Starting phenix.real_space_refine on Thu Jul 25 15:48:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syg_40873/07_2024/8syg_40873.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syg_40873/07_2024/8syg_40873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syg_40873/07_2024/8syg_40873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syg_40873/07_2024/8syg_40873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syg_40873/07_2024/8syg_40873.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syg_40873/07_2024/8syg_40873.cif" } resolution = 2.6 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= 0.001 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 9632 2.51 5 N 2730 2.21 5 O 2786 1.98 5 H 14714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 445": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 453": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 457": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 458": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29932 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "A" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "C" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "D" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "E" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "F" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "G" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "H" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "I" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "J" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "K" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "L" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "M" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "N" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2138 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126} Time building chain proxies: 13.94, per 1000 atoms: 0.47 Number of scatterers: 29932 At special positions: 0 Unit cell: (135.603, 133.38, 71.877, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 O 2786 8.00 N 2730 7.00 C 9632 6.00 H 14714 1.00 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: 22.50 Conformation dependent library (CDL) restraints added in 2.8 seconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 14 sheets defined 32.1% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'B' and resid 345 through 364 removed outlier: 4.068A pdb=" N GLU B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 350 " --> pdb=" O ARG B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE B 397 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 364 removed outlier: 3.765A pdb=" N ILE C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 381 through 385 Processing helix chain 'C' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR C 398 " --> pdb=" O PHE C 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 364 removed outlier: 3.763A pdb=" N ILE E 350 " --> pdb=" O ARG E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE E 397 " --> pdb=" O ASP E 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR E 398 " --> pdb=" O PHE E 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE F 350 " --> pdb=" O ARG F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 372 Processing helix chain 'F' and resid 381 through 385 Processing helix chain 'F' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE F 397 " --> pdb=" O ASP F 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 364 removed outlier: 3.765A pdb=" N ILE G 350 " --> pdb=" O ARG G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 372 Processing helix chain 'G' and resid 381 through 385 Processing helix chain 'G' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE H 350 " --> pdb=" O ARG H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 372 Processing helix chain 'H' and resid 381 through 385 Processing helix chain 'H' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE H 397 " --> pdb=" O ASP H 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE I 350 " --> pdb=" O ARG I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 372 Processing helix chain 'I' and resid 381 through 385 Processing helix chain 'I' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE I 397 " --> pdb=" O ASP I 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 364 removed outlier: 3.765A pdb=" N ILE J 350 " --> pdb=" O ARG J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 372 Processing helix chain 'J' and resid 381 through 385 Processing helix chain 'J' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE J 397 " --> pdb=" O ASP J 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR J 398 " --> pdb=" O PHE J 394 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 372 Processing helix chain 'K' and resid 381 through 385 Processing helix chain 'K' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR K 398 " --> pdb=" O PHE K 394 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE L 350 " --> pdb=" O ARG L 346 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 372 Processing helix chain 'L' and resid 381 through 385 Processing helix chain 'L' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE L 397 " --> pdb=" O ASP L 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR L 398 " --> pdb=" O PHE L 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE M 350 " --> pdb=" O ARG M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 372 Processing helix chain 'M' and resid 381 through 385 Processing helix chain 'M' and resid 392 through 402 removed outlier: 3.839A pdb=" N PHE M 397 " --> pdb=" O ASP M 393 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N TYR M 398 " --> pdb=" O PHE M 394 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 364 removed outlier: 3.764A pdb=" N ILE N 350 " --> pdb=" O ARG N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 372 Processing helix chain 'N' and resid 381 through 385 Processing helix chain 'N' and resid 392 through 402 removed outlier: 3.840A pdb=" N PHE N 397 " --> pdb=" O ASP N 393 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR N 398 " --> pdb=" O PHE N 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS B 466 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY B 376 " --> pdb=" O HIS B 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS B 468 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR B 378 " --> pdb=" O HIS B 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER B 470 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE B 380 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 458 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE B 464 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS B 456 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS B 466 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER B 426 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU B 421 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS B 428 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE B 419 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 430 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS A 466 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N GLY A 376 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS A 468 " --> pdb=" O GLY A 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR A 378 " --> pdb=" O HIS A 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER A 470 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE A 380 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 458 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE A 464 " --> pdb=" O HIS A 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS A 456 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS A 466 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER A 426 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU A 421 " --> pdb=" O SER A 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS A 428 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 419 " --> pdb=" O CYS A 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 430 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS C 466 " --> pdb=" O ASP C 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY C 376 " --> pdb=" O HIS C 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS C 468 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR C 378 " --> pdb=" O HIS C 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER C 470 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N PHE C 380 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG C 458 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE C 464 " --> pdb=" O HIS C 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS C 456 " --> pdb=" O ILE C 464 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS C 466 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER C 426 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU C 421 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS C 428 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE C 419 " --> pdb=" O CYS C 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 430 " --> pdb=" O PRO C 417 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS D 466 " --> pdb=" O ASP D 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY D 376 " --> pdb=" O HIS D 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS D 468 " --> pdb=" O GLY D 376 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N THR D 378 " --> pdb=" O HIS D 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER D 470 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE D 380 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG D 458 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE D 464 " --> pdb=" O HIS D 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS D 456 " --> pdb=" O ILE D 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS D 466 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER D 426 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU D 421 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS D 428 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE D 419 " --> pdb=" O CYS D 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA D 430 " --> pdb=" O PRO D 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS E 466 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY E 376 " --> pdb=" O HIS E 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS E 468 " --> pdb=" O GLY E 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR E 378 " --> pdb=" O HIS E 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER E 470 " --> pdb=" O THR E 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE E 380 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG E 458 " --> pdb=" O TRP E 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE E 464 " --> pdb=" O HIS E 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS E 456 " --> pdb=" O ILE E 464 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS E 466 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER E 426 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU E 421 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS E 428 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE E 419 " --> pdb=" O CYS E 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA E 430 " --> pdb=" O PRO E 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS F 466 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY F 376 " --> pdb=" O HIS F 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS F 468 " --> pdb=" O GLY F 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR F 378 " --> pdb=" O HIS F 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER F 470 " --> pdb=" O THR F 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE F 380 " --> pdb=" O SER F 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG F 458 " --> pdb=" O TRP F 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE F 464 " --> pdb=" O HIS F 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS F 456 " --> pdb=" O ILE F 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS F 466 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER F 426 " --> pdb=" O LEU F 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU F 421 " --> pdb=" O SER F 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS F 428 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE F 419 " --> pdb=" O CYS F 428 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA F 430 " --> pdb=" O PRO F 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS G 466 " --> pdb=" O ASP G 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY G 376 " --> pdb=" O HIS G 466 " (cutoff:3.500A) removed outlier: 11.978A pdb=" N HIS G 468 " --> pdb=" O GLY G 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR G 378 " --> pdb=" O HIS G 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER G 470 " --> pdb=" O THR G 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE G 380 " --> pdb=" O SER G 470 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TRP G 462 " --> pdb=" O ARG G 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG G 458 " --> pdb=" O TRP G 462 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE G 464 " --> pdb=" O HIS G 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS G 456 " --> pdb=" O ILE G 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS G 466 " --> pdb=" O VAL G 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER G 426 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU G 421 " --> pdb=" O SER G 426 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS G 428 " --> pdb=" O ILE G 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE G 419 " --> pdb=" O CYS G 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA G 430 " --> pdb=" O PRO G 417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS H 466 " --> pdb=" O ASP H 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY H 376 " --> pdb=" O HIS H 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS H 468 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR H 378 " --> pdb=" O HIS H 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER H 470 " --> pdb=" O THR H 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE H 380 " --> pdb=" O SER H 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP H 462 " --> pdb=" O ARG H 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG H 458 " --> pdb=" O TRP H 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE H 464 " --> pdb=" O HIS H 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS H 456 " --> pdb=" O ILE H 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS H 466 " --> pdb=" O VAL H 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER H 426 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU H 421 " --> pdb=" O SER H 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS H 428 " --> pdb=" O ILE H 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE H 419 " --> pdb=" O CYS H 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA H 430 " --> pdb=" O PRO H 417 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS I 466 " --> pdb=" O ASP I 374 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N GLY I 376 " --> pdb=" O HIS I 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS I 468 " --> pdb=" O GLY I 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR I 378 " --> pdb=" O HIS I 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER I 470 " --> pdb=" O THR I 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE I 380 " --> pdb=" O SER I 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP I 462 " --> pdb=" O ARG I 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG I 458 " --> pdb=" O TRP I 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE I 464 " --> pdb=" O HIS I 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS I 456 " --> pdb=" O ILE I 464 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS I 466 " --> pdb=" O VAL I 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER I 426 " --> pdb=" O LEU I 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU I 421 " --> pdb=" O SER I 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS I 428 " --> pdb=" O ILE I 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE I 419 " --> pdb=" O CYS I 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA I 430 " --> pdb=" O PRO I 417 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS J 466 " --> pdb=" O ASP J 374 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N GLY J 376 " --> pdb=" O HIS J 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS J 468 " --> pdb=" O GLY J 376 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N THR J 378 " --> pdb=" O HIS J 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER J 470 " --> pdb=" O THR J 378 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N PHE J 380 " --> pdb=" O SER J 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP J 462 " --> pdb=" O ARG J 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG J 458 " --> pdb=" O TRP J 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE J 464 " --> pdb=" O HIS J 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS J 456 " --> pdb=" O ILE J 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS J 466 " --> pdb=" O VAL J 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER J 426 " --> pdb=" O LEU J 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU J 421 " --> pdb=" O SER J 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS J 428 " --> pdb=" O ILE J 419 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE J 419 " --> pdb=" O CYS J 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA J 430 " --> pdb=" O PRO J 417 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS K 466 " --> pdb=" O ASP K 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY K 376 " --> pdb=" O HIS K 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS K 468 " --> pdb=" O GLY K 376 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N THR K 378 " --> pdb=" O HIS K 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER K 470 " --> pdb=" O THR K 378 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N PHE K 380 " --> pdb=" O SER K 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP K 462 " --> pdb=" O ARG K 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG K 458 " --> pdb=" O TRP K 462 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE K 464 " --> pdb=" O HIS K 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS K 456 " --> pdb=" O ILE K 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS K 466 " --> pdb=" O VAL K 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER K 426 " --> pdb=" O LEU K 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU K 421 " --> pdb=" O SER K 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS K 428 " --> pdb=" O ILE K 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE K 419 " --> pdb=" O CYS K 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA K 430 " --> pdb=" O PRO K 417 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS L 466 " --> pdb=" O ASP L 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY L 376 " --> pdb=" O HIS L 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS L 468 " --> pdb=" O GLY L 376 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N THR L 378 " --> pdb=" O HIS L 468 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N SER L 470 " --> pdb=" O THR L 378 " (cutoff:3.500A) removed outlier: 10.993A pdb=" N PHE L 380 " --> pdb=" O SER L 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP L 462 " --> pdb=" O ARG L 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG L 458 " --> pdb=" O TRP L 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE L 464 " --> pdb=" O HIS L 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS L 456 " --> pdb=" O ILE L 464 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS L 466 " --> pdb=" O VAL L 454 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER L 426 " --> pdb=" O LEU L 421 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU L 421 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS L 428 " --> pdb=" O ILE L 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE L 419 " --> pdb=" O CYS L 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA L 430 " --> pdb=" O PRO L 417 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS M 466 " --> pdb=" O ASP M 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY M 376 " --> pdb=" O HIS M 466 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N HIS M 468 " --> pdb=" O GLY M 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR M 378 " --> pdb=" O HIS M 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER M 470 " --> pdb=" O THR M 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE M 380 " --> pdb=" O SER M 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP M 462 " --> pdb=" O ARG M 458 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG M 458 " --> pdb=" O TRP M 462 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE M 464 " --> pdb=" O HIS M 456 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N HIS M 456 " --> pdb=" O ILE M 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS M 466 " --> pdb=" O VAL M 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER M 426 " --> pdb=" O LEU M 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU M 421 " --> pdb=" O SER M 426 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS M 428 " --> pdb=" O ILE M 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE M 419 " --> pdb=" O CYS M 428 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA M 430 " --> pdb=" O PRO M 417 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 389 through 390 removed outlier: 7.473A pdb=" N HIS N 466 " --> pdb=" O ASP N 374 " (cutoff:3.500A) removed outlier: 11.048A pdb=" N GLY N 376 " --> pdb=" O HIS N 466 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N HIS N 468 " --> pdb=" O GLY N 376 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N THR N 378 " --> pdb=" O HIS N 468 " (cutoff:3.500A) removed outlier: 12.004A pdb=" N SER N 470 " --> pdb=" O THR N 378 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N PHE N 380 " --> pdb=" O SER N 470 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP N 462 " --> pdb=" O ARG N 458 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG N 458 " --> pdb=" O TRP N 462 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE N 464 " --> pdb=" O HIS N 456 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS N 456 " --> pdb=" O ILE N 464 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS N 466 " --> pdb=" O VAL N 454 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER N 426 " --> pdb=" O LEU N 421 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU N 421 " --> pdb=" O SER N 426 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS N 428 " --> pdb=" O ILE N 419 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE N 419 " --> pdb=" O CYS N 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA N 430 " --> pdb=" O PRO N 417 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2016 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: 11.82 Time building geometry restraints manager: 23.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 14686 1.12 - 1.30: 2559 1.30 - 1.47: 5381 1.47 - 1.64: 7614 1.64 - 1.81: 112 Bond restraints: 30352 Sorted by residual: bond pdb=" N THR L 413 " pdb=" H THR L 413 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" ND2 ASN J 406 " pdb="HD21 ASN J 406 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N GLU C 349 " pdb=" H GLU C 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NE2 HIS J 411 " pdb=" HE2 HIS J 411 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" ND2 ASN G 406 " pdb="HD21 ASN G 406 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 ... (remaining 30347 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.47: 308 104.47 - 112.14: 32213 112.14 - 119.81: 11821 119.81 - 127.48: 10072 127.48 - 135.15: 228 Bond angle restraints: 54642 Sorted by residual: angle pdb=" CA HIS G 468 " pdb=" CB HIS G 468 " pdb=" CG HIS G 468 " ideal model delta sigma weight residual 113.80 119.31 -5.51 1.00e+00 1.00e+00 3.04e+01 angle pdb=" CA HIS I 468 " pdb=" CB HIS I 468 " pdb=" CG HIS I 468 " ideal model delta sigma weight residual 113.80 119.30 -5.50 1.00e+00 1.00e+00 3.03e+01 angle pdb=" CA HIS L 468 " pdb=" CB HIS L 468 " pdb=" CG HIS L 468 " ideal model delta sigma weight residual 113.80 119.29 -5.49 1.00e+00 1.00e+00 3.01e+01 angle pdb=" CA HIS D 468 " pdb=" CB HIS D 468 " pdb=" CG HIS D 468 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" CA HIS K 468 " pdb=" CB HIS K 468 " pdb=" CG HIS K 468 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 ... (remaining 54637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 12824 14.25 - 28.51: 896 28.51 - 42.76: 280 42.76 - 57.02: 154 57.02 - 71.27: 196 Dihedral angle restraints: 14350 sinusoidal: 7686 harmonic: 6664 Sorted by residual: dihedral pdb=" CA GLU G 425 " pdb=" C GLU G 425 " pdb=" N SER G 426 " pdb=" CA SER G 426 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU I 425 " pdb=" C GLU I 425 " pdb=" N SER I 426 " pdb=" CA SER I 426 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU B 425 " pdb=" C GLU B 425 " pdb=" N SER B 426 " pdb=" CA SER B 426 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 14347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 932 0.046 - 0.093: 764 0.093 - 0.139: 356 0.139 - 0.186: 132 0.186 - 0.232: 56 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA PHE I 467 " pdb=" N PHE I 467 " pdb=" C PHE I 467 " pdb=" CB PHE I 467 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PHE J 467 " pdb=" N PHE J 467 " pdb=" C PHE J 467 " pdb=" CB PHE J 467 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PHE A 467 " pdb=" N PHE A 467 " pdb=" C PHE A 467 " pdb=" CB PHE A 467 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2237 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 469 " 0.288 9.50e-02 1.11e+02 1.32e-01 1.96e+02 pdb=" NE ARG N 469 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG N 469 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG N 469 " 0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG N 469 " -0.018 2.00e-02 2.50e+03 pdb="HH11 ARG N 469 " -0.203 2.00e-02 2.50e+03 pdb="HH12 ARG N 469 " 0.130 2.00e-02 2.50e+03 pdb="HH21 ARG N 469 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG N 469 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 469 " -0.288 9.50e-02 1.11e+02 1.32e-01 1.95e+02 pdb=" NE ARG K 469 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG K 469 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG K 469 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG K 469 " 0.019 2.00e-02 2.50e+03 pdb="HH11 ARG K 469 " 0.203 2.00e-02 2.50e+03 pdb="HH12 ARG K 469 " -0.130 2.00e-02 2.50e+03 pdb="HH21 ARG K 469 " 0.043 2.00e-02 2.50e+03 pdb="HH22 ARG K 469 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 469 " -0.289 9.50e-02 1.11e+02 1.32e-01 1.95e+02 pdb=" NE ARG J 469 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG J 469 " -0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG J 469 " -0.072 2.00e-02 2.50e+03 pdb=" NH2 ARG J 469 " 0.019 2.00e-02 2.50e+03 pdb="HH11 ARG J 469 " 0.203 2.00e-02 2.50e+03 pdb="HH12 ARG J 469 " -0.130 2.00e-02 2.50e+03 pdb="HH21 ARG J 469 " 0.044 2.00e-02 2.50e+03 pdb="HH22 ARG J 469 " 0.056 2.00e-02 2.50e+03 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2702 2.23 - 2.82: 54871 2.82 - 3.42: 81798 3.42 - 4.01: 110980 4.01 - 4.60: 161929 Nonbonded interactions: 412280 Sorted by model distance: nonbonded pdb=" HH TYR J 431 " pdb=" OE1 GLU J 451 " model vdw 1.641 1.850 nonbonded pdb=" HH TYR E 431 " pdb=" OE1 GLU E 451 " model vdw 1.642 1.850 nonbonded pdb=" HH TYR L 431 " pdb=" OE1 GLU L 451 " model vdw 1.642 1.850 nonbonded pdb=" HH TYR K 431 " pdb=" OE1 GLU K 451 " model vdw 1.642 1.850 nonbonded pdb=" HH TYR F 431 " pdb=" OE1 GLU F 451 " model vdw 1.642 1.850 ... (remaining 412275 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' } 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 individual isotropic 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: 4.100 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: 0.430 Extract box with map and model: 1.040 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 95.220 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.140 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.013 0.037 15638 Z= 0.865 Angle : 1.786 6.818 21210 Z= 1.230 Chirality : 0.082 0.232 2240 Planarity : 0.016 0.092 2772 Dihedral : 12.962 71.272 5740 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1848 helix: -1.28 (0.19), residues: 518 sheet: 3.90 (0.19), residues: 574 loop : 0.08 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.014 TRP A 403 HIS 0.016 0.004 HIS A 456 PHE 0.030 0.011 PHE E 394 TYR 0.127 0.034 TYR C 398 ARG 0.008 0.002 ARG D 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 2.352 Fit side-chains REVERT: B 352 LYS cc_start: 0.7860 (tttt) cc_final: 0.7575 (ttpt) REVERT: B 353 VAL cc_start: 0.8279 (p) cc_final: 0.7937 (m) REVERT: B 359 GLU cc_start: 0.8330 (tt0) cc_final: 0.8079 (tt0) REVERT: B 396 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7976 (ttm-80) REVERT: B 425 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7727 (mm-30) REVERT: A 352 LYS cc_start: 0.7993 (tttt) cc_final: 0.7636 (ttpt) REVERT: A 353 VAL cc_start: 0.8328 (p) cc_final: 0.8047 (m) REVERT: A 359 GLU cc_start: 0.8139 (tt0) cc_final: 0.7902 (tt0) REVERT: A 396 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7938 (ttm170) REVERT: A 398 TYR cc_start: 0.8091 (m-80) cc_final: 0.7871 (m-80) REVERT: A 425 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7745 (mm-30) REVERT: C 352 LYS cc_start: 0.7920 (tttt) cc_final: 0.7583 (ttpt) REVERT: C 353 VAL cc_start: 0.8267 (p) cc_final: 0.8006 (m) REVERT: C 359 GLU cc_start: 0.8278 (tt0) cc_final: 0.7996 (tt0) REVERT: C 396 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.8003 (ttm170) REVERT: C 398 TYR cc_start: 0.8138 (m-80) cc_final: 0.7899 (m-80) REVERT: C 425 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7741 (mm-30) REVERT: D 352 LYS cc_start: 0.7971 (tttt) cc_final: 0.7696 (tmmt) REVERT: D 353 VAL cc_start: 0.8303 (p) cc_final: 0.7992 (m) REVERT: D 359 GLU cc_start: 0.8219 (tt0) cc_final: 0.7982 (tt0) REVERT: D 396 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7958 (ttp-170) REVERT: D 425 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7842 (mm-30) REVERT: E 352 LYS cc_start: 0.7941 (tttt) cc_final: 0.7647 (ttpt) REVERT: E 353 VAL cc_start: 0.8244 (p) cc_final: 0.7977 (m) REVERT: E 359 GLU cc_start: 0.8357 (tt0) cc_final: 0.8085 (tt0) REVERT: E 396 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7965 (ttm-80) REVERT: E 398 TYR cc_start: 0.8149 (m-80) cc_final: 0.7910 (m-80) REVERT: E 425 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7895 (mm-30) REVERT: F 352 LYS cc_start: 0.7969 (tttt) cc_final: 0.7746 (ttpt) REVERT: F 353 VAL cc_start: 0.8132 (p) cc_final: 0.7842 (m) REVERT: F 359 GLU cc_start: 0.8210 (tt0) cc_final: 0.7947 (tt0) REVERT: F 396 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7947 (ttm-80) REVERT: F 425 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7808 (mm-30) REVERT: G 353 VAL cc_start: 0.8217 (p) cc_final: 0.7952 (m) REVERT: G 396 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7919 (ttm170) REVERT: G 425 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7775 (mm-30) REVERT: H 352 LYS cc_start: 0.7805 (tttt) cc_final: 0.7532 (ttpt) REVERT: H 353 VAL cc_start: 0.8279 (p) cc_final: 0.7943 (m) REVERT: H 359 GLU cc_start: 0.8350 (tt0) cc_final: 0.8100 (tt0) REVERT: H 396 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.8000 (ttm-80) REVERT: H 425 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7753 (mm-30) REVERT: I 352 LYS cc_start: 0.7947 (tttt) cc_final: 0.7634 (ttpt) REVERT: I 353 VAL cc_start: 0.8229 (p) cc_final: 0.7949 (m) REVERT: I 359 GLU cc_start: 0.8176 (tt0) cc_final: 0.7949 (tt0) REVERT: I 396 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7941 (ttm170) REVERT: I 398 TYR cc_start: 0.8081 (m-80) cc_final: 0.7838 (m-80) REVERT: I 425 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7758 (mm-30) REVERT: J 352 LYS cc_start: 0.8004 (tttt) cc_final: 0.7675 (ttpt) REVERT: J 353 VAL cc_start: 0.8229 (p) cc_final: 0.7972 (m) REVERT: J 359 GLU cc_start: 0.8316 (tt0) cc_final: 0.8053 (tt0) REVERT: J 396 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7954 (ttm170) REVERT: J 398 TYR cc_start: 0.8156 (m-80) cc_final: 0.7908 (m-80) REVERT: J 425 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7734 (mm-30) REVERT: K 352 LYS cc_start: 0.7995 (tttt) cc_final: 0.7711 (tmmt) REVERT: K 353 VAL cc_start: 0.8290 (p) cc_final: 0.7984 (m) REVERT: K 359 GLU cc_start: 0.8241 (tt0) cc_final: 0.8012 (tt0) REVERT: K 396 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7996 (ttp-170) REVERT: K 398 TYR cc_start: 0.8109 (m-80) cc_final: 0.7906 (m-80) REVERT: K 425 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7826 (mm-30) REVERT: L 352 LYS cc_start: 0.7938 (tttt) cc_final: 0.7638 (ttpt) REVERT: L 353 VAL cc_start: 0.8181 (p) cc_final: 0.7953 (m) REVERT: L 359 GLU cc_start: 0.8236 (tt0) cc_final: 0.7970 (tt0) REVERT: L 396 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7934 (ttm-80) REVERT: L 398 TYR cc_start: 0.8149 (m-80) cc_final: 0.7915 (m-80) REVERT: L 425 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7750 (mm-30) REVERT: M 352 LYS cc_start: 0.7972 (tttt) cc_final: 0.7607 (tmmt) REVERT: M 353 VAL cc_start: 0.8392 (p) cc_final: 0.8043 (m) REVERT: M 359 GLU cc_start: 0.8205 (tt0) cc_final: 0.7936 (tt0) REVERT: M 396 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.8086 (ttm170) REVERT: M 425 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7775 (mm-30) REVERT: N 352 LYS cc_start: 0.7824 (tttt) cc_final: 0.7605 (ttpt) REVERT: N 353 VAL cc_start: 0.8240 (p) cc_final: 0.7954 (m) REVERT: N 396 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7899 (ttm170) REVERT: N 425 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7798 (mm-30) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 3.5785 time to fit residues: 1429.2783 Evaluate side-chains 314 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15638 Z= 0.217 Angle : 0.608 4.769 21210 Z= 0.341 Chirality : 0.043 0.126 2240 Planarity : 0.006 0.032 2772 Dihedral : 5.514 20.412 2058 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.59 % Allowed : 7.94 % Favored : 90.48 % 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: 2.15 (0.21), residues: 1848 helix: 0.27 (0.24), residues: 532 sheet: 3.08 (0.19), residues: 686 loop : 0.61 (0.28), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 455 HIS 0.004 0.001 HIS I 478 PHE 0.013 0.002 PHE K 467 TYR 0.009 0.002 TYR H 398 ARG 0.004 0.001 ARG I 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 340 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 VAL cc_start: 0.5070 (t) cc_final: 0.4043 (p) REVERT: B 352 LYS cc_start: 0.7917 (tttt) cc_final: 0.7674 (ttpt) REVERT: B 353 VAL cc_start: 0.8108 (p) cc_final: 0.7841 (m) REVERT: A 345 VAL cc_start: 0.5288 (t) cc_final: 0.4176 (p) REVERT: A 352 LYS cc_start: 0.7901 (tttt) cc_final: 0.7659 (ttpt) REVERT: A 353 VAL cc_start: 0.8074 (p) cc_final: 0.7857 (m) REVERT: A 396 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7912 (ttm-80) REVERT: C 345 VAL cc_start: 0.5087 (t) cc_final: 0.4074 (p) REVERT: C 352 LYS cc_start: 0.7851 (tttt) cc_final: 0.7543 (ttpt) REVERT: C 464 ILE cc_start: 0.8261 (mp) cc_final: 0.8030 (tt) REVERT: D 345 VAL cc_start: 0.5053 (t) cc_final: 0.3952 (p) REVERT: D 352 LYS cc_start: 0.7957 (tttt) cc_final: 0.7754 (ttpp) REVERT: D 353 VAL cc_start: 0.8125 (p) cc_final: 0.7904 (m) REVERT: D 396 ARG cc_start: 0.8122 (ttm-80) cc_final: 0.7817 (ttm-80) REVERT: E 345 VAL cc_start: 0.5216 (t) cc_final: 0.4194 (p) REVERT: E 349 GLU cc_start: 0.7891 (tt0) cc_final: 0.7498 (tt0) REVERT: E 352 LYS cc_start: 0.7911 (tttt) cc_final: 0.7602 (ttpp) REVERT: E 353 VAL cc_start: 0.8119 (p) cc_final: 0.7901 (m) REVERT: E 396 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7951 (ttm-80) REVERT: E 398 TYR cc_start: 0.8061 (m-80) cc_final: 0.7734 (m-80) REVERT: F 345 VAL cc_start: 0.5142 (t) cc_final: 0.4259 (p) REVERT: F 353 VAL cc_start: 0.7971 (p) cc_final: 0.7770 (m) REVERT: F 396 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7937 (ttm-80) REVERT: G 353 VAL cc_start: 0.8012 (p) cc_final: 0.7779 (m) REVERT: H 345 VAL cc_start: 0.5083 (t) cc_final: 0.4075 (p) REVERT: H 352 LYS cc_start: 0.7866 (tttt) cc_final: 0.7620 (ttpt) REVERT: H 353 VAL cc_start: 0.8119 (p) cc_final: 0.7847 (m) REVERT: H 425 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7815 (mm-30) REVERT: I 345 VAL cc_start: 0.5404 (t) cc_final: 0.4438 (p) REVERT: I 352 LYS cc_start: 0.7899 (tttt) cc_final: 0.7668 (ttpt) REVERT: I 353 VAL cc_start: 0.8069 (p) cc_final: 0.7853 (m) REVERT: I 396 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7925 (ttm-80) REVERT: J 345 VAL cc_start: 0.5145 (t) cc_final: 0.4147 (p) REVERT: J 349 GLU cc_start: 0.7770 (tt0) cc_final: 0.7502 (tt0) REVERT: J 352 LYS cc_start: 0.7926 (tttt) cc_final: 0.7636 (ttpt) REVERT: J 396 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7893 (ttm170) REVERT: J 464 ILE cc_start: 0.8316 (mp) cc_final: 0.8090 (tt) REVERT: K 345 VAL cc_start: 0.5131 (t) cc_final: 0.4031 (p) REVERT: K 352 LYS cc_start: 0.7974 (tttt) cc_final: 0.7769 (ttpp) REVERT: K 353 VAL cc_start: 0.8060 (p) cc_final: 0.7838 (m) REVERT: K 396 ARG cc_start: 0.8183 (ttm-80) cc_final: 0.7883 (ttm-80) REVERT: K 398 TYR cc_start: 0.7932 (m-80) cc_final: 0.7607 (m-80) REVERT: L 345 VAL cc_start: 0.5137 (t) cc_final: 0.4139 (p) REVERT: L 352 LYS cc_start: 0.7894 (tttt) cc_final: 0.7606 (ttpp) REVERT: L 396 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7935 (ttm-80) REVERT: L 398 TYR cc_start: 0.8051 (m-80) cc_final: 0.7731 (m-80) REVERT: M 352 LYS cc_start: 0.7940 (tttt) cc_final: 0.7729 (ttpt) REVERT: M 353 VAL cc_start: 0.8177 (p) cc_final: 0.7931 (m) REVERT: M 396 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.8042 (ttm-80) REVERT: M 425 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7745 (mm-30) REVERT: N 353 VAL cc_start: 0.8028 (p) cc_final: 0.7795 (m) REVERT: N 396 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7945 (ttm-80) outliers start: 26 outliers final: 3 residues processed: 354 average time/residue: 3.6247 time to fit residues: 1386.5533 Evaluate side-chains 312 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 309 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 402 LEU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain K residue 402 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15638 Z= 0.205 Angle : 0.552 4.355 21210 Z= 0.303 Chirality : 0.045 0.126 2240 Planarity : 0.006 0.061 2772 Dihedral : 4.887 17.396 2058 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.89 % Allowed : 10.44 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.21), residues: 1848 helix: 0.71 (0.24), residues: 518 sheet: 3.12 (0.19), residues: 686 loop : 0.30 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 455 HIS 0.004 0.001 HIS N 395 PHE 0.015 0.002 PHE J 467 TYR 0.007 0.002 TYR A 398 ARG 0.007 0.001 ARG N 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 348 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 VAL cc_start: 0.5690 (t) cc_final: 0.4685 (p) REVERT: B 352 LYS cc_start: 0.7921 (tttt) cc_final: 0.7688 (ttpp) REVERT: B 353 VAL cc_start: 0.8026 (p) cc_final: 0.7802 (m) REVERT: A 345 VAL cc_start: 0.5359 (t) cc_final: 0.4257 (p) REVERT: A 352 LYS cc_start: 0.7870 (tttt) cc_final: 0.7622 (ttpt) REVERT: C 345 VAL cc_start: 0.5366 (t) cc_final: 0.4362 (p) REVERT: C 352 LYS cc_start: 0.7793 (tttt) cc_final: 0.7511 (ttpp) REVERT: D 345 VAL cc_start: 0.5176 (t) cc_final: 0.4082 (p) REVERT: D 349 GLU cc_start: 0.8015 (tt0) cc_final: 0.7624 (tt0) REVERT: D 352 LYS cc_start: 0.7973 (tttt) cc_final: 0.7660 (tmmt) REVERT: D 353 VAL cc_start: 0.8071 (p) cc_final: 0.7857 (m) REVERT: D 396 ARG cc_start: 0.8111 (ttm-80) cc_final: 0.7835 (ttm-80) REVERT: D 451 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8925 (mt-10) REVERT: E 345 VAL cc_start: 0.5424 (t) cc_final: 0.4409 (p) REVERT: E 352 LYS cc_start: 0.7909 (tttt) cc_final: 0.7584 (ttpt) REVERT: E 396 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7982 (ttm-80) REVERT: E 398 TYR cc_start: 0.8047 (m-80) cc_final: 0.7819 (m-80) REVERT: F 345 VAL cc_start: 0.5358 (t) cc_final: 0.4443 (p) REVERT: F 396 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7944 (ttm170) REVERT: G 345 VAL cc_start: 0.5358 (t) cc_final: 0.4411 (p) REVERT: G 349 GLU cc_start: 0.7837 (tt0) cc_final: 0.7511 (tt0) REVERT: G 353 VAL cc_start: 0.8021 (p) cc_final: 0.7800 (m) REVERT: H 345 VAL cc_start: 0.5717 (t) cc_final: 0.4727 (p) REVERT: H 352 LYS cc_start: 0.7870 (tttt) cc_final: 0.7638 (ttpp) REVERT: H 353 VAL cc_start: 0.8039 (p) cc_final: 0.7807 (m) REVERT: I 345 VAL cc_start: 0.5471 (t) cc_final: 0.4506 (p) REVERT: I 352 LYS cc_start: 0.7869 (tttt) cc_final: 0.7636 (ttpt) REVERT: J 345 VAL cc_start: 0.5410 (t) cc_final: 0.4419 (p) REVERT: J 349 GLU cc_start: 0.7856 (tt0) cc_final: 0.7622 (tt0) REVERT: J 352 LYS cc_start: 0.7861 (tttt) cc_final: 0.7594 (ttpp) REVERT: K 345 VAL cc_start: 0.5267 (t) cc_final: 0.4186 (p) REVERT: K 349 GLU cc_start: 0.7938 (tt0) cc_final: 0.7613 (tt0) REVERT: K 352 LYS cc_start: 0.7986 (tttt) cc_final: 0.7678 (tmmt) REVERT: K 353 VAL cc_start: 0.8055 (p) cc_final: 0.7854 (m) REVERT: K 396 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7894 (ttm-80) REVERT: K 398 TYR cc_start: 0.7962 (m-80) cc_final: 0.7650 (m-80) REVERT: K 451 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8927 (mt-10) REVERT: L 345 VAL cc_start: 0.5338 (t) cc_final: 0.4379 (p) REVERT: L 352 LYS cc_start: 0.7874 (tttt) cc_final: 0.7548 (ttpt) REVERT: L 396 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7958 (ttm-80) REVERT: L 398 TYR cc_start: 0.8035 (m-80) cc_final: 0.7819 (m-80) REVERT: M 345 VAL cc_start: 0.5302 (t) cc_final: 0.4198 (p) REVERT: M 352 LYS cc_start: 0.7917 (tttt) cc_final: 0.7677 (ttpt) REVERT: M 353 VAL cc_start: 0.8100 (p) cc_final: 0.7895 (m) REVERT: M 425 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7688 (mm-30) REVERT: N 345 VAL cc_start: 0.5266 (t) cc_final: 0.4292 (p) REVERT: N 353 VAL cc_start: 0.8007 (p) cc_final: 0.7761 (m) outliers start: 31 outliers final: 14 residues processed: 352 average time/residue: 3.5938 time to fit residues: 1361.5687 Evaluate side-chains 349 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 333 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain H residue 355 GLU Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 355 GLU Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15638 Z= 0.161 Angle : 0.500 4.353 21210 Z= 0.273 Chirality : 0.043 0.127 2240 Planarity : 0.005 0.068 2772 Dihedral : 4.595 17.515 2058 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.83 % Allowed : 10.93 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.21), residues: 1848 helix: 0.84 (0.24), residues: 518 sheet: 2.79 (0.20), residues: 714 loop : 0.49 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 455 HIS 0.003 0.001 HIS G 395 PHE 0.012 0.001 PHE D 467 TYR 0.006 0.001 TYR J 398 ARG 0.006 0.001 ARG C 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 332 time to evaluate : 2.404 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: B 345 VAL cc_start: 0.5590 (t) cc_final: 0.4598 (p) REVERT: B 349 GLU cc_start: 0.7919 (tt0) cc_final: 0.7555 (tt0) REVERT: B 352 LYS cc_start: 0.7898 (tttt) cc_final: 0.7683 (ttpp) REVERT: A 345 VAL cc_start: 0.5558 (t) cc_final: 0.4442 (p) REVERT: A 352 LYS cc_start: 0.7729 (tttt) cc_final: 0.7479 (ttpt) REVERT: C 345 VAL cc_start: 0.5457 (t) cc_final: 0.4469 (p) REVERT: C 352 LYS cc_start: 0.7776 (tttt) cc_final: 0.7488 (ttpp) REVERT: D 345 VAL cc_start: 0.5279 (t) cc_final: 0.4183 (p) REVERT: D 349 GLU cc_start: 0.8016 (tt0) cc_final: 0.7634 (tt0) REVERT: D 352 LYS cc_start: 0.7951 (tttt) cc_final: 0.7648 (tmmt) REVERT: D 396 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7857 (ttm-80) REVERT: D 451 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8928 (mt-10) REVERT: E 345 VAL cc_start: 0.5535 (t) cc_final: 0.4514 (p) REVERT: E 352 LYS cc_start: 0.7845 (tttt) cc_final: 0.7537 (ttpt) REVERT: F 345 VAL cc_start: 0.5436 (t) cc_final: 0.4518 (p) REVERT: G 345 VAL cc_start: 0.5492 (t) cc_final: 0.4548 (p) REVERT: G 353 VAL cc_start: 0.7993 (p) cc_final: 0.7789 (m) REVERT: H 345 VAL cc_start: 0.5619 (t) cc_final: 0.4641 (p) REVERT: H 349 GLU cc_start: 0.7948 (tt0) cc_final: 0.7552 (tt0) REVERT: H 352 LYS cc_start: 0.7846 (tttt) cc_final: 0.7630 (ttpp) REVERT: H 353 VAL cc_start: 0.8036 (p) cc_final: 0.7828 (m) REVERT: I 345 VAL cc_start: 0.5678 (t) cc_final: 0.4716 (p) REVERT: I 352 LYS cc_start: 0.7741 (tttt) cc_final: 0.7514 (ttpt) REVERT: J 345 VAL cc_start: 0.5525 (t) cc_final: 0.4546 (p) REVERT: J 349 GLU cc_start: 0.7863 (tt0) cc_final: 0.7622 (tt0) REVERT: J 352 LYS cc_start: 0.7809 (tttt) cc_final: 0.7537 (ttpp) REVERT: K 345 VAL cc_start: 0.5368 (t) cc_final: 0.4282 (p) REVERT: K 349 GLU cc_start: 0.7929 (tt0) cc_final: 0.7617 (tt0) REVERT: K 352 LYS cc_start: 0.7960 (tttt) cc_final: 0.7662 (tmmt) REVERT: K 396 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7891 (ttm-80) REVERT: K 398 TYR cc_start: 0.7877 (m-80) cc_final: 0.7596 (m-80) REVERT: K 451 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.8919 (mt-10) REVERT: L 345 VAL cc_start: 0.5423 (t) cc_final: 0.4458 (p) REVERT: L 352 LYS cc_start: 0.7844 (tttt) cc_final: 0.7529 (ttpt) REVERT: L 396 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7954 (ttm-80) REVERT: M 345 VAL cc_start: 0.5389 (t) cc_final: 0.4285 (p) REVERT: M 352 LYS cc_start: 0.7887 (tttt) cc_final: 0.7651 (ttpt) REVERT: N 345 VAL cc_start: 0.5421 (t) cc_final: 0.4446 (p) REVERT: N 353 VAL cc_start: 0.8001 (p) cc_final: 0.7791 (m) outliers start: 30 outliers final: 16 residues processed: 343 average time/residue: 3.6443 time to fit residues: 1343.6324 Evaluate side-chains 343 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 325 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 396 ARG Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 396 ARG Chi-restraints excluded: chain N residue 424 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 0.0170 chunk 150 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15638 Z= 0.178 Angle : 0.505 4.635 21210 Z= 0.275 Chirality : 0.043 0.128 2240 Planarity : 0.005 0.046 2772 Dihedral : 4.458 17.327 2058 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.89 % Allowed : 11.72 % Favored : 86.39 % 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: 2.21 (0.21), residues: 1848 helix: 0.88 (0.23), residues: 518 sheet: 2.79 (0.20), residues: 714 loop : 0.39 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 455 HIS 0.003 0.001 HIS I 395 PHE 0.013 0.002 PHE C 467 TYR 0.006 0.002 TYR J 398 ARG 0.005 0.001 ARG N 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 335 time to evaluate : 2.282 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: B 345 VAL cc_start: 0.5558 (t) cc_final: 0.4609 (p) REVERT: B 352 LYS cc_start: 0.7810 (tttt) cc_final: 0.7603 (ttpp) REVERT: A 345 VAL cc_start: 0.5637 (t) cc_final: 0.4535 (p) REVERT: A 352 LYS cc_start: 0.7747 (tttt) cc_final: 0.7527 (ttpt) REVERT: C 345 VAL cc_start: 0.5614 (t) cc_final: 0.4625 (p) REVERT: C 352 LYS cc_start: 0.7748 (tttt) cc_final: 0.7467 (ttpp) REVERT: D 345 VAL cc_start: 0.5327 (t) cc_final: 0.4238 (p) REVERT: D 349 GLU cc_start: 0.7988 (tt0) cc_final: 0.7669 (tt0) REVERT: D 396 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7850 (ttm-80) REVERT: D 451 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8933 (mt-10) REVERT: E 345 VAL cc_start: 0.5544 (t) cc_final: 0.4502 (p) REVERT: E 349 GLU cc_start: 0.7894 (tt0) cc_final: 0.7557 (tt0) REVERT: E 352 LYS cc_start: 0.7815 (tttt) cc_final: 0.7511 (ttpt) REVERT: F 345 VAL cc_start: 0.5476 (t) cc_final: 0.4564 (p) REVERT: G 345 VAL cc_start: 0.5468 (t) cc_final: 0.4550 (p) REVERT: H 345 VAL cc_start: 0.5584 (t) cc_final: 0.4643 (p) REVERT: H 352 LYS cc_start: 0.7817 (tttt) cc_final: 0.7599 (ttpp) REVERT: H 353 VAL cc_start: 0.8048 (p) cc_final: 0.7842 (m) REVERT: I 345 VAL cc_start: 0.5737 (t) cc_final: 0.4785 (p) REVERT: I 352 LYS cc_start: 0.7758 (tttt) cc_final: 0.7554 (ttpt) REVERT: J 345 VAL cc_start: 0.5698 (t) cc_final: 0.4722 (p) REVERT: J 352 LYS cc_start: 0.7816 (tttt) cc_final: 0.7552 (ttpp) REVERT: K 345 VAL cc_start: 0.5499 (t) cc_final: 0.4442 (p) REVERT: K 349 GLU cc_start: 0.7896 (tt0) cc_final: 0.7641 (tt0) REVERT: K 396 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7907 (ttm-80) REVERT: K 398 TYR cc_start: 0.7877 (m-80) cc_final: 0.7596 (m-80) REVERT: K 451 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8936 (mt-10) REVERT: L 345 VAL cc_start: 0.5386 (t) cc_final: 0.4413 (p) REVERT: L 352 LYS cc_start: 0.7813 (tttt) cc_final: 0.7494 (ttpt) REVERT: M 345 VAL cc_start: 0.5468 (t) cc_final: 0.4371 (p) REVERT: M 349 GLU cc_start: 0.7861 (tt0) cc_final: 0.7637 (tt0) REVERT: M 352 LYS cc_start: 0.7866 (tttt) cc_final: 0.7645 (ttpt) REVERT: M 381 GLU cc_start: 0.8857 (pt0) cc_final: 0.8655 (pt0) REVERT: N 345 VAL cc_start: 0.5408 (t) cc_final: 0.4459 (p) REVERT: N 353 VAL cc_start: 0.7995 (p) cc_final: 0.7780 (m) outliers start: 31 outliers final: 16 residues processed: 342 average time/residue: 3.7690 time to fit residues: 1387.3022 Evaluate side-chains 352 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 334 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 396 ARG Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 396 ARG Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 424 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15638 Z= 0.145 Angle : 0.474 4.553 21210 Z= 0.255 Chirality : 0.043 0.126 2240 Planarity : 0.005 0.049 2772 Dihedral : 4.286 17.398 2058 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.10 % Allowed : 12.45 % Favored : 86.45 % 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: 2.30 (0.21), residues: 1848 helix: 1.00 (0.23), residues: 518 sheet: 2.81 (0.20), residues: 714 loop : 0.43 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 455 HIS 0.002 0.001 HIS H 468 PHE 0.011 0.001 PHE J 467 TYR 0.005 0.001 TYR J 398 ARG 0.007 0.001 ARG N 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 324 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 VAL cc_start: 0.5556 (t) cc_final: 0.4626 (p) REVERT: B 352 LYS cc_start: 0.7820 (tttt) cc_final: 0.7607 (ttpp) REVERT: A 345 VAL cc_start: 0.5749 (t) cc_final: 0.4664 (p) REVERT: A 352 LYS cc_start: 0.7747 (tttt) cc_final: 0.7531 (ttpt) REVERT: C 345 VAL cc_start: 0.5895 (t) cc_final: 0.4958 (p) REVERT: C 352 LYS cc_start: 0.7727 (tttt) cc_final: 0.7456 (ttpp) REVERT: C 359 GLU cc_start: 0.8182 (tt0) cc_final: 0.7805 (tp30) REVERT: C 464 ILE cc_start: 0.8155 (mt) cc_final: 0.7858 (tt) REVERT: D 345 VAL cc_start: 0.5332 (t) cc_final: 0.4353 (p) REVERT: D 396 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7844 (ttm-80) REVERT: D 451 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8904 (mt-10) REVERT: E 345 VAL cc_start: 0.5448 (t) cc_final: 0.4432 (p) REVERT: E 352 LYS cc_start: 0.7773 (tttt) cc_final: 0.7470 (ttpt) REVERT: E 359 GLU cc_start: 0.8233 (tt0) cc_final: 0.7919 (pt0) REVERT: F 345 VAL cc_start: 0.5467 (t) cc_final: 0.4555 (p) REVERT: F 359 GLU cc_start: 0.8223 (tt0) cc_final: 0.7844 (pt0) REVERT: G 345 VAL cc_start: 0.5439 (t) cc_final: 0.4514 (p) REVERT: H 345 VAL cc_start: 0.5586 (t) cc_final: 0.4666 (p) REVERT: H 352 LYS cc_start: 0.7812 (tttt) cc_final: 0.7604 (ttpp) REVERT: I 345 VAL cc_start: 0.5891 (t) cc_final: 0.4949 (p) REVERT: I 352 LYS cc_start: 0.7736 (tttt) cc_final: 0.7535 (ttpt) REVERT: J 345 VAL cc_start: 0.5804 (t) cc_final: 0.4853 (p) REVERT: J 349 GLU cc_start: 0.7775 (tt0) cc_final: 0.7566 (tt0) REVERT: J 352 LYS cc_start: 0.7830 (tttt) cc_final: 0.7577 (ttpp) REVERT: K 345 VAL cc_start: 0.5415 (t) cc_final: 0.4405 (p) REVERT: K 396 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7905 (ttm-80) REVERT: K 398 TYR cc_start: 0.7864 (m-80) cc_final: 0.7594 (m-80) REVERT: K 451 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8902 (mt-10) REVERT: L 345 VAL cc_start: 0.5379 (t) cc_final: 0.4414 (p) REVERT: L 352 LYS cc_start: 0.7760 (tttt) cc_final: 0.7456 (ttpt) REVERT: L 359 GLU cc_start: 0.8131 (tt0) cc_final: 0.7829 (pt0) REVERT: M 345 VAL cc_start: 0.5414 (t) cc_final: 0.4321 (p) REVERT: M 352 LYS cc_start: 0.7829 (tttt) cc_final: 0.7622 (ttpt) REVERT: M 359 GLU cc_start: 0.8228 (tt0) cc_final: 0.7842 (pt0) REVERT: N 345 VAL cc_start: 0.5359 (t) cc_final: 0.4403 (p) outliers start: 18 outliers final: 10 residues processed: 328 average time/residue: 3.8664 time to fit residues: 1359.9912 Evaluate side-chains 329 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 317 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 396 ARG Chi-restraints excluded: chain M residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15638 Z= 0.261 Angle : 0.558 4.721 21210 Z= 0.304 Chirality : 0.044 0.129 2240 Planarity : 0.006 0.048 2772 Dihedral : 4.495 17.124 2058 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.77 % Allowed : 12.52 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.21), residues: 1848 helix: 0.71 (0.23), residues: 532 sheet: 2.81 (0.20), residues: 714 loop : 0.38 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 455 HIS 0.003 0.001 HIS K 468 PHE 0.018 0.002 PHE J 467 TYR 0.008 0.003 TYR J 398 ARG 0.006 0.001 ARG L 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 324 time to evaluate : 2.160 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: B 345 VAL cc_start: 0.5542 (t) cc_final: 0.4635 (p) REVERT: B 352 LYS cc_start: 0.7827 (tttt) cc_final: 0.7594 (ttpp) REVERT: A 345 VAL cc_start: 0.5785 (t) cc_final: 0.4761 (p) REVERT: A 352 LYS cc_start: 0.7793 (tttt) cc_final: 0.7564 (ttpt) REVERT: A 461 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7536 (tmtt) REVERT: C 345 VAL cc_start: 0.5872 (t) cc_final: 0.4934 (p) REVERT: C 352 LYS cc_start: 0.7787 (tttt) cc_final: 0.7507 (ttpp) REVERT: C 464 ILE cc_start: 0.8202 (mt) cc_final: 0.7900 (tt) REVERT: D 345 VAL cc_start: 0.5442 (t) cc_final: 0.4456 (p) REVERT: D 396 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7886 (ttm-80) REVERT: D 451 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.8967 (mt-10) REVERT: E 345 VAL cc_start: 0.5649 (t) cc_final: 0.4610 (p) REVERT: E 349 GLU cc_start: 0.7941 (tt0) cc_final: 0.7614 (tt0) REVERT: E 352 LYS cc_start: 0.7775 (tttt) cc_final: 0.7488 (ttpp) REVERT: F 345 VAL cc_start: 0.5532 (t) cc_final: 0.4617 (p) REVERT: G 345 VAL cc_start: 0.5494 (t) cc_final: 0.4552 (p) REVERT: H 345 VAL cc_start: 0.5571 (t) cc_final: 0.4672 (p) REVERT: H 352 LYS cc_start: 0.7797 (tttt) cc_final: 0.7579 (ttpp) REVERT: I 345 VAL cc_start: 0.5912 (t) cc_final: 0.5021 (p) REVERT: I 352 LYS cc_start: 0.7784 (tttt) cc_final: 0.7568 (ttpt) REVERT: I 461 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7599 (tmtt) REVERT: J 345 VAL cc_start: 0.5948 (t) cc_final: 0.5024 (p) REVERT: J 352 LYS cc_start: 0.7850 (tttt) cc_final: 0.7560 (ttpp) REVERT: K 345 VAL cc_start: 0.5488 (t) cc_final: 0.4505 (p) REVERT: K 396 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7940 (ttm-80) REVERT: K 398 TYR cc_start: 0.7906 (m-80) cc_final: 0.7638 (m-80) REVERT: K 451 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.8964 (mt-10) REVERT: L 345 VAL cc_start: 0.5553 (t) cc_final: 0.4584 (p) REVERT: L 352 LYS cc_start: 0.7766 (tttt) cc_final: 0.7435 (ttpt) REVERT: M 345 VAL cc_start: 0.5500 (t) cc_final: 0.4409 (p) REVERT: M 352 LYS cc_start: 0.7829 (tttt) cc_final: 0.7613 (ttpt) REVERT: N 345 VAL cc_start: 0.5439 (t) cc_final: 0.4467 (p) outliers start: 29 outliers final: 17 residues processed: 334 average time/residue: 3.8614 time to fit residues: 1396.4459 Evaluate side-chains 343 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 324 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 396 ARG Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15638 Z= 0.233 Angle : 0.540 4.881 21210 Z= 0.295 Chirality : 0.044 0.129 2240 Planarity : 0.006 0.051 2772 Dihedral : 4.486 17.142 2058 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.95 % Allowed : 12.70 % Favored : 85.35 % 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: 2.10 (0.21), residues: 1848 helix: 0.70 (0.23), residues: 532 sheet: 2.83 (0.20), residues: 714 loop : 0.26 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 403 HIS 0.004 0.001 HIS N 395 PHE 0.015 0.002 PHE K 467 TYR 0.007 0.002 TYR B 398 ARG 0.008 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 320 time to evaluate : 2.373 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: B 345 VAL cc_start: 0.5723 (t) cc_final: 0.4824 (p) REVERT: A 345 VAL cc_start: 0.5764 (t) cc_final: 0.4725 (p) REVERT: A 352 LYS cc_start: 0.7753 (tttt) cc_final: 0.7514 (ttpt) REVERT: A 461 LYS cc_start: 0.7834 (ttpt) cc_final: 0.7550 (tmtt) REVERT: C 345 VAL cc_start: 0.5927 (t) cc_final: 0.4978 (p) REVERT: C 352 LYS cc_start: 0.7772 (tttt) cc_final: 0.7469 (ttpt) REVERT: C 464 ILE cc_start: 0.8204 (mt) cc_final: 0.7909 (tt) REVERT: D 345 VAL cc_start: 0.5470 (t) cc_final: 0.4490 (p) REVERT: D 396 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7903 (ttm-80) REVERT: D 451 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8967 (mt-10) REVERT: E 345 VAL cc_start: 0.5675 (t) cc_final: 0.4667 (p) REVERT: E 352 LYS cc_start: 0.7712 (tttt) cc_final: 0.7379 (ttpt) REVERT: E 359 GLU cc_start: 0.8263 (tt0) cc_final: 0.7970 (pt0) REVERT: F 345 VAL cc_start: 0.5631 (t) cc_final: 0.4712 (p) REVERT: G 345 VAL cc_start: 0.5634 (t) cc_final: 0.4711 (p) REVERT: H 345 VAL cc_start: 0.5753 (t) cc_final: 0.4863 (p) REVERT: H 352 LYS cc_start: 0.7739 (tttt) cc_final: 0.7505 (ttpp) REVERT: I 345 VAL cc_start: 0.5935 (t) cc_final: 0.5036 (p) REVERT: I 352 LYS cc_start: 0.7759 (tttt) cc_final: 0.7536 (ttpt) REVERT: I 461 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7600 (tmtt) REVERT: J 345 VAL cc_start: 0.5994 (t) cc_final: 0.5060 (p) REVERT: J 352 LYS cc_start: 0.7838 (tttt) cc_final: 0.7550 (ttpt) REVERT: K 345 VAL cc_start: 0.5512 (t) cc_final: 0.4535 (p) REVERT: K 396 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7946 (ttm-80) REVERT: K 398 TYR cc_start: 0.7918 (m-80) cc_final: 0.7620 (m-80) REVERT: K 451 GLU cc_start: 0.9339 (OUTLIER) cc_final: 0.8971 (mt-10) REVERT: L 345 VAL cc_start: 0.5534 (t) cc_final: 0.4594 (p) REVERT: L 352 LYS cc_start: 0.7714 (tttt) cc_final: 0.7397 (ttpt) REVERT: M 345 VAL cc_start: 0.5578 (t) cc_final: 0.4483 (p) REVERT: M 352 LYS cc_start: 0.7817 (tttt) cc_final: 0.7596 (ttpt) REVERT: M 359 GLU cc_start: 0.8230 (tt0) cc_final: 0.7878 (pt0) REVERT: N 345 VAL cc_start: 0.5564 (t) cc_final: 0.4608 (p) outliers start: 32 outliers final: 21 residues processed: 329 average time/residue: 3.7133 time to fit residues: 1313.1673 Evaluate side-chains 343 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 320 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 424 ASP Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 396 ARG Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 424 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.4980 chunk 168 optimal weight: 0.6980 chunk 153 optimal weight: 0.1980 chunk 163 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15638 Z= 0.145 Angle : 0.482 6.264 21210 Z= 0.258 Chirality : 0.043 0.126 2240 Planarity : 0.006 0.099 2772 Dihedral : 4.253 17.701 2058 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.40 % Allowed : 14.16 % Favored : 84.43 % 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: 2.27 (0.21), residues: 1848 helix: 0.90 (0.23), residues: 532 sheet: 2.86 (0.21), residues: 714 loop : 0.37 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 455 HIS 0.002 0.001 HIS K 395 PHE 0.010 0.001 PHE J 467 TYR 0.006 0.001 TYR B 398 ARG 0.015 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 318 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 VAL cc_start: 0.5688 (t) cc_final: 0.4765 (p) REVERT: A 345 VAL cc_start: 0.5737 (t) cc_final: 0.4698 (p) REVERT: A 352 LYS cc_start: 0.7706 (tttt) cc_final: 0.7484 (ttpt) REVERT: A 461 LYS cc_start: 0.7817 (ttpt) cc_final: 0.7516 (tmtt) REVERT: C 345 VAL cc_start: 0.5911 (t) cc_final: 0.4965 (p) REVERT: C 352 LYS cc_start: 0.7711 (tttt) cc_final: 0.7440 (ttpp) REVERT: C 464 ILE cc_start: 0.8192 (mt) cc_final: 0.7912 (tt) REVERT: D 345 VAL cc_start: 0.5600 (t) cc_final: 0.4595 (p) REVERT: D 396 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7893 (ttm-80) REVERT: D 451 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8900 (mt-10) REVERT: E 345 VAL cc_start: 0.5609 (t) cc_final: 0.4598 (p) REVERT: E 352 LYS cc_start: 0.7709 (tttt) cc_final: 0.7393 (ttpt) REVERT: E 359 GLU cc_start: 0.8267 (tt0) cc_final: 0.7959 (pt0) REVERT: F 345 VAL cc_start: 0.5686 (t) cc_final: 0.4767 (p) REVERT: F 359 GLU cc_start: 0.8234 (tt0) cc_final: 0.7899 (pt0) REVERT: G 345 VAL cc_start: 0.5612 (t) cc_final: 0.4691 (p) REVERT: G 359 GLU cc_start: 0.8221 (tt0) cc_final: 0.7878 (pt0) REVERT: H 345 VAL cc_start: 0.5714 (t) cc_final: 0.4797 (p) REVERT: H 352 LYS cc_start: 0.7701 (tttt) cc_final: 0.7491 (ttpp) REVERT: I 345 VAL cc_start: 0.5873 (t) cc_final: 0.4975 (p) REVERT: I 352 LYS cc_start: 0.7715 (tttt) cc_final: 0.7495 (ttpt) REVERT: I 461 LYS cc_start: 0.7845 (ttpt) cc_final: 0.7553 (tmtt) REVERT: J 345 VAL cc_start: 0.5989 (t) cc_final: 0.5058 (p) REVERT: J 352 LYS cc_start: 0.7758 (tttt) cc_final: 0.7496 (ttpp) REVERT: J 359 GLU cc_start: 0.8175 (tt0) cc_final: 0.7866 (pt0) REVERT: K 345 VAL cc_start: 0.5459 (t) cc_final: 0.4484 (p) REVERT: K 396 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7928 (ttm-80) REVERT: K 398 TYR cc_start: 0.7884 (m-80) cc_final: 0.7588 (m-80) REVERT: K 451 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8901 (mt-10) REVERT: L 345 VAL cc_start: 0.5469 (t) cc_final: 0.4522 (p) REVERT: L 352 LYS cc_start: 0.7699 (tttt) cc_final: 0.7495 (ttpp) REVERT: L 359 GLU cc_start: 0.8158 (tt0) cc_final: 0.7858 (pt0) REVERT: M 345 VAL cc_start: 0.5634 (t) cc_final: 0.4545 (p) REVERT: M 352 LYS cc_start: 0.7763 (tttt) cc_final: 0.7546 (ttpt) REVERT: M 359 GLU cc_start: 0.8228 (tt0) cc_final: 0.7889 (pt0) REVERT: N 345 VAL cc_start: 0.5543 (t) cc_final: 0.4588 (p) outliers start: 23 outliers final: 16 residues processed: 327 average time/residue: 3.8560 time to fit residues: 1351.3199 Evaluate side-chains 333 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 315 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 396 ARG Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Chi-restraints excluded: chain N residue 424 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.0980 chunk 172 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 181 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15638 Z= 0.137 Angle : 0.459 4.942 21210 Z= 0.243 Chirality : 0.042 0.124 2240 Planarity : 0.006 0.084 2772 Dihedral : 4.017 17.690 2058 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.16 % Allowed : 14.16 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.21), residues: 1848 helix: 1.12 (0.23), residues: 532 sheet: 2.90 (0.21), residues: 714 loop : 0.48 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 403 HIS 0.002 0.000 HIS H 395 PHE 0.010 0.001 PHE J 467 TYR 0.005 0.001 TYR D 398 ARG 0.015 0.001 ARG F 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 310 time to evaluate : 2.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 345 VAL cc_start: 0.5706 (t) cc_final: 0.4776 (p) REVERT: B 349 GLU cc_start: 0.7821 (tt0) cc_final: 0.7564 (tt0) REVERT: B 359 GLU cc_start: 0.8225 (tt0) cc_final: 0.7890 (pt0) REVERT: B 381 GLU cc_start: 0.8555 (pt0) cc_final: 0.8319 (pt0) REVERT: A 345 VAL cc_start: 0.5820 (t) cc_final: 0.4750 (p) REVERT: A 396 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7531 (ttt180) REVERT: A 461 LYS cc_start: 0.7788 (ttpt) cc_final: 0.7504 (tmtt) REVERT: C 345 VAL cc_start: 0.5864 (t) cc_final: 0.4914 (p) REVERT: C 352 LYS cc_start: 0.7727 (tttt) cc_final: 0.7475 (ttpp) REVERT: D 345 VAL cc_start: 0.5676 (t) cc_final: 0.4649 (p) REVERT: D 396 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7836 (ttm-80) REVERT: D 451 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8846 (mt-10) REVERT: E 345 VAL cc_start: 0.5587 (t) cc_final: 0.4589 (p) REVERT: E 352 LYS cc_start: 0.7713 (tttt) cc_final: 0.7497 (ttpp) REVERT: E 359 GLU cc_start: 0.8282 (tt0) cc_final: 0.7970 (pt0) REVERT: E 425 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7798 (mm-30) REVERT: F 345 VAL cc_start: 0.5676 (t) cc_final: 0.4753 (p) REVERT: F 359 GLU cc_start: 0.8247 (tt0) cc_final: 0.7940 (pt0) REVERT: G 345 VAL cc_start: 0.5603 (t) cc_final: 0.4676 (p) REVERT: G 349 GLU cc_start: 0.7837 (tt0) cc_final: 0.7603 (tt0) REVERT: G 359 GLU cc_start: 0.8232 (tt0) cc_final: 0.7943 (pt0) REVERT: H 345 VAL cc_start: 0.5734 (t) cc_final: 0.4809 (p) REVERT: H 352 LYS cc_start: 0.7698 (tttt) cc_final: 0.7479 (ttpp) REVERT: H 359 GLU cc_start: 0.8236 (tt0) cc_final: 0.7927 (pt0) REVERT: H 381 GLU cc_start: 0.8645 (pt0) cc_final: 0.8441 (pt0) REVERT: I 345 VAL cc_start: 0.5965 (t) cc_final: 0.5034 (p) REVERT: I 359 GLU cc_start: 0.8134 (tt0) cc_final: 0.7859 (pt0) REVERT: I 396 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7563 (ttt180) REVERT: I 461 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7555 (tmtt) REVERT: J 345 VAL cc_start: 0.5877 (t) cc_final: 0.4933 (p) REVERT: J 352 LYS cc_start: 0.7754 (tttt) cc_final: 0.7494 (ttpp) REVERT: J 359 GLU cc_start: 0.8180 (tt0) cc_final: 0.7892 (pt0) REVERT: K 345 VAL cc_start: 0.5620 (t) cc_final: 0.4615 (p) REVERT: K 396 ARG cc_start: 0.8130 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: K 398 TYR cc_start: 0.7881 (m-80) cc_final: 0.7592 (m-80) REVERT: K 451 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8844 (mt-10) REVERT: L 345 VAL cc_start: 0.5473 (t) cc_final: 0.4532 (p) REVERT: L 352 LYS cc_start: 0.7705 (tttt) cc_final: 0.7497 (ttpp) REVERT: L 359 GLU cc_start: 0.8192 (tt0) cc_final: 0.7892 (pt0) REVERT: L 424 ASP cc_start: 0.8115 (m-30) cc_final: 0.7883 (m-30) REVERT: L 425 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7639 (mm-30) REVERT: M 345 VAL cc_start: 0.5627 (t) cc_final: 0.4545 (p) REVERT: M 352 LYS cc_start: 0.7751 (tttt) cc_final: 0.7544 (ttpp) REVERT: M 359 GLU cc_start: 0.8252 (tt0) cc_final: 0.7943 (pt0) REVERT: N 345 VAL cc_start: 0.5607 (t) cc_final: 0.4627 (p) REVERT: N 349 GLU cc_start: 0.7889 (tt0) cc_final: 0.7582 (tt0) REVERT: N 359 GLU cc_start: 0.8280 (tt0) cc_final: 0.7532 (tp30) outliers start: 19 outliers final: 13 residues processed: 316 average time/residue: 4.0487 time to fit residues: 1369.8184 Evaluate side-chains 327 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 310 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 396 ARG Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain G residue 464 ILE Chi-restraints excluded: chain I residue 396 ARG Chi-restraints excluded: chain J residue 426 SER Chi-restraints excluded: chain J residue 464 ILE Chi-restraints excluded: chain K residue 451 GLU Chi-restraints excluded: chain L residue 464 ILE Chi-restraints excluded: chain M residue 396 ARG Chi-restraints excluded: chain M residue 426 SER Chi-restraints excluded: chain M residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.174572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141516 restraints weight = 37778.853| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.08 r_work: 0.3311 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15638 Z= 0.256 Angle : 0.542 5.136 21210 Z= 0.294 Chirality : 0.043 0.128 2240 Planarity : 0.006 0.090 2772 Dihedral : 4.275 17.214 2058 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.16 % Allowed : 14.35 % Favored : 84.49 % 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: 2.30 (0.21), residues: 1848 helix: 0.92 (0.23), residues: 532 sheet: 2.96 (0.21), residues: 714 loop : 0.27 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 403 HIS 0.004 0.001 HIS M 468 PHE 0.017 0.002 PHE J 467 TYR 0.007 0.002 TYR A 398 ARG 0.011 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17997.26 seconds wall clock time: 309 minutes 27.75 seconds (18567.75 seconds total)