tttm) REVERT: F 83 LYS cc_start: 0.9140 (mtpt) cc_final: 0.8924 (mtpp) REVERT: G 15 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8658 (tp) REVERT: G 40 LYS cc_start: 0.9243 (tppt) cc_final: 0.8998 (mttm) REVERT: G 58 ARG cc_start: 0.8230 (mtm110) cc_final: 0.7853 (mtt90) REVERT: G 86 LYS cc_start: 0.9156 (mttt) cc_final: 0.8914 (mttm) REVERT: G 89 ASP cc_start: 0.8367 (m-30) cc_final: 0.8130 (m-30) REVERT: G 96 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8279 (tm-30) REVERT: H 30 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8375 (p) REVERT: H 31 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8612 (tm-30) REVERT: H 32 GLU cc_start: 0.9039 (tp30) cc_final: 0.8650 (tp30) REVERT: H 60 ASP cc_start: 0.8419 (t70) cc_final: 0.8146 (t0) REVERT: H 66 GLU cc_start: 0.8581 (tp30) cc_final: 0.8133 (mt-10) REVERT: I 32 GLU cc_start: 0.8879 (tp30) cc_final: 0.8475 (tp30) REVERT: I 86 LYS cc_start: 0.8899 (mttt) cc_final: 0.8573 (mtpp) REVERT: I 96 GLN cc_start: 0.9258 (tm-30) cc_final: 0.8762 (tm-30) REVERT: J 15 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8982 (tp) REVERT: K 31 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8605 (tm-30) REVERT: K 63 ASP cc_start: 0.8713 (m-30) cc_final: 0.8465 (m-30) REVERT: L 30 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8595 (t) REVERT: L 83 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8829 (mmtt) REVERT: L 96 GLN cc_start: 0.8911 (tm-30) cc_final: 0.7567 (tm-30) REVERT: M 31 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8583 (tm-30) REVERT: M 33 GLN cc_start: 0.8359 (mt0) cc_final: 0.7920 (mt0) REVERT: M 57 GLU cc_start: 0.8665 (tt0) cc_final: 0.8184 (tt0) REVERT: M 83 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8920 (mtpp) REVERT: N 15 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8454 (tp) REVERT: N 40 LYS cc_start: 0.9169 (tppt) cc_final: 0.8937 (mttm) REVERT: N 58 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7850 (mtt180) REVERT: N 86 LYS cc_start: 0.9247 (mttt) cc_final: 0.8978 (mttp) REVERT: N 89 ASP cc_start: 0.8293 (m-30) cc_final: 0.8015 (m-30) REVERT: N 96 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8213 (tm-30) REVERT: O 30 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8183 (p) REVERT: O 31 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8568 (tm-30) REVERT: O 32 GLU cc_start: 0.8946 (tp30) cc_final: 0.8686 (tp30) REVERT: O 66 GLU cc_start: 0.8287 (tp30) cc_final: 0.7786 (mt-10) REVERT: P 31 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8722 (tm-30) REVERT: P 35 LYS cc_start: 0.9056 (tttt) cc_final: 0.8829 (tptm) REVERT: P 66 GLU cc_start: 0.8309 (tp30) cc_final: 0.8081 (tm-30) REVERT: P 86 LYS cc_start: 0.8869 (mttt) cc_final: 0.8536 (mtpp) REVERT: P 96 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8742 (tm-30) REVERT: Q 31 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8294 (tm-30) REVERT: Q 35 LYS cc_start: 0.9295 (tttt) cc_final: 0.9005 (tttp) REVERT: Q 63 ASP cc_start: 0.8693 (m-30) cc_final: 0.8492 (m-30) REVERT: R 31 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8600 (tm-30) REVERT: R 32 GLU cc_start: 0.8848 (tp30) cc_final: 0.8623 (tp30) REVERT: R 57 GLU cc_start: 0.8076 (tt0) cc_final: 0.7689 (tt0) REVERT: R 83 LYS cc_start: 0.9198 (mtpt) cc_final: 0.8912 (mtpp) REVERT: R 89 ASP cc_start: 0.8241 (m-30) cc_final: 0.8033 (m-30) REVERT: S 63 ASP cc_start: 0.8885 (m-30) cc_final: 0.8608 (m-30) REVERT: S 83 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8872 (mmtt) REVERT: T 31 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8642 (tm-30) REVERT: T 33 GLN cc_start: 0.8288 (mt0) cc_final: 0.7737 (mt0) REVERT: T 35 LYS cc_start: 0.9169 (tttt) cc_final: 0.8898 (tttm) REVERT: T 57 GLU cc_start: 0.8675 (tt0) cc_final: 0.8215 (tt0) REVERT: T 79 GLU cc_start: 0.8233 (tp30) cc_final: 0.7812 (tp30) REVERT: T 83 LYS cc_start: 0.9169 (mtpt) cc_final: 0.8769 (mtpp) REVERT: V 40 LYS cc_start: 0.9277 (tppt) cc_final: 0.9011 (mttm) REVERT: V 57 GLU cc_start: 0.7907 (tt0) cc_final: 0.7617 (tt0) REVERT: V 58 ARG cc_start: 0.8360 (mtm110) cc_final: 0.7858 (mtt180) REVERT: V 86 LYS cc_start: 0.9196 (mttt) cc_final: 0.8923 (mttm) REVERT: V 89 ASP cc_start: 0.8205 (m-30) cc_final: 0.7971 (m-30) REVERT: V 96 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 42 outliers final: 11 residues processed: 599 average time/residue: 0.3185 time to fit residues: 265.3980 Evaluate side-chains 436 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 418 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain P residue 30 SER Chi-restraints excluded: chain Q residue 30 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain T residue 30 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN C 33 GLN C 39 HIS C 70 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS D 96 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 103 GLN J 33 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN M 39 HIS O 70 GLN O 96 GLN R 39 HIS R 70 GLN R 96 GLN S 96 GLN T 39 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15645 Z= 0.233 Angle : 0.584 8.232 21021 Z= 0.301 Chirality : 0.038 0.156 2289 Planarity : 0.005 0.034 2835 Dihedral : 4.745 38.403 2227 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.35 % Allowed : 15.72 % Favored : 81.93 % 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: -4.64 (0.15), residues: 1869 helix: -3.23 (0.11), residues: 1176 sheet: None (None), residues: 0 loop : -2.47 (0.19), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 53 HIS 0.003 0.001 HIS Q 39 PHE 0.007 0.001 PHE H 37 TYR 0.005 0.001 TYR P 72 ARG 0.006 0.000 ARG E 58 *********************** 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 486 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 450 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8256 (tp30) cc_final: 0.7855 (tm-30) REVERT: A 86 LYS cc_start: 0.9044 (mttt) cc_final: 0.8661 (mtpp) REVERT: B 30 SER cc_start: 0.8327 (t) cc_final: 0.7668 (p) REVERT: B 31 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8422 (tm-30) REVERT: B 32 GLU cc_start: 0.8785 (tp30) cc_final: 0.8325 (tp30) REVERT: B 66 GLU cc_start: 0.8650 (tp30) cc_final: 0.8178 (tm-30) REVERT: B 83 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8007 (mmtt) REVERT: B 96 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8886 (tm-30) REVERT: D 31 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8398 (tm-30) REVERT: D 35 LYS cc_start: 0.9300 (tttp) cc_final: 0.9059 (tttp) REVERT: D 39 HIS cc_start: 0.7240 (t-90) cc_final: 0.6227 (t-90) REVERT: D 57 GLU cc_start: 0.7729 (tt0) cc_final: 0.7343 (tt0) REVERT: D 99 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8094 (tm-30) REVERT: E 20 GLU cc_start: 0.8684 (tp30) cc_final: 0.8394 (tm-30) REVERT: E 32 GLU cc_start: 0.8325 (tp30) cc_final: 0.7836 (tp30) REVERT: F 32 GLU cc_start: 0.8547 (tp30) cc_final: 0.8281 (tp30) REVERT: F 35 LYS cc_start: 0.9302 (tttt) cc_final: 0.9067 (tttp) REVERT: G 40 LYS cc_start: 0.9139 (tppt) cc_final: 0.8928 (mttm) REVERT: G 58 ARG cc_start: 0.8357 (mtm110) cc_final: 0.7929 (mtt-85) REVERT: G 89 ASP cc_start: 0.8432 (m-30) cc_final: 0.8154 (m-30) REVERT: G 96 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8488 (tm-30) REVERT: H 30 SER cc_start: 0.8454 (t) cc_final: 0.7768 (p) REVERT: H 31 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8338 (tm-30) REVERT: H 32 GLU cc_start: 0.8761 (tp30) cc_final: 0.8409 (tp30) REVERT: H 57 GLU cc_start: 0.8343 (tt0) cc_final: 0.8112 (mt-10) REVERT: H 66 GLU cc_start: 0.8476 (tp30) cc_final: 0.8017 (tp30) REVERT: J 21 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8957 (mp) REVERT: K 31 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8391 (tm-30) REVERT: L 32 GLU cc_start: 0.8535 (tp30) cc_final: 0.8014 (tp30) REVERT: L 83 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8776 (mmtm) REVERT: L 89 ASP cc_start: 0.7838 (m-30) cc_final: 0.7577 (m-30) REVERT: M 28 GLU cc_start: 0.8962 (tp30) cc_final: 0.8762 (tp30) REVERT: M 31 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8548 (tm-30) REVERT: N 20 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7890 (mm-30) REVERT: N 31 GLN cc_start: 0.8629 (tt0) cc_final: 0.8241 (pt0) REVERT: N 58 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7946 (mtt-85) REVERT: N 96 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8437 (tm-30) REVERT: O 30 SER cc_start: 0.8393 (t) cc_final: 0.7367 (p) REVERT: O 31 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8350 (tm-30) REVERT: O 32 GLU cc_start: 0.8612 (tp30) cc_final: 0.8329 (tp30) REVERT: O 33 GLN cc_start: 0.9026 (mt0) cc_final: 0.8292 (mt0) REVERT: O 66 GLU cc_start: 0.8264 (tp30) cc_final: 0.7852 (tm-30) REVERT: P 20 GLU cc_start: 0.8507 (tt0) cc_final: 0.8283 (tt0) REVERT: P 31 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8563 (tm-30) REVERT: P 66 GLU cc_start: 0.8221 (tp30) cc_final: 0.7975 (tm-30) REVERT: R 31 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8336 (tm-30) REVERT: R 32 GLU cc_start: 0.8687 (tp30) cc_final: 0.7995 (tp30) REVERT: R 79 GLU cc_start: 0.8436 (tp30) cc_final: 0.7613 (tp30) REVERT: R 83 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8356 (ttmm) REVERT: R 99 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: S 32 GLU cc_start: 0.8333 (tp30) cc_final: 0.7759 (tp30) REVERT: S 83 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8779 (mmtt) REVERT: S 99 GLU cc_start: 0.8524 (pt0) cc_final: 0.7981 (tm-30) REVERT: T 31 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8634 (tm-30) REVERT: T 79 GLU cc_start: 0.8352 (tp30) cc_final: 0.8025 (tp30) REVERT: T 83 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8761 (mtpp) REVERT: V 20 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7984 (mm-30) REVERT: V 58 ARG cc_start: 0.8445 (mtm110) cc_final: 0.7982 (mtt-85) REVERT: V 89 ASP cc_start: 0.8307 (m-30) cc_final: 0.8015 (m-30) REVERT: V 96 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8249 (tm-30) outliers start: 36 outliers final: 18 residues processed: 464 average time/residue: 0.2883 time to fit residues: 191.6004 Evaluate side-chains 419 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 398 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain F residue 39 HIS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 70 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain S residue 96 GLN Chi-restraints excluded: chain T residue 39 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN F 33 GLN F 39 HIS F 96 GLN I 96 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN P 39 HIS P 96 GLN Q 31 GLN R 70 GLN ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15645 Z= 0.232 Angle : 0.537 5.778 21021 Z= 0.280 Chirality : 0.037 0.132 2289 Planarity : 0.004 0.034 2835 Dihedral : 3.953 16.144 2205 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.35 % Allowed : 19.05 % Favored : 78.60 % 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: -2.30 (0.13), residues: 1176 sheet: None (None), residues: 0 loop : -2.10 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 53 HIS 0.011 0.001 HIS F 39 PHE 0.007 0.001 PHE H 37 TYR 0.005 0.001 TYR F 72 ARG 0.004 0.000 ARG E 58 *********************** 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 451 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 415 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8227 (tp30) cc_final: 0.7917 (tm-30) REVERT: B 30 SER cc_start: 0.8506 (t) cc_final: 0.7622 (p) REVERT: B 31 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 32 GLU cc_start: 0.8735 (tp30) cc_final: 0.8301 (tp30) REVERT: B 33 GLN cc_start: 0.9213 (mt0) cc_final: 0.8800 (mt0) REVERT: B 66 GLU cc_start: 0.8593 (tp30) cc_final: 0.8213 (tm-30) REVERT: B 75 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8250 (tt0) REVERT: B 83 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8157 (mmtt) REVERT: D 31 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8436 (tm-30) REVERT: D 32 GLU cc_start: 0.8707 (tp30) cc_final: 0.8207 (tp30) REVERT: D 99 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: E 20 GLU cc_start: 0.8698 (tp30) cc_final: 0.8343 (tm-30) REVERT: E 32 GLU cc_start: 0.8350 (tp30) cc_final: 0.7817 (tp30) REVERT: E 79 GLU cc_start: 0.8679 (tp30) cc_final: 0.8144 (tp30) REVERT: F 32 GLU cc_start: 0.8550 (tp30) cc_final: 0.8185 (tp30) REVERT: F 66 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7589 (mt-10) REVERT: G 58 ARG cc_start: 0.8386 (mtm110) cc_final: 0.7935 (mtt-85) REVERT: G 89 ASP cc_start: 0.8422 (m-30) cc_final: 0.8155 (m-30) REVERT: G 96 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8090 (tm-30) REVERT: H 30 SER cc_start: 0.8333 (t) cc_final: 0.7612 (p) REVERT: H 31 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8360 (tm-30) REVERT: H 32 GLU cc_start: 0.8720 (tp30) cc_final: 0.8396 (tp30) REVERT: H 66 GLU cc_start: 0.8494 (tp30) cc_final: 0.8198 (tp30) REVERT: H 83 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7936 (mmtt) REVERT: J 21 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8995 (mp) REVERT: J 70 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: K 31 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8370 (tm-30) REVERT: L 20 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8197 (tm-30) REVERT: L 31 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8651 (tm-30) REVERT: L 32 GLU cc_start: 0.8584 (tp30) cc_final: 0.8095 (tp30) REVERT: L 83 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8711 (mmtt) REVERT: L 89 ASP cc_start: 0.7803 (m-30) cc_final: 0.7561 (m-30) REVERT: L 99 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8072 (tm-30) REVERT: M 28 GLU cc_start: 0.8925 (tp30) cc_final: 0.8723 (tp30) REVERT: M 31 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8586 (tm-30) REVERT: N 20 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7940 (mm-30) REVERT: N 31 GLN cc_start: 0.8486 (tt0) cc_final: 0.8128 (pt0) REVERT: N 58 ARG cc_start: 0.8229 (mtm110) cc_final: 0.8012 (mtt-85) REVERT: N 96 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8329 (tm-30) REVERT: O 30 SER cc_start: 0.8580 (t) cc_final: 0.7628 (p) REVERT: O 31 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8393 (tm-30) REVERT: O 32 GLU cc_start: 0.8558 (tp30) cc_final: 0.8263 (tp30) REVERT: O 33 GLN cc_start: 0.9024 (mt0) cc_final: 0.8334 (mt0) REVERT: O 66 GLU cc_start: 0.8312 (tp30) cc_final: 0.7988 (tm-30) REVERT: P 31 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8688 (tm-30) REVERT: R 31 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8386 (tm-30) REVERT: R 32 GLU cc_start: 0.8639 (tp30) cc_final: 0.7936 (tp30) REVERT: R 79 GLU cc_start: 0.8374 (tp30) cc_final: 0.7570 (tp30) REVERT: R 83 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8323 (ttmm) REVERT: R 99 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: S 32 GLU cc_start: 0.8374 (tp30) cc_final: 0.7765 (tp30) REVERT: S 63 ASP cc_start: 0.9047 (m-30) cc_final: 0.8808 (m-30) REVERT: S 83 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8761 (mmtt) REVERT: S 99 GLU cc_start: 0.8564 (pt0) cc_final: 0.7987 (tm-30) REVERT: T 35 LYS cc_start: 0.9259 (tttm) cc_final: 0.8975 (tttm) REVERT: T 79 GLU cc_start: 0.8238 (tp30) cc_final: 0.7951 (tp30) REVERT: T 83 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8722 (mtpp) REVERT: V 20 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7970 (mm-30) REVERT: V 40 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8924 (ttmm) REVERT: V 58 ARG cc_start: 0.8523 (mtm110) cc_final: 0.8080 (mtt-85) REVERT: V 92 ASP cc_start: 0.8445 (p0) cc_final: 0.8008 (t0) REVERT: V 96 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8277 (tm-30) outliers start: 36 outliers final: 18 residues processed: 425 average time/residue: 0.2691 time to fit residues: 167.1086 Evaluate side-chains 413 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 389 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 53 TRP Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 39 HIS Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 70 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 39 HIS A 96 GLN B 96 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** G 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 GLN I 70 GLN I 96 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 HIS Q 39 HIS Q 67 GLN ** Q 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 GLN ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 GLN T 96 GLN V 39 HIS V 103 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15645 Z= 0.258 Angle : 0.537 8.577 21021 Z= 0.279 Chirality : 0.038 0.135 2289 Planarity : 0.004 0.034 2835 Dihedral : 3.837 16.178 2205 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.13 % Allowed : 20.35 % Favored : 76.52 % 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: -2.93 (0.18), residues: 1869 helix: -1.84 (0.13), residues: 1260 sheet: None (None), residues: 0 loop : -1.76 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 53 HIS 0.007 0.001 HIS P 39 PHE 0.008 0.001 PHE H 37 TYR 0.005 0.001 TYR F 72 ARG 0.003 0.000 ARG K 58 *********************** 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 450 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 402 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 66 GLU cc_start: 0.8206 (tp30) cc_final: 0.7911 (tm-30) REVERT: A 75 GLU cc_start: 0.9053 (tp30) cc_final: 0.8748 (tp30) REVERT: B 30 SER cc_start: 0.8412 (t) cc_final: 0.7549 (p) REVERT: B 31 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8407 (tm-30) REVERT: B 32 GLU cc_start: 0.8692 (tp30) cc_final: 0.8460 (tp30) REVERT: B 33 GLN cc_start: 0.9184 (mt0) cc_final: 0.8765 (mt0) REVERT: B 66 GLU cc_start: 0.8640 (tp30) cc_final: 0.8246 (tm-30) REVERT: B 83 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8127 (mmtt) REVERT: D 31 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8482 (tm-30) REVERT: D 32 GLU cc_start: 0.8686 (tp30) cc_final: 0.8107 (tp30) REVERT: D 79 GLU cc_start: 0.8028 (tp30) cc_final: 0.7665 (tp30) REVERT: E 20 GLU cc_start: 0.8725 (tp30) cc_final: 0.8367 (tm-30) REVERT: E 32 GLU cc_start: 0.8405 (tp30) cc_final: 0.7791 (tp30) REVERT: E 57 GLU cc_start: 0.7623 (tt0) cc_final: 0.7387 (tt0) REVERT: E 79 GLU cc_start: 0.8661 (tp30) cc_final: 0.8105 (tp30) REVERT: F 31 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8226 (tm-30) REVERT: F 32 GLU cc_start: 0.8635 (tp30) cc_final: 0.8269 (tp30) REVERT: F 57 GLU cc_start: 0.8520 (tt0) cc_final: 0.8207 (tt0) REVERT: F 63 ASP cc_start: 0.8215 (t70) cc_final: 0.8003 (t70) REVERT: G 58 ARG cc_start: 0.8353 (mtm110) cc_final: 0.7924 (mtt-85) REVERT: G 89 ASP cc_start: 0.8450 (m-30) cc_final: 0.8178 (m-30) REVERT: G 96 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8044 (tm-30) REVERT: H 30 SER cc_start: 0.8349 (t) cc_final: 0.7573 (p) REVERT: H 31 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8373 (tm-30) REVERT: H 32 GLU cc_start: 0.8708 (tp30) cc_final: 0.8377 (tp30) REVERT: H 66 GLU cc_start: 0.8534 (tp30) cc_final: 0.8309 (tp30) REVERT: H 83 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7939 (mmtt) REVERT: I 31 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8605 (tm-30) REVERT: J 21 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9015 (mp) REVERT: K 31 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8449 (tm-30) REVERT: K 32 GLU cc_start: 0.8584 (tp30) cc_final: 0.8366 (tp30) REVERT: L 20 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8197 (tm-30) REVERT: L 32 GLU cc_start: 0.8595 (tp30) cc_final: 0.8072 (tp30) REVERT: L 83 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8697 (mmtt) REVERT: L 89 ASP cc_start: 0.7838 (m-30) cc_final: 0.7609 (m-30) REVERT: L 99 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: L 100 ARG cc_start: 0.8480 (mtm180) cc_final: 0.8265 (mtm180) REVERT: M 31 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8532 (tm-30) REVERT: N 20 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8048 (mm-30) REVERT: N 31 GLN cc_start: 0.8512 (tt0) cc_final: 0.8124 (pt0) REVERT: N 58 ARG cc_start: 0.8278 (mtm110) cc_final: 0.8040 (mtt-85) REVERT: O 30 SER cc_start: 0.8553 (t) cc_final: 0.7605 (p) REVERT: O 31 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8360 (tm-30) REVERT: O 32 GLU cc_start: 0.8547 (tp30) cc_final: 0.8254 (tp30) REVERT: O 33 GLN cc_start: 0.9084 (mt0) cc_final: 0.8422 (mt0) REVERT: O 66 GLU cc_start: 0.8366 (tp30) cc_final: 0.8093 (tm-30) REVERT: P 31 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8693 (tm-30) REVERT: P 66 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8095 (tm-30) REVERT: Q 57 GLU cc_start: 0.7947 (tt0) cc_final: 0.7649 (tt0) REVERT: R 31 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8401 (tm-30) REVERT: R 32 GLU cc_start: 0.8653 (tp30) cc_final: 0.7932 (tp30) REVERT: R 83 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8822 (mtpp) REVERT: R 99 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: S 32 GLU cc_start: 0.8415 (tp30) cc_final: 0.7807 (tp30) REVERT: S 83 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8732 (mmtt) REVERT: S 99 GLU cc_start: 0.8646 (pt0) cc_final: 0.8153 (tm-30) REVERT: T 35 LYS cc_start: 0.9289 (tttm) cc_final: 0.9056 (tttm) REVERT: T 66 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7829 (tm-30) REVERT: T 79 GLU cc_start: 0.8240 (tp30) cc_final: 0.7944 (tp30) REVERT: T 83 LYS cc_start: 0.8967 (mtpt) cc_final: 0.8733 (mtpp) REVERT: V 20 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8025 (mm-30) REVERT: V 32 GLU cc_start: 0.8557 (tp30) cc_final: 0.8344 (tp30) REVERT: V 40 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8950 (ttmm) REVERT: V 58 ARG cc_start: 0.8592 (mtm110) cc_final: 0.8094 (mtt-85) REVERT: V 92 ASP cc_start: 0.8726 (p0) cc_final: 0.7937 (t0) REVERT: V 96 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8236 (tm-30) outliers start: 48 outliers final: 26 residues processed: 417 average time/residue: 0.2777 time to fit residues: 168.9074 Evaluate side-chains 418 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 388 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 39 HIS Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 39 HIS Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 70 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.0060 chunk 163 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN C 31 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 HIS E 96 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN I 39 HIS I 96 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 HIS ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 33 GLN L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 96 GLN O 33 GLN P 39 HIS Q 70 GLN ** S 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 67 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15645 Z= 0.159 Angle : 0.493 7.313 21021 Z= 0.258 Chirality : 0.035 0.124 2289 Planarity : 0.003 0.034 2835 Dihedral : 3.581 15.089 2205 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.67 % Allowed : 22.05 % Favored : 75.28 % 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: -2.07 (0.19), residues: 1869 helix: -1.00 (0.14), residues: 1218 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 53 HIS 0.005 0.001 HIS P 39 PHE 0.004 0.001 PHE J 71 TYR 0.003 0.001 TYR M 72 ARG 0.002 0.000 ARG K 58 *********************** 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 454 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 413 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 66 GLU cc_start: 0.8151 (tp30) cc_final: 0.7881 (tm-30) REVERT: A 75 GLU cc_start: 0.9006 (tp30) cc_final: 0.8708 (tp30) REVERT: B 30 SER cc_start: 0.8377 (t) cc_final: 0.7559 (p) REVERT: B 31 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 32 GLU cc_start: 0.8556 (tp30) cc_final: 0.8313 (tp30) REVERT: B 33 GLN cc_start: 0.9134 (mt0) cc_final: 0.8780 (mt0) REVERT: B 83 LYS cc_start: 0.8304 (mmtt) cc_final: 0.8079 (mmtt) REVERT: D 31 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8410 (tm-30) REVERT: D 32 GLU cc_start: 0.8568 (tp30) cc_final: 0.7992 (tp30) REVERT: D 39 HIS cc_start: 0.6769 (t70) cc_final: 0.6554 (t70) REVERT: D 99 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8315 (tm-30) REVERT: E 20 GLU cc_start: 0.8735 (tp30) cc_final: 0.8347 (tm-30) REVERT: E 32 GLU cc_start: 0.8286 (tp30) cc_final: 0.7976 (tp30) REVERT: E 63 ASP cc_start: 0.8860 (m-30) cc_final: 0.8647 (m-30) REVERT: E 79 GLU cc_start: 0.8605 (tp30) cc_final: 0.7997 (tp30) REVERT: E 96 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8899 (tm-30) REVERT: E 99 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: F 31 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8206 (tm-30) REVERT: F 32 GLU cc_start: 0.8641 (tp30) cc_final: 0.8260 (tp30) REVERT: G 58 ARG cc_start: 0.8321 (mtm110) cc_final: 0.7893 (mtt-85) REVERT: G 75 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8178 (mm-30) REVERT: G 96 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8002 (tm-30) REVERT: H 31 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8479 (tm-30) REVERT: H 32 GLU cc_start: 0.8549 (tp30) cc_final: 0.8261 (tp30) REVERT: H 66 GLU cc_start: 0.8478 (tp30) cc_final: 0.8123 (tm-30) REVERT: H 83 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7896 (mmtt) REVERT: I 31 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8502 (tm-30) REVERT: I 75 GLU cc_start: 0.9010 (tp30) cc_final: 0.8511 (mm-30) REVERT: I 98 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8891 (mm-40) REVERT: J 67 GLN cc_start: 0.8210 (mt0) cc_final: 0.7877 (mt0) REVERT: K 31 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8368 (tm-30) REVERT: K 32 GLU cc_start: 0.8555 (tp30) cc_final: 0.8197 (tp30) REVERT: K 99 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8197 (tm-30) REVERT: L 20 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8185 (tm-30) REVERT: L 32 GLU cc_start: 0.8481 (tp30) cc_final: 0.7833 (tp30) REVERT: L 66 GLU cc_start: 0.7819 (tp30) cc_final: 0.7577 (tp30) REVERT: L 89 ASP cc_start: 0.7833 (m-30) cc_final: 0.7585 (m-30) REVERT: L 99 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: M 31 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8276 (tm-30) REVERT: N 20 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8054 (mm-30) REVERT: N 31 GLN cc_start: 0.8515 (tt0) cc_final: 0.8084 (pt0) REVERT: N 58 ARG cc_start: 0.8258 (mtm110) cc_final: 0.8015 (mtt-85) REVERT: N 96 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: O 31 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8474 (tm-30) REVERT: O 32 GLU cc_start: 0.8469 (tp30) cc_final: 0.8181 (tp30) REVERT: O 66 GLU cc_start: 0.8327 (tp30) cc_final: 0.8113 (tm-30) REVERT: O 99 GLU cc_start: 0.8613 (pt0) cc_final: 0.8367 (pt0) REVERT: P 31 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8469 (tm-30) REVERT: P 32 GLU cc_start: 0.8715 (tp30) cc_final: 0.8503 (tp30) REVERT: P 66 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8040 (tm-30) REVERT: P 98 GLN cc_start: 0.9215 (mm-40) cc_final: 0.9014 (mm-40) REVERT: Q 57 GLU cc_start: 0.7889 (tt0) cc_final: 0.7616 (tt0) REVERT: R 31 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8361 (tm-30) REVERT: R 32 GLU cc_start: 0.8506 (tp30) cc_final: 0.7764 (tp30) REVERT: R 99 GLU cc_start: 0.8632 (pt0) cc_final: 0.8245 (tm-30) REVERT: S 32 GLU cc_start: 0.8392 (tp30) cc_final: 0.7732 (tp30) REVERT: S 99 GLU cc_start: 0.8601 (pt0) cc_final: 0.8205 (tm-30) REVERT: T 31 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8180 (tm-30) REVERT: T 35 LYS cc_start: 0.9208 (tttm) cc_final: 0.8976 (tttm) REVERT: T 66 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7900 (tm-30) REVERT: T 79 GLU cc_start: 0.8136 (tp30) cc_final: 0.7835 (tp30) REVERT: T 83 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8596 (mtpp) REVERT: V 20 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8030 (mm-30) REVERT: V 32 GLU cc_start: 0.8522 (tp30) cc_final: 0.8221 (tp30) REVERT: V 58 ARG cc_start: 0.8576 (mtm110) cc_final: 0.8087 (mtt-85) REVERT: V 96 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8218 (tm-30) outliers start: 41 outliers final: 14 residues processed: 423 average time/residue: 0.2813 time to fit residues: 176.6382 Evaluate side-chains 403 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 384 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain K residue 39 HIS Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 70 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 151 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 70 GLN B 96 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN I 96 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 L 39 HIS L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 GLN N 96 GLN R 39 HIS ** S 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15645 Z= 0.160 Angle : 0.488 6.467 21021 Z= 0.256 Chirality : 0.035 0.120 2289 Planarity : 0.003 0.031 2835 Dihedral : 3.397 14.452 2205 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.13 % Allowed : 22.31 % Favored : 74.56 % 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: -1.32 (0.19), residues: 1869 helix: -0.46 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -1.55 (0.27), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 53 HIS 0.003 0.000 HIS P 39 PHE 0.004 0.001 PHE V 37 TYR 0.004 0.001 TYR O 72 ARG 0.003 0.000 ARG D 58 *********************** 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 441 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 393 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8649 (tm-30) REVERT: A 75 GLU cc_start: 0.8914 (tp30) cc_final: 0.8548 (mm-30) REVERT: B 31 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8473 (tm-30) REVERT: B 32 GLU cc_start: 0.8515 (tp30) cc_final: 0.8288 (tp30) REVERT: D 31 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8300 (tm-30) REVERT: D 32 GLU cc_start: 0.8521 (tp30) cc_final: 0.7763 (tp30) REVERT: D 99 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8343 (tm-30) REVERT: E 20 GLU cc_start: 0.8738 (tp30) cc_final: 0.8367 (tm-30) REVERT: E 32 GLU cc_start: 0.8323 (tp30) cc_final: 0.7590 (tp30) REVERT: E 57 GLU cc_start: 0.7222 (tt0) cc_final: 0.7015 (tt0) REVERT: E 79 GLU cc_start: 0.8601 (tp30) cc_final: 0.8054 (tp30) REVERT: E 96 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8721 (tm-30) REVERT: E 99 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: F 31 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8179 (tm-30) REVERT: F 32 GLU cc_start: 0.8640 (tp30) cc_final: 0.8259 (tp30) REVERT: G 58 ARG cc_start: 0.8382 (mtm110) cc_final: 0.7919 (mtt-85) REVERT: G 75 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8147 (mm-30) REVERT: G 89 ASP cc_start: 0.8328 (m-30) cc_final: 0.8111 (m-30) REVERT: G 96 GLN cc_start: 0.8593 (tm-30) cc_final: 0.7940 (tm-30) REVERT: H 31 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8477 (tm-30) REVERT: H 32 GLU cc_start: 0.8539 (tp30) cc_final: 0.8261 (tp30) REVERT: H 66 GLU cc_start: 0.8446 (tp30) cc_final: 0.8171 (tm-30) REVERT: I 31 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8551 (tm-30) REVERT: I 75 GLU cc_start: 0.8957 (tp30) cc_final: 0.8549 (mm-30) REVERT: I 83 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8484 (mtpp) REVERT: K 31 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8413 (tm-30) REVERT: K 32 GLU cc_start: 0.8546 (tp30) cc_final: 0.8196 (tp30) REVERT: K 99 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8191 (tm-30) REVERT: L 20 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8227 (tm-30) REVERT: L 32 GLU cc_start: 0.8404 (tp30) cc_final: 0.7890 (tp30) REVERT: L 63 ASP cc_start: 0.8920 (m-30) cc_final: 0.8568 (m-30) REVERT: L 89 ASP cc_start: 0.7820 (m-30) cc_final: 0.7488 (m-30) REVERT: L 99 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: M 31 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8332 (tm-30) REVERT: N 31 GLN cc_start: 0.8491 (tt0) cc_final: 0.8010 (pt0) REVERT: N 58 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7974 (mtt-85) REVERT: N 96 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: O 31 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8513 (tm-30) REVERT: O 32 GLU cc_start: 0.8483 (tp30) cc_final: 0.8194 (tp30) REVERT: O 99 GLU cc_start: 0.8578 (pt0) cc_final: 0.8300 (pt0) REVERT: P 31 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8533 (tm-30) REVERT: P 32 GLU cc_start: 0.8774 (tp30) cc_final: 0.8529 (tp30) REVERT: P 66 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7981 (tm-30) REVERT: Q 32 GLU cc_start: 0.8485 (tp30) cc_final: 0.8250 (tp30) REVERT: Q 57 GLU cc_start: 0.7850 (tt0) cc_final: 0.7647 (tt0) REVERT: R 31 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8406 (tm-30) REVERT: R 32 GLU cc_start: 0.8464 (tp30) cc_final: 0.7720 (tp30) REVERT: R 99 GLU cc_start: 0.8615 (pt0) cc_final: 0.8252 (tm-30) REVERT: S 32 GLU cc_start: 0.8409 (tp30) cc_final: 0.7735 (tp30) REVERT: S 99 GLU cc_start: 0.8598 (pt0) cc_final: 0.8239 (tm-30) REVERT: T 31 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8209 (tm-30) REVERT: T 35 LYS cc_start: 0.9193 (tttm) cc_final: 0.8940 (tttp) REVERT: T 66 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7807 (tm-30) REVERT: T 79 GLU cc_start: 0.8096 (tp30) cc_final: 0.7844 (tp30) REVERT: T 83 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8666 (mtpp) REVERT: V 20 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8045 (mm-30) REVERT: V 32 GLU cc_start: 0.8511 (tp30) cc_final: 0.8266 (tp30) REVERT: V 58 ARG cc_start: 0.8577 (mtm110) cc_final: 0.8086 (mtt-85) REVERT: V 89 ASP cc_start: 0.8327 (m-30) cc_final: 0.8094 (m-30) REVERT: V 96 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8230 (tm-30) outliers start: 48 outliers final: 15 residues processed: 405 average time/residue: 0.2516 time to fit residues: 151.1486 Evaluate side-chains 396 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 377 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain N residue 96 GLN Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 70 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 102 optimal weight: 0.0050 chunk 182 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 chunk 111 optimal weight: 0.3980 chunk 84 optimal weight: 0.6980 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN E 39 HIS E 96 GLN I 96 GLN J 70 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS T 67 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15645 Z= 0.168 Angle : 0.495 6.806 21021 Z= 0.259 Chirality : 0.035 0.117 2289 Planarity : 0.003 0.031 2835 Dihedral : 3.308 13.980 2205 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.67 % Allowed : 22.96 % Favored : 74.36 % 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: -0.81 (0.20), residues: 1869 helix: -0.02 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 53 HIS 0.004 0.001 HIS K 39 PHE 0.005 0.001 PHE N 37 TYR 0.005 0.001 TYR J 72 ARG 0.003 0.000 ARG D 58 *********************** 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 420 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 379 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8018 (tm-30) REVERT: A 75 GLU cc_start: 0.8889 (tp30) cc_final: 0.8535 (mm-30) REVERT: B 31 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8464 (tm-30) REVERT: B 32 GLU cc_start: 0.8519 (tp30) cc_final: 0.8266 (tp30) REVERT: D 31 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8325 (tm-30) REVERT: D 32 GLU cc_start: 0.8472 (tp30) cc_final: 0.7737 (tp30) REVERT: D 99 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8373 (tm-30) REVERT: E 20 GLU cc_start: 0.8725 (tp30) cc_final: 0.8374 (tm-30) REVERT: E 32 GLU cc_start: 0.8270 (tp30) cc_final: 0.7505 (tp30) REVERT: E 79 GLU cc_start: 0.8571 (tp30) cc_final: 0.8038 (tp30) REVERT: E 99 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: F 31 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8178 (tm-30) REVERT: F 32 GLU cc_start: 0.8650 (tp30) cc_final: 0.8288 (tp30) REVERT: G 58 ARG cc_start: 0.8393 (mtm110) cc_final: 0.7920 (mtt-85) REVERT: G 89 ASP cc_start: 0.8319 (m-30) cc_final: 0.8086 (m-30) REVERT: G 96 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7940 (tm-30) REVERT: H 31 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8440 (tm-30) REVERT: H 32 GLU cc_start: 0.8560 (tp30) cc_final: 0.8242 (tp30) REVERT: H 66 GLU cc_start: 0.8427 (tp30) cc_final: 0.8170 (tm-30) REVERT: H 83 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7978 (mmtt) REVERT: I 31 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8622 (tm-30) REVERT: I 66 GLU cc_start: 0.8291 (tm-30) cc_final: 0.8048 (tm-30) REVERT: I 75 GLU cc_start: 0.8938 (tp30) cc_final: 0.8556 (mm-30) REVERT: I 83 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8474 (mtpp) REVERT: I 99 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7902 (tm-30) REVERT: K 31 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8419 (tm-30) REVERT: K 32 GLU cc_start: 0.8573 (tp30) cc_final: 0.8175 (tp30) REVERT: K 99 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8201 (tm-30) REVERT: L 20 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8249 (tm-30) REVERT: L 32 GLU cc_start: 0.8382 (tp30) cc_final: 0.7857 (tp30) REVERT: L 66 GLU cc_start: 0.7883 (tp30) cc_final: 0.7682 (tp30) REVERT: L 89 ASP cc_start: 0.7838 (m-30) cc_final: 0.7504 (m-30) REVERT: L 99 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: M 31 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8319 (tm-30) REVERT: N 31 GLN cc_start: 0.8512 (tt0) cc_final: 0.8051 (pt0) REVERT: N 58 ARG cc_start: 0.8257 (mtm110) cc_final: 0.8011 (mtt-85) REVERT: N 96 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8168 (tm-30) REVERT: O 31 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8444 (tm-30) REVERT: O 32 GLU cc_start: 0.8543 (tp30) cc_final: 0.8275 (tp30) REVERT: O 66 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8034 (tm-30) REVERT: O 99 GLU cc_start: 0.8557 (pt0) cc_final: 0.8284 (pt0) REVERT: P 31 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8488 (tm-30) REVERT: P 66 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7929 (tm-30) REVERT: Q 32 GLU cc_start: 0.8500 (tp30) cc_final: 0.8218 (tp30) REVERT: R 31 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8432 (tm-30) REVERT: R 32 GLU cc_start: 0.8466 (tp30) cc_final: 0.8004 (tp30) REVERT: R 99 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8378 (tm-30) REVERT: S 32 GLU cc_start: 0.8412 (tp30) cc_final: 0.7728 (tp30) REVERT: S 99 GLU cc_start: 0.8561 (pt0) cc_final: 0.8178 (tm-30) REVERT: T 31 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8240 (tm-30) REVERT: T 35 LYS cc_start: 0.9190 (tttm) cc_final: 0.8909 (tttp) REVERT: T 66 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7912 (tm-30) REVERT: T 79 GLU cc_start: 0.8107 (tp30) cc_final: 0.7894 (tp30) REVERT: V 32 GLU cc_start: 0.8439 (tp30) cc_final: 0.8222 (tp30) REVERT: V 55 ARG cc_start: 0.8856 (ptp90) cc_final: 0.8568 (mtp180) REVERT: V 58 ARG cc_start: 0.8582 (mtm110) cc_final: 0.8078 (mtt-85) REVERT: V 89 ASP cc_start: 0.8342 (m-30) cc_final: 0.8091 (m-30) REVERT: V 96 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8153 (tm-30) outliers start: 41 outliers final: 21 residues processed: 389 average time/residue: 0.2663 time to fit residues: 155.7470 Evaluate side-chains 395 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 370 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 70 GLN Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 83 LYS Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 60 ASP Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 70 GLN D 98 GLN E 96 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 HIS ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN L 96 GLN M 98 GLN O 96 GLN R 98 GLN R 103 GLN ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 15645 Z= 0.515 Angle : 0.714 5.209 21021 Z= 0.361 Chirality : 0.045 0.153 2289 Planarity : 0.005 0.036 2835 Dihedral : 4.076 16.259 2205 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.07 % Allowed : 23.94 % Favored : 72.99 % 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: -1.41 (0.20), residues: 1869 helix: -0.72 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -1.08 (0.31), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 53 HIS 0.008 0.001 HIS K 39 PHE 0.023 0.003 PHE J 71 TYR 0.012 0.002 TYR J 72 ARG 0.006 0.001 ARG E 55 *********************** 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 438 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 391 time to evaluate : 2.114 Fit side-chains revert: symmetry clash REVERT: B 27 GLU cc_start: 0.8403 (pt0) cc_final: 0.8167 (pt0) REVERT: B 31 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8346 (tm-30) REVERT: B 32 GLU cc_start: 0.8839 (tp30) cc_final: 0.8507 (tp30) REVERT: D 31 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8273 (tm-30) REVERT: D 32 GLU cc_start: 0.8679 (tp30) cc_final: 0.8085 (tp30) REVERT: D 99 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8406 (tm-30) REVERT: E 20 GLU cc_start: 0.8689 (tp30) cc_final: 0.8408 (tm-30) REVERT: E 31 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8797 (tm-30) REVERT: E 32 GLU cc_start: 0.8705 (tp30) cc_final: 0.8061 (tp30) REVERT: F 20 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: F 31 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8421 (tm-30) REVERT: G 58 ARG cc_start: 0.8554 (mtm110) cc_final: 0.8283 (mtt-85) REVERT: G 75 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7987 (mm-30) REVERT: G 89 ASP cc_start: 0.8520 (m-30) cc_final: 0.8288 (m-30) REVERT: G 96 GLN cc_start: 0.8547 (tm-30) cc_final: 0.7909 (tm-30) REVERT: H 27 GLU cc_start: 0.8199 (pt0) cc_final: 0.7913 (pt0) REVERT: H 28 GLU cc_start: 0.8437 (tp30) cc_final: 0.8198 (tp30) REVERT: H 31 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8478 (tm-30) REVERT: H 32 GLU cc_start: 0.8871 (tp30) cc_final: 0.8477 (tp30) REVERT: H 33 GLN cc_start: 0.9062 (mt0) cc_final: 0.8528 (mp10) REVERT: H 66 GLU cc_start: 0.8704 (tp30) cc_final: 0.8326 (tp30) REVERT: I 31 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8771 (tm-30) REVERT: K 31 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8470 (tm-30) REVERT: K 32 GLU cc_start: 0.8865 (tp30) cc_final: 0.8651 (tp30) REVERT: K 66 GLU cc_start: 0.8401 (tp30) cc_final: 0.8147 (tm-30) REVERT: K 99 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8291 (tm-30) REVERT: L 20 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8216 (tm-30) REVERT: L 32 GLU cc_start: 0.8769 (tp30) cc_final: 0.8325 (tp30) REVERT: L 99 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: M 31 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8574 (tm-30) REVERT: N 58 ARG cc_start: 0.8419 (mtm110) cc_final: 0.8198 (mtt-85) REVERT: O 31 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8400 (tm-30) REVERT: O 32 GLU cc_start: 0.8818 (tp30) cc_final: 0.8440 (tp30) REVERT: O 33 GLN cc_start: 0.9015 (mt0) cc_final: 0.8725 (mt0) REVERT: O 66 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8164 (tm-30) REVERT: P 31 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8435 (tm-30) REVERT: P 66 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8133 (tm-30) REVERT: P 70 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: R 31 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8538 (tm-30) REVERT: R 32 GLU cc_start: 0.8843 (tp30) cc_final: 0.8229 (tp30) REVERT: R 99 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8271 (tm-30) REVERT: S 32 GLU cc_start: 0.8642 (tp30) cc_final: 0.7997 (tp30) REVERT: S 99 GLU cc_start: 0.8616 (pt0) cc_final: 0.8226 (tm-30) REVERT: T 31 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8503 (tm-30) REVERT: T 35 LYS cc_start: 0.9307 (tttm) cc_final: 0.9035 (tttm) REVERT: T 79 GLU cc_start: 0.8235 (tp30) cc_final: 0.7709 (tp30) REVERT: V 58 ARG cc_start: 0.8640 (mtm110) cc_final: 0.8275 (mtt-85) REVERT: V 96 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8113 (tm-30) outliers start: 47 outliers final: 29 residues processed: 400 average time/residue: 0.2572 time to fit residues: 153.5992 Evaluate side-chains 414 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 381 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain I residue 70 GLN Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain Q residue 99 GLU Chi-restraints excluded: chain R residue 99 GLU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 96 GLN Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 7.9990 chunk 159 optimal weight: 0.4980 chunk 169 optimal weight: 6.9990 chunk 102 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN C 31 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 33 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN I 103 GLN J 96 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN O 96 GLN ** S 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 HIS ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4617 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= 0.286 Angle : 0.597 9.509 21021 Z= 0.310 Chirality : 0.039 0.135 2289 Planarity : 0.004 0.038 2835 Dihedral : 3.804 15.719 2205 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.87 % Allowed : 24.66 % Favored : 72.47 % 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: -1.01 (0.20), residues: 1869 helix: -0.38 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -1.02 (0.31), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 53 HIS 0.006 0.001 HIS K 39 PHE 0.009 0.001 PHE O 37 TYR 0.005 0.001 TYR D 72 ARG 0.003 0.000 ARG C 55 *********************** 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 425 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 381 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8306 (tm-30) REVERT: B 32 GLU cc_start: 0.8749 (tp30) cc_final: 0.8415 (tp30) REVERT: C 57 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: D 31 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8421 (tm-30) REVERT: D 32 GLU cc_start: 0.8521 (tp30) cc_final: 0.7839 (tp30) REVERT: D 63 ASP cc_start: 0.8638 (m-30) cc_final: 0.8408 (m-30) REVERT: D 99 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8385 (tm-30) REVERT: E 20 GLU cc_start: 0.8650 (tp30) cc_final: 0.8367 (tm-30) REVERT: E 32 GLU cc_start: 0.8563 (tp30) cc_final: 0.8042 (tp30) REVERT: F 20 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7739 (tm-30) REVERT: G 58 ARG cc_start: 0.8559 (mtm110) cc_final: 0.8290 (mtt-85) REVERT: G 89 ASP cc_start: 0.8461 (m-30) cc_final: 0.8215 (m-30) REVERT: G 96 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7884 (tm-30) REVERT: H 27 GLU cc_start: 0.8128 (pt0) cc_final: 0.7830 (pt0) REVERT: H 31 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8358 (tm-30) REVERT: H 32 GLU cc_start: 0.8784 (tp30) cc_final: 0.8402 (tp30) REVERT: H 33 GLN cc_start: 0.9023 (mt0) cc_final: 0.8728 (mt0) REVERT: H 66 GLU cc_start: 0.8619 (tp30) cc_final: 0.8381 (tp30) REVERT: I 31 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8752 (tm-30) REVERT: J 33 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: K 31 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8432 (tm-30) REVERT: K 32 GLU cc_start: 0.8749 (tp30) cc_final: 0.8479 (tp30) REVERT: K 99 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8272 (tm-30) REVERT: L 20 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8177 (tm-30) REVERT: L 32 GLU cc_start: 0.8639 (tp30) cc_final: 0.8147 (tp30) REVERT: L 89 ASP cc_start: 0.7831 (m-30) cc_final: 0.7530 (m-30) REVERT: L 99 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: M 31 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8532 (tm-30) REVERT: M 33 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: N 58 ARG cc_start: 0.8400 (mtm110) cc_final: 0.8148 (mtt-85) REVERT: N 96 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8234 (tm-30) REVERT: O 31 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8426 (tm-30) REVERT: O 32 GLU cc_start: 0.8739 (tp30) cc_final: 0.8425 (tp30) REVERT: O 33 GLN cc_start: 0.8993 (mt0) cc_final: 0.8708 (mp10) REVERT: O 66 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8035 (tm-30) REVERT: P 31 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8421 (tm-30) REVERT: P 66 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8244 (tm-30) REVERT: R 31 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8433 (tm-30) REVERT: R 32 GLU cc_start: 0.8648 (tp30) cc_final: 0.7929 (tp30) REVERT: S 31 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8681 (tm-30) REVERT: S 32 GLU cc_start: 0.8598 (tp30) cc_final: 0.8012 (tp30) REVERT: S 99 GLU cc_start: 0.8618 (pt0) cc_final: 0.8249 (tm-30) REVERT: T 31 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8433 (tm-30) REVERT: T 35 LYS cc_start: 0.9309 (tttm) cc_final: 0.9082 (tttm) REVERT: T 79 GLU cc_start: 0.8194 (tp30) cc_final: 0.7758 (tp30) REVERT: V 58 ARG cc_start: 0.8608 (mtm110) cc_final: 0.8256 (mtt-85) REVERT: V 96 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8092 (tm-30) outliers start: 44 outliers final: 25 residues processed: 392 average time/residue: 0.2558 time to fit residues: 150.8499 Evaluate side-chains 407 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 377 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain D residue 33 GLN Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 33 GLN Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain V residue 43 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN K 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN P 70 GLN ** S 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4700 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= 0.256 Angle : 0.589 9.305 21021 Z= 0.307 Chirality : 0.038 0.132 2289 Planarity : 0.003 0.037 2835 Dihedral : 3.688 15.122 2205 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 2.41 % Allowed : 24.85 % Favored : 72.73 % 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: -0.78 (0.21), residues: 1869 helix: -0.15 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -1.04 (0.31), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 53 HIS 0.005 0.001 HIS K 39 PHE 0.009 0.001 PHE N 37 TYR 0.004 0.001 TYR T 72 ARG 0.003 0.000 ARG K 58 ********************** 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 416 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 379 time to evaluate : 1.628 Fit side-chains REVERT: B 31 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8289 (tm-30) REVERT: B 32 GLU cc_start: 0.8709 (tp30) cc_final: 0.8381 (tp30) REVERT: B 33 GLN cc_start: 0.8860 (mt0) cc_final: 0.8416 (mt0) REVERT: C 57 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: D 31 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8188 (tm-30) REVERT: D 32 GLU cc_start: 0.8475 (tp30) cc_final: 0.7661 (tp30) REVERT: D 99 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8357 (tm-30) REVERT: E 20 GLU cc_start: 0.8665 (tp30) cc_final: 0.8388 (tm-30) REVERT: E 31 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8710 (tm-30) REVERT: E 32 GLU cc_start: 0.8557 (tp30) cc_final: 0.7955 (tp30) REVERT: E 71 PHE cc_start: 0.8749 (t80) cc_final: 0.8507 (t80) REVERT: F 20 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: F 79 GLU cc_start: 0.8254 (tp30) cc_final: 0.7973 (tp30) REVERT: G 58 ARG cc_start: 0.8548 (mtm110) cc_final: 0.8293 (mtt-85) REVERT: G 75 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8148 (mm-30) REVERT: G 89 ASP cc_start: 0.8457 (m-30) cc_final: 0.8212 (m-30) REVERT: G 96 GLN cc_start: 0.8555 (tm-30) cc_final: 0.7862 (tm-30) REVERT: H 27 GLU cc_start: 0.8138 (pt0) cc_final: 0.7840 (pt0) REVERT: H 31 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8345 (tm-30) REVERT: H 32 GLU cc_start: 0.8781 (tp30) cc_final: 0.8369 (tp30) REVERT: H 33 GLN cc_start: 0.8941 (mt0) cc_final: 0.8405 (mp10) REVERT: H 66 GLU cc_start: 0.8562 (tp30) cc_final: 0.8315 (tp30) REVERT: I 31 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8725 (tm-30) REVERT: I 98 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8902 (mm-40) REVERT: J 33 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7805 (mt0) REVERT: K 31 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8441 (tm-30) REVERT: K 32 GLU cc_start: 0.8720 (tp30) cc_final: 0.8427 (tp30) REVERT: K 99 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8269 (tm-30) REVERT: L 20 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8204 (tm-30) REVERT: L 32 GLU cc_start: 0.8661 (tp30) cc_final: 0.8161 (tp30) REVERT: L 89 ASP cc_start: 0.7793 (m-30) cc_final: 0.7486 (m-30) REVERT: L 99 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: M 31 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8369 (tm-30) REVERT: M 33 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: N 58 ARG cc_start: 0.8376 (mtm110) cc_final: 0.8130 (mtt-85) REVERT: N 96 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8230 (tm-30) REVERT: O 31 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8376 (tm-30) REVERT: O 32 GLU cc_start: 0.8732 (tp30) cc_final: 0.8417 (tp30) REVERT: O 33 GLN cc_start: 0.8926 (mt0) cc_final: 0.8647 (mp10) REVERT: O 66 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8036 (tm-30) REVERT: P 31 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8406 (tm-30) REVERT: P 66 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8204 (tm-30) REVERT: R 31 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8447 (tm-30) REVERT: R 32 GLU cc_start: 0.8596 (tp30) cc_final: 0.7855 (tp30) REVERT: S 31 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8666 (tm-30) REVERT: S 32 GLU cc_start: 0.8565 (tp30) cc_final: 0.7989 (tp30) REVERT: S 99 GLU cc_start: 0.8611 (pt0) cc_final: 0.8239 (tm-30) REVERT: T 31 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8447 (tm-30) REVERT: T 35 LYS cc_start: 0.9261 (tttm) cc_final: 0.9032 (tttm) REVERT: T 79 GLU cc_start: 0.8185 (tp30) cc_final: 0.7789 (tp30) REVERT: V 58 ARG cc_start: 0.8596 (mtm110) cc_final: 0.8238 (mtt-85) REVERT: V 96 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8087 (tm-30) outliers start: 37 outliers final: 25 residues processed: 387 average time/residue: 0.2437 time to fit residues: 142.6249 Evaluate side-chains 407 residues out of total 1533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 377 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain F residue 20 GLU Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 57 GLU Chi-restraints excluded: chain J residue 33 GLN Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain L residue 99 GLU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 43 ASP Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 96 GLN Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 70 GLN Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 96 GLN Chi-restraints excluded: chain T residue 20 GLU Chi-restraints excluded: chain V residue 43 ASP 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: 5.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 0.0980 chunk 62 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN B 96 GLN C 31 GLN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN D 33 GLN ** E 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** K 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 GLN P 70 GLN ** Q 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 33 GLN ** S 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.089075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.075273 restraints weight = 34817.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.077853 restraints weight = 18105.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079521 restraints weight = 11453.790| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15645 Z= 0.250 Angle : 0.588 9.183 21021 Z= 0.307 Chirality : 0.038 0.130 2289 Planarity : 0.003 0.037 2835 Dihedral : 3.670 14.872 2205 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.67 % Allowed : 24.79 % Favored : 72.54 % 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: -0.64 (0.21), residues: 1869 helix: -0.03 (0.15), residues: 1260 sheet: None (None), residues: 0 loop : -1.04 (0.31), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 53 HIS 0.005 0.001 HIS K 39 PHE 0.009 0.001 PHE N 37 TYR 0.010 0.001 TYR P 72 ARG 0.003 0.000 ARG K 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3355.03 seconds wall clock time: 60 minutes 24.14 seconds (3624.14 seconds total)