Starting phenix.real_space_refine on Mon Mar 25 02:07:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytl_10919/03_2024/6ytl_10919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytl_10919/03_2024/6ytl_10919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytl_10919/03_2024/6ytl_10919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytl_10919/03_2024/6ytl_10919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytl_10919/03_2024/6ytl_10919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ytl_10919/03_2024/6ytl_10919.pdb" } resolution = 3.82 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= 0.007 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: 4 Type Number sf(0) Gaussians S 440 5.16 5 C 29480 2.51 5 N 7678 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F GLU 230": "OE1" <-> "OE2" Residue "F GLU 233": "OE1" <-> "OE2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G GLU 230": "OE1" <-> "OE2" Residue "G GLU 233": "OE1" <-> "OE2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H ARG 174": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H GLU 230": "OE1" <-> "OE2" Residue "H GLU 233": "OE1" <-> "OE2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H GLU 259": "OE1" <-> "OE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 174": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I GLU 230": "OE1" <-> "OE2" Residue "I GLU 233": "OE1" <-> "OE2" Residue "I ARG 247": "NH1" <-> "NH2" Residue "I GLU 259": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "J GLU 230": "OE1" <-> "OE2" Residue "J GLU 233": "OE1" <-> "OE2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "J GLU 259": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "K GLU 230": "OE1" <-> "OE2" Residue "K GLU 233": "OE1" <-> "OE2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "K GLU 259": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L ARG 164": "NH1" <-> "NH2" Residue "L ARG 174": "NH1" <-> "NH2" Residue "L ARG 182": "NH1" <-> "NH2" Residue "L GLU 233": "OE1" <-> "OE2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "L GLU 259": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M ARG 174": "NH1" <-> "NH2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 233": "OE1" <-> "OE2" Residue "M ARG 247": "NH1" <-> "NH2" Residue "M GLU 259": "OE1" <-> "OE2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N ARG 164": "NH1" <-> "NH2" Residue "N ARG 174": "NH1" <-> "NH2" Residue "N ARG 182": "NH1" <-> "NH2" Residue "N GLU 233": "OE1" <-> "OE2" Residue "N ARG 247": "NH1" <-> "NH2" Residue "N GLU 259": "OE1" <-> "OE2" Residue "O GLU 155": "OE1" <-> "OE2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O ARG 174": "NH1" <-> "NH2" Residue "O ARG 182": "NH1" <-> "NH2" Residue "O GLU 233": "OE1" <-> "OE2" Residue "O ARG 247": "NH1" <-> "NH2" Residue "O GLU 259": "OE1" <-> "OE2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P ARG 164": "NH1" <-> "NH2" Residue "P ARG 174": "NH1" <-> "NH2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P GLU 233": "OE1" <-> "OE2" Residue "P ARG 247": "NH1" <-> "NH2" Residue "P GLU 259": "OE1" <-> "OE2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "Q ARG 174": "NH1" <-> "NH2" Residue "Q ARG 182": "NH1" <-> "NH2" Residue "Q GLU 233": "OE1" <-> "OE2" Residue "Q ARG 247": "NH1" <-> "NH2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "R GLU 155": "OE1" <-> "OE2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 174": "NH1" <-> "NH2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R GLU 233": "OE1" <-> "OE2" Residue "R ARG 247": "NH1" <-> "NH2" Residue "R GLU 259": "OE1" <-> "OE2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S ARG 174": "NH1" <-> "NH2" Residue "S ARG 182": "NH1" <-> "NH2" Residue "S GLU 233": "OE1" <-> "OE2" Residue "S ARG 247": "NH1" <-> "NH2" Residue "S GLU 259": "OE1" <-> "OE2" Residue "T GLU 155": "OE1" <-> "OE2" Residue "T ARG 164": "NH1" <-> "NH2" Residue "T ARG 174": "NH1" <-> "NH2" Residue "T ARG 182": "NH1" <-> "NH2" Residue "T GLU 233": "OE1" <-> "OE2" Residue "T ARG 247": "NH1" <-> "NH2" Residue "T GLU 259": "OE1" <-> "OE2" Residue "U GLU 155": "OE1" <-> "OE2" Residue "U ARG 164": "NH1" <-> "NH2" Residue "U ARG 174": "NH1" <-> "NH2" Residue "U ARG 182": "NH1" <-> "NH2" Residue "U GLU 233": "OE1" <-> "OE2" Residue "U ARG 247": "NH1" <-> "NH2" Residue "U GLU 259": "OE1" <-> "OE2" Residue "V GLU 155": "OE1" <-> "OE2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V ARG 174": "NH1" <-> "NH2" Residue "V ARG 182": "NH1" <-> "NH2" Residue "V GLU 233": "OE1" <-> "OE2" Residue "V ARG 247": "NH1" <-> "NH2" Residue "V GLU 259": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 45782 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "B" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "C" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "E" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "F" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "G" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "H" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "I" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "J" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "K" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "M" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "N" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "O" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "P" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "Q" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "R" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "S" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "T" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "U" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Chain: "V" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2081 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 11, 'TRANS': 255} Chain breaks: 1 Time building chain proxies: 23.63, per 1000 atoms: 0.52 Number of scatterers: 45782 At special positions: 0 Unit cell: (140.7, 140.7, 207.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 440 16.00 O 8184 8.00 N 7678 7.00 C 29480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 162 " distance=2.04 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 162 " distance=2.03 Simple disulfide: pdb=" SG CYS N 41 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 162 " distance=2.03 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 131 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 162 " distance=2.03 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 162 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 41 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 162 " distance=2.03 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 131 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 162 " distance=2.03 Simple disulfide: pdb=" SG CYS S 41 " - pdb=" SG CYS S 131 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 162 " distance=2.03 Simple disulfide: pdb=" SG CYS T 41 " - pdb=" SG CYS T 131 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 162 " distance=2.03 Simple disulfide: pdb=" SG CYS U 41 " - pdb=" SG CYS U 131 " distance=2.03 Simple disulfide: pdb=" SG CYS U 43 " - pdb=" SG CYS U 162 " distance=2.03 Simple disulfide: pdb=" SG CYS V 41 " - pdb=" SG CYS V 131 " distance=2.03 Simple disulfide: pdb=" SG CYS V 43 " - pdb=" SG CYS V 162 " distance=2.03 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: 17.27 Conformation dependent library (CDL) restraints added in 8.4 seconds 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11176 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.70 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 removed outlier: 3.725A pdb=" N PHE A 55 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 167 through 211 Processing helix chain 'A' and resid 216 through 253 Processing helix chain 'A' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 Processing helix chain 'B' and resid 167 through 211 Processing helix chain 'B' and resid 216 through 253 Processing helix chain 'B' and resid 268 through 276 removed outlier: 4.099A pdb=" N TRP B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 167 through 211 Processing helix chain 'C' and resid 216 through 253 Processing helix chain 'C' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 158 Processing helix chain 'D' and resid 167 through 211 Processing helix chain 'D' and resid 216 through 253 Processing helix chain 'D' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.552A pdb=" N LEU E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 167 through 211 Processing helix chain 'E' and resid 216 through 253 Processing helix chain 'E' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP E 272 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS E 273 " --> pdb=" O CYS E 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 70 removed outlier: 3.725A pdb=" N PHE F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.730A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 112 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 158 Processing helix chain 'F' and resid 167 through 211 Processing helix chain 'F' and resid 216 through 253 Processing helix chain 'F' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP F 272 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS F 273 " --> pdb=" O CYS F 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 15 through 39 removed outlier: 3.591A pdb=" N PHE G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 70 removed outlier: 3.725A pdb=" N PHE G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU G 116 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'G' and resid 167 through 211 Processing helix chain 'G' and resid 216 through 253 Processing helix chain 'G' and resid 268 through 276 removed outlier: 4.097A pdb=" N TRP G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS G 273 " --> pdb=" O CYS G 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 70 removed outlier: 3.723A pdb=" N PHE H 55 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 112 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 158 Processing helix chain 'H' and resid 167 through 211 Processing helix chain 'H' and resid 216 through 253 Processing helix chain 'H' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP H 272 " --> pdb=" O SER H 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS H 273 " --> pdb=" O CYS H 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 15 through 39 removed outlier: 3.591A pdb=" N PHE I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 70 removed outlier: 3.724A pdb=" N PHE I 55 " --> pdb=" O TYR I 51 " (cutoff:3.500A) Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 112 Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.552A pdb=" N LEU I 116 " --> pdb=" O VAL I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 158 Processing helix chain 'I' and resid 167 through 211 Processing helix chain 'I' and resid 216 through 253 Processing helix chain 'I' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP I 272 " --> pdb=" O SER I 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS I 273 " --> pdb=" O CYS I 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 70 removed outlier: 3.723A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 112 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.553A pdb=" N LEU J 116 " --> pdb=" O VAL J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 158 Processing helix chain 'J' and resid 167 through 211 Processing helix chain 'J' and resid 216 through 253 Processing helix chain 'J' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP J 272 " --> pdb=" O SER J 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS J 273 " --> pdb=" O CYS J 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 15 through 39 removed outlier: 3.591A pdb=" N PHE K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 70 removed outlier: 3.725A pdb=" N PHE K 55 " --> pdb=" O TYR K 51 " (cutoff:3.500A) Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 71 through 82 removed outlier: 3.729A pdb=" N TRP K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 112 Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.552A pdb=" N LEU K 116 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.740A pdb=" N CYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 167 through 211 Processing helix chain 'K' and resid 216 through 253 Processing helix chain 'K' and resid 268 through 276 removed outlier: 4.098A pdb=" N TRP K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS K 273 " --> pdb=" O CYS K 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE L 55 " --> pdb=" O TYR L 51 " (cutoff:3.500A) Proline residue: L 59 - end of helix Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 112 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU L 116 " --> pdb=" O VAL L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 158 Processing helix chain 'L' and resid 167 through 211 Processing helix chain 'L' and resid 216 through 253 Processing helix chain 'L' and resid 268 through 276 removed outlier: 4.070A pdb=" N TRP L 272 " --> pdb=" O SER L 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS L 273 " --> pdb=" O CYS L 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE M 55 " --> pdb=" O TYR M 51 " (cutoff:3.500A) Proline residue: M 59 - end of helix Processing helix chain 'M' and resid 71 through 82 removed outlier: 3.747A pdb=" N TRP M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 112 Processing helix chain 'M' and resid 112 through 126 removed outlier: 3.576A pdb=" N LEU M 116 " --> pdb=" O VAL M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 158 Processing helix chain 'M' and resid 167 through 211 Processing helix chain 'M' and resid 216 through 253 Processing helix chain 'M' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP M 272 " --> pdb=" O SER M 268 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS M 273 " --> pdb=" O CYS M 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 70 removed outlier: 3.714A pdb=" N PHE N 55 " --> pdb=" O TYR N 51 " (cutoff:3.500A) Proline residue: N 59 - end of helix Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 112 Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU N 116 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS N 131 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 158 Processing helix chain 'N' and resid 167 through 211 Processing helix chain 'N' and resid 216 through 253 Processing helix chain 'N' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP N 272 " --> pdb=" O SER N 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS N 273 " --> pdb=" O CYS N 269 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE O 55 " --> pdb=" O TYR O 51 " (cutoff:3.500A) Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 112 Processing helix chain 'O' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU O 116 " --> pdb=" O VAL O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 158 Processing helix chain 'O' and resid 167 through 211 Processing helix chain 'O' and resid 216 through 253 Processing helix chain 'O' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS O 273 " --> pdb=" O CYS O 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE P 55 " --> pdb=" O TYR P 51 " (cutoff:3.500A) Proline residue: P 59 - end of helix Processing helix chain 'P' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP P 75 " --> pdb=" O ARG P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 112 Processing helix chain 'P' and resid 112 through 126 removed outlier: 3.576A pdb=" N LEU P 116 " --> pdb=" O VAL P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS P 131 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 158 Processing helix chain 'P' and resid 167 through 211 Processing helix chain 'P' and resid 216 through 253 Processing helix chain 'P' and resid 268 through 276 removed outlier: 4.070A pdb=" N TRP P 272 " --> pdb=" O SER P 268 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS P 273 " --> pdb=" O CYS P 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE Q 55 " --> pdb=" O TYR Q 51 " (cutoff:3.500A) Proline residue: Q 59 - end of helix Processing helix chain 'Q' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP Q 75 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 112 Processing helix chain 'Q' and resid 112 through 126 removed outlier: 3.576A pdb=" N LEU Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS Q 131 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 158 Processing helix chain 'Q' and resid 167 through 211 Processing helix chain 'Q' and resid 216 through 253 Processing helix chain 'Q' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP Q 272 " --> pdb=" O SER Q 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS Q 273 " --> pdb=" O CYS Q 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE R 55 " --> pdb=" O TYR R 51 " (cutoff:3.500A) Proline residue: R 59 - end of helix Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 112 Processing helix chain 'R' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU R 116 " --> pdb=" O VAL R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS R 131 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 158 Processing helix chain 'R' and resid 167 through 211 Processing helix chain 'R' and resid 216 through 253 Processing helix chain 'R' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP R 272 " --> pdb=" O SER R 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS R 273 " --> pdb=" O CYS R 269 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE S 39 " --> pdb=" O SER S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 70 removed outlier: 3.714A pdb=" N PHE S 55 " --> pdb=" O TYR S 51 " (cutoff:3.500A) Proline residue: S 59 - end of helix Processing helix chain 'S' and resid 71 through 82 removed outlier: 3.745A pdb=" N TRP S 75 " --> pdb=" O ARG S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 112 Processing helix chain 'S' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU S 116 " --> pdb=" O VAL S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS S 131 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 158 Processing helix chain 'S' and resid 167 through 211 Processing helix chain 'S' and resid 216 through 253 Processing helix chain 'S' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP S 272 " --> pdb=" O SER S 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS S 273 " --> pdb=" O CYS S 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 15 through 39 removed outlier: 3.591A pdb=" N PHE T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE T 55 " --> pdb=" O TYR T 51 " (cutoff:3.500A) Proline residue: T 59 - end of helix Processing helix chain 'T' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP T 75 " --> pdb=" O ARG T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 112 Processing helix chain 'T' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU T 116 " --> pdb=" O VAL T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS T 131 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 158 Processing helix chain 'T' and resid 167 through 211 Processing helix chain 'T' and resid 216 through 253 Processing helix chain 'T' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP T 272 " --> pdb=" O SER T 268 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS T 273 " --> pdb=" O CYS T 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 15 Processing helix chain 'U' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE U 39 " --> pdb=" O SER U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 70 removed outlier: 3.713A pdb=" N PHE U 55 " --> pdb=" O TYR U 51 " (cutoff:3.500A) Proline residue: U 59 - end of helix Processing helix chain 'U' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP U 75 " --> pdb=" O ARG U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 112 Processing helix chain 'U' and resid 112 through 126 removed outlier: 3.575A pdb=" N LEU U 116 " --> pdb=" O VAL U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 126 through 133 removed outlier: 3.742A pdb=" N CYS U 131 " --> pdb=" O THR U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 158 Processing helix chain 'U' and resid 167 through 211 Processing helix chain 'U' and resid 216 through 253 Processing helix chain 'U' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP U 272 " --> pdb=" O SER U 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS U 273 " --> pdb=" O CYS U 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 15 Processing helix chain 'V' and resid 15 through 39 removed outlier: 3.590A pdb=" N PHE V 39 " --> pdb=" O SER V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 47 through 70 removed outlier: 3.712A pdb=" N PHE V 55 " --> pdb=" O TYR V 51 " (cutoff:3.500A) Proline residue: V 59 - end of helix Processing helix chain 'V' and resid 71 through 82 removed outlier: 3.746A pdb=" N TRP V 75 " --> pdb=" O ARG V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 95 through 112 Processing helix chain 'V' and resid 112 through 126 removed outlier: 3.576A pdb=" N LEU V 116 " --> pdb=" O VAL V 112 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 133 removed outlier: 3.741A pdb=" N CYS V 131 " --> pdb=" O THR V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 158 Processing helix chain 'V' and resid 167 through 211 Processing helix chain 'V' and resid 216 through 253 Processing helix chain 'V' and resid 268 through 276 removed outlier: 4.071A pdb=" N TRP V 272 " --> pdb=" O SER V 268 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS V 273 " --> pdb=" O CYS V 269 " (cutoff:3.500A) 3543 hydrogen bonds defined for protein. 10629 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: 16.32 Time building geometry restraints manager: 18.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14476 1.34 - 1.46: 11338 1.46 - 1.58: 20474 1.58 - 1.71: 0 1.71 - 1.83: 550 Bond restraints: 46838 Sorted by residual: bond pdb=" CA ILE M 58 " pdb=" CB ILE M 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.29e+00 bond pdb=" CA ILE V 58 " pdb=" CB ILE V 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.29e+00 bond pdb=" CA ILE P 58 " pdb=" CB ILE P 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.20e+00 bond pdb=" CA ILE N 58 " pdb=" CB ILE N 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.14e+00 bond pdb=" CA ILE T 58 " pdb=" CB ILE T 58 " ideal model delta sigma weight residual 1.537 1.528 0.009 5.00e-03 4.00e+04 3.00e+00 ... (remaining 46833 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.81: 1363 106.81 - 113.65: 26382 113.65 - 120.49: 19959 120.49 - 127.32: 15359 127.32 - 134.16: 539 Bond angle restraints: 63602 Sorted by residual: angle pdb=" CA LYS R 262 " pdb=" CB LYS R 262 " pdb=" CG LYS R 262 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.74e+00 angle pdb=" CA LYS S 262 " pdb=" CB LYS S 262 " pdb=" CG LYS S 262 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.73e+00 angle pdb=" CA LYS V 262 " pdb=" CB LYS V 262 " pdb=" CG LYS V 262 " ideal model delta sigma weight residual 114.10 120.01 -5.91 2.00e+00 2.50e-01 8.72e+00 angle pdb=" CA LYS T 262 " pdb=" CB LYS T 262 " pdb=" CG LYS T 262 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.71e+00 angle pdb=" CA LYS M 262 " pdb=" CB LYS M 262 " pdb=" CG LYS M 262 " ideal model delta sigma weight residual 114.10 119.99 -5.89 2.00e+00 2.50e-01 8.69e+00 ... (remaining 63597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 25214 17.94 - 35.88: 2341 35.88 - 53.81: 319 53.81 - 71.75: 44 71.75 - 89.69: 66 Dihedral angle restraints: 27984 sinusoidal: 10802 harmonic: 17182 Sorted by residual: dihedral pdb=" CB CYS N 41 " pdb=" SG CYS N 41 " pdb=" SG CYS N 131 " pdb=" CB CYS N 131 " ideal model delta sinusoidal sigma weight residual -86.00 -170.40 84.40 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS O 41 " pdb=" SG CYS O 41 " pdb=" SG CYS O 131 " pdb=" CB CYS O 131 " ideal model delta sinusoidal sigma weight residual -86.00 -170.39 84.39 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS Q 41 " pdb=" SG CYS Q 41 " pdb=" SG CYS Q 131 " pdb=" CB CYS Q 131 " ideal model delta sinusoidal sigma weight residual -86.00 -170.38 84.38 1 1.00e+01 1.00e-02 8.66e+01 ... (remaining 27981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 5504 0.044 - 0.087: 1317 0.087 - 0.131: 483 0.131 - 0.174: 99 0.174 - 0.218: 11 Chirality restraints: 7414 Sorted by residual: chirality pdb=" CB VAL B 148 " pdb=" CA VAL B 148 " pdb=" CG1 VAL B 148 " pdb=" CG2 VAL B 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL A 148 " pdb=" CA VAL A 148 " pdb=" CG1 VAL A 148 " pdb=" CG2 VAL A 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL E 148 " pdb=" CA VAL E 148 " pdb=" CG1 VAL E 148 " pdb=" CG2 VAL E 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 7411 not shown) Planarity restraints: 7898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU J 228 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" CD GLU J 228 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU J 228 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU J 228 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 228 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" CD GLU B 228 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU B 228 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU B 228 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 228 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" CD GLU G 228 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU G 228 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU G 228 " -0.015 2.00e-02 2.50e+03 ... (remaining 7895 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 239 2.52 - 3.12: 36698 3.12 - 3.71: 71526 3.71 - 4.31: 87756 4.31 - 4.90: 154040 Nonbonded interactions: 350259 Sorted by model distance: nonbonded pdb=" OG SER I 40 " pdb=" NH1 ARG J 182 " model vdw 1.929 2.520 nonbonded pdb=" OG SER A 40 " pdb=" NH1 ARG B 182 " model vdw 2.028 2.520 nonbonded pdb=" OG SER R 40 " pdb=" NH1 ARG S 182 " model vdw 2.047 2.520 nonbonded pdb=" OG SER Q 40 " pdb=" NH1 ARG R 182 " model vdw 2.082 2.520 nonbonded pdb=" OG SER T 40 " pdb=" NH1 ARG U 182 " model vdw 2.140 2.520 ... (remaining 350254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.040 Extract box with map and model: 5.510 Check model and map are aligned: 0.710 Set scattering table: 0.390 Process input model: 115.420 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.005 0.052 46838 Z= 0.346 Angle : 0.763 6.116 63602 Z= 0.441 Chirality : 0.046 0.218 7414 Planarity : 0.005 0.035 7898 Dihedral : 13.893 89.688 16676 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % 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: -0.15 (0.10), residues: 5786 helix: 0.69 (0.07), residues: 4466 sheet: None (None), residues: 0 loop : -2.76 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 75 HIS 0.003 0.001 HIS M 239 PHE 0.027 0.002 PHE N 55 TYR 0.011 0.002 TYR A 128 ARG 0.005 0.001 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1074 time to evaluate : 5.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TYR cc_start: 0.9019 (t80) cc_final: 0.8763 (t80) REVERT: A 192 LEU cc_start: 0.9041 (tp) cc_final: 0.8810 (tt) REVERT: A 195 LEU cc_start: 0.8739 (tt) cc_final: 0.8412 (mm) REVERT: A 229 ARG cc_start: 0.8049 (tpt90) cc_final: 0.7659 (tpp80) REVERT: A 258 SER cc_start: 0.8505 (m) cc_final: 0.8076 (t) REVERT: B 14 ARG cc_start: 0.7727 (mtm110) cc_final: 0.6526 (ptm160) REVERT: B 74 MET cc_start: 0.8359 (tmm) cc_final: 0.7669 (tmm) REVERT: B 163 CYS cc_start: 0.6909 (p) cc_final: 0.6635 (t) REVERT: B 195 LEU cc_start: 0.8483 (tt) cc_final: 0.8169 (mm) REVERT: B 208 LYS cc_start: 0.8627 (tptp) cc_final: 0.8316 (mmtp) REVERT: C 48 ASN cc_start: 0.8024 (t0) cc_final: 0.7568 (t0) REVERT: C 187 MET cc_start: 0.9262 (mmp) cc_final: 0.8401 (mmm) REVERT: C 191 ILE cc_start: 0.9266 (mt) cc_final: 0.8878 (mt) REVERT: C 195 LEU cc_start: 0.8763 (tt) cc_final: 0.8461 (mm) REVERT: C 229 ARG cc_start: 0.7984 (tpt90) cc_final: 0.7717 (tpp80) REVERT: D 31 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8250 (tm-30) REVERT: D 187 MET cc_start: 0.9244 (mmp) cc_final: 0.8852 (tpp) REVERT: D 208 LYS cc_start: 0.8703 (tptp) cc_final: 0.8323 (tppt) REVERT: D 215 SER cc_start: 0.8749 (t) cc_final: 0.8417 (p) REVERT: D 237 GLU cc_start: 0.8251 (tm-30) cc_final: 0.8021 (tm-30) REVERT: E 50 TYR cc_start: 0.8584 (m-80) cc_final: 0.8328 (m-80) REVERT: E 187 MET cc_start: 0.8900 (mmp) cc_final: 0.8533 (mmm) REVERT: E 229 ARG cc_start: 0.7925 (tpt90) cc_final: 0.7453 (tpp80) REVERT: E 244 MET cc_start: 0.8147 (tpt) cc_final: 0.7913 (tpt) REVERT: F 141 HIS cc_start: 0.7637 (p-80) cc_final: 0.6951 (p-80) REVERT: F 192 LEU cc_start: 0.8676 (tp) cc_final: 0.8415 (tt) REVERT: F 195 LEU cc_start: 0.8585 (tt) cc_final: 0.8268 (mm) REVERT: F 208 LYS cc_start: 0.8718 (tptp) cc_final: 0.8220 (mmtm) REVERT: F 229 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7434 (tpp80) REVERT: G 74 MET cc_start: 0.7526 (tmm) cc_final: 0.7220 (tmm) REVERT: G 141 HIS cc_start: 0.7198 (p-80) cc_final: 0.6612 (p-80) REVERT: G 187 MET cc_start: 0.9275 (mmp) cc_final: 0.8933 (mmm) REVERT: G 229 ARG cc_start: 0.8221 (tpt90) cc_final: 0.7800 (tpp80) REVERT: G 274 ASP cc_start: 0.7267 (m-30) cc_final: 0.7046 (m-30) REVERT: H 187 MET cc_start: 0.9212 (mmp) cc_final: 0.8997 (mmm) REVERT: H 195 LEU cc_start: 0.8661 (tt) cc_final: 0.8224 (mm) REVERT: H 208 LYS cc_start: 0.8719 (tptp) cc_final: 0.8360 (tppt) REVERT: H 229 ARG cc_start: 0.8206 (tpt90) cc_final: 0.7870 (tpp80) REVERT: H 258 SER cc_start: 0.8747 (m) cc_final: 0.8420 (t) REVERT: H 274 ASP cc_start: 0.7679 (m-30) cc_final: 0.7457 (m-30) REVERT: I 208 LYS cc_start: 0.8957 (tptp) cc_final: 0.8249 (mmtm) REVERT: I 229 ARG cc_start: 0.7872 (tpt90) cc_final: 0.7592 (tpp80) REVERT: J 14 ARG cc_start: 0.8044 (mtm110) cc_final: 0.6692 (ptm160) REVERT: J 155 GLU cc_start: 0.8445 (tp30) cc_final: 0.7984 (tm-30) REVERT: J 186 GLN cc_start: 0.7995 (mt0) cc_final: 0.7788 (mt0) REVERT: J 215 SER cc_start: 0.8752 (t) cc_final: 0.8188 (p) REVERT: K 31 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8348 (tm-30) REVERT: K 129 TYR cc_start: 0.8860 (t80) cc_final: 0.8537 (t80) REVERT: K 187 MET cc_start: 0.9126 (mmp) cc_final: 0.8854 (mmm) REVERT: K 229 ARG cc_start: 0.8007 (tpt90) cc_final: 0.7662 (tpp80) REVERT: K 258 SER cc_start: 0.8276 (m) cc_final: 0.8065 (t) REVERT: L 104 PHE cc_start: 0.8190 (t80) cc_final: 0.7966 (t80) REVERT: L 142 TYR cc_start: 0.6386 (m-80) cc_final: 0.6153 (m-10) REVERT: L 155 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7954 (tp30) REVERT: L 187 MET cc_start: 0.9323 (mmp) cc_final: 0.8990 (mmp) REVERT: L 195 LEU cc_start: 0.8674 (tt) cc_final: 0.8364 (mm) REVERT: L 208 LYS cc_start: 0.9051 (tptp) cc_final: 0.8472 (mmtm) REVERT: L 229 ARG cc_start: 0.7970 (tpt90) cc_final: 0.7621 (tpp80) REVERT: M 128 TYR cc_start: 0.9088 (m-10) cc_final: 0.8880 (m-10) REVERT: M 187 MET cc_start: 0.9258 (mmp) cc_final: 0.8948 (mmp) REVERT: M 195 LEU cc_start: 0.8659 (tt) cc_final: 0.8347 (mm) REVERT: M 208 LYS cc_start: 0.8991 (tptp) cc_final: 0.8342 (mmtm) REVERT: M 229 ARG cc_start: 0.8282 (tpt90) cc_final: 0.7811 (tpp80) REVERT: N 74 MET cc_start: 0.7695 (tmm) cc_final: 0.7451 (tmm) REVERT: N 195 LEU cc_start: 0.8708 (tt) cc_final: 0.8336 (mm) REVERT: N 208 LYS cc_start: 0.8941 (tptp) cc_final: 0.8667 (tppt) REVERT: N 229 ARG cc_start: 0.8087 (tpt90) cc_final: 0.7853 (tpp80) REVERT: N 237 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7990 (tm-30) REVERT: N 258 SER cc_start: 0.8343 (m) cc_final: 0.7896 (t) REVERT: N 274 ASP cc_start: 0.8043 (m-30) cc_final: 0.7816 (m-30) REVERT: O 129 TYR cc_start: 0.9021 (t80) cc_final: 0.8629 (t80) REVERT: O 195 LEU cc_start: 0.8832 (tt) cc_final: 0.8463 (tp) REVERT: O 208 LYS cc_start: 0.8881 (tptp) cc_final: 0.8434 (mmtm) REVERT: O 229 ARG cc_start: 0.8050 (tpt90) cc_final: 0.7574 (tpp80) REVERT: O 230 GLU cc_start: 0.7748 (tp30) cc_final: 0.7472 (tp30) REVERT: P 14 ARG cc_start: 0.8271 (mtm110) cc_final: 0.8034 (mtp-110) REVERT: P 31 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8354 (tm-30) REVERT: P 241 ARG cc_start: 0.7934 (ttt180) cc_final: 0.7698 (ttt-90) REVERT: Q 142 TYR cc_start: 0.6669 (m-80) cc_final: 0.6445 (m-10) REVERT: Q 208 LYS cc_start: 0.8621 (tptp) cc_final: 0.8089 (mmtm) REVERT: R 141 HIS cc_start: 0.7500 (p-80) cc_final: 0.6939 (p-80) REVERT: R 142 TYR cc_start: 0.6171 (m-80) cc_final: 0.5926 (m-80) REVERT: R 198 ILE cc_start: 0.9146 (mm) cc_final: 0.8900 (tt) REVERT: R 208 LYS cc_start: 0.8868 (tptp) cc_final: 0.8564 (tppt) REVERT: R 229 ARG cc_start: 0.8025 (tpt90) cc_final: 0.7597 (tpp80) REVERT: R 274 ASP cc_start: 0.7895 (m-30) cc_final: 0.7632 (m-30) REVERT: S 51 TYR cc_start: 0.9114 (t80) cc_final: 0.8802 (t80) REVERT: S 187 MET cc_start: 0.9340 (mmp) cc_final: 0.8881 (mmm) REVERT: S 208 LYS cc_start: 0.8891 (tptp) cc_final: 0.8433 (mmtm) REVERT: S 215 SER cc_start: 0.8767 (t) cc_final: 0.8476 (p) REVERT: T 141 HIS cc_start: 0.7908 (p-80) cc_final: 0.7317 (p-80) REVERT: T 187 MET cc_start: 0.9410 (mmp) cc_final: 0.9055 (mmp) REVERT: T 195 LEU cc_start: 0.8780 (tt) cc_final: 0.8349 (mm) REVERT: T 229 ARG cc_start: 0.8106 (tpt90) cc_final: 0.7726 (tpp80) REVERT: T 237 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7987 (tm-30) REVERT: T 249 LYS cc_start: 0.8703 (tttt) cc_final: 0.8469 (tttp) REVERT: T 250 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8435 (ttpp) REVERT: U 229 ARG cc_start: 0.8074 (tpt90) cc_final: 0.7779 (tpp80) REVERT: V 195 LEU cc_start: 0.8746 (tt) cc_final: 0.8209 (mm) REVERT: V 208 LYS cc_start: 0.8859 (tptp) cc_final: 0.8466 (mmtp) REVERT: V 229 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7576 (tpp80) outliers start: 0 outliers final: 0 residues processed: 1074 average time/residue: 0.7120 time to fit residues: 1169.4177 Evaluate side-chains 666 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 8.9990 chunk 433 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 448 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 333 optimal weight: 0.7980 chunk 519 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 184 GLN B 20 ASN B 184 GLN C 20 ASN C 184 GLN D 20 ASN D 181 HIS D 184 GLN E 184 GLN E 234 GLN F 20 ASN F 184 GLN G 20 ASN G 184 GLN H 20 ASN H 184 GLN I 20 ASN I 184 GLN I 234 GLN J 184 GLN K 20 ASN K 184 GLN K 234 GLN L 20 ASN L 184 GLN M 20 ASN M 184 GLN N 20 ASN N 184 GLN O 20 ASN O 184 GLN P 184 GLN P 234 GLN Q 184 GLN Q 234 GLN R 20 ASN R 184 GLN S 20 ASN S 184 GLN T 20 ASN T 184 GLN U 20 ASN U 184 GLN V 20 ASN V 184 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 46838 Z= 0.423 Angle : 0.679 7.540 63602 Z= 0.371 Chirality : 0.044 0.147 7414 Planarity : 0.006 0.054 7898 Dihedral : 4.261 17.250 6270 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.87 % Allowed : 15.84 % Favored : 81.29 % 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: 1.25 (0.10), residues: 5786 helix: 1.66 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.44 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 221 HIS 0.006 0.001 HIS J 239 PHE 0.023 0.002 PHE M 55 TYR 0.014 0.002 TYR F 50 ARG 0.007 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 712 time to evaluate : 5.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TYR cc_start: 0.9179 (t80) cc_final: 0.8744 (t80) REVERT: A 195 LEU cc_start: 0.8718 (tt) cc_final: 0.8211 (mm) REVERT: B 74 MET cc_start: 0.8395 (tmm) cc_final: 0.7600 (tmm) REVERT: B 104 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: B 155 GLU cc_start: 0.8262 (tp30) cc_final: 0.7777 (tm-30) REVERT: B 195 LEU cc_start: 0.8795 (tt) cc_final: 0.8365 (mm) REVERT: B 234 GLN cc_start: 0.8321 (tp-100) cc_final: 0.8090 (tp-100) REVERT: B 244 MET cc_start: 0.8259 (tpp) cc_final: 0.7943 (tpt) REVERT: C 104 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: C 187 MET cc_start: 0.9127 (mmp) cc_final: 0.8582 (mmm) REVERT: C 195 LEU cc_start: 0.8648 (tt) cc_final: 0.8342 (mm) REVERT: C 229 ARG cc_start: 0.8175 (tpt90) cc_final: 0.7816 (tpp80) REVERT: D 171 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8159 (tt) REVERT: D 198 ILE cc_start: 0.9350 (mm) cc_final: 0.9079 (tt) REVERT: D 208 LYS cc_start: 0.8905 (tptp) cc_final: 0.8635 (tppt) REVERT: D 229 ARG cc_start: 0.8094 (tpp-160) cc_final: 0.7658 (tpp80) REVERT: D 230 GLU cc_start: 0.7953 (tp30) cc_final: 0.7752 (tp30) REVERT: D 237 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7865 (tm-30) REVERT: E 104 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7259 (m-80) REVERT: E 153 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8057 (tpp80) REVERT: E 187 MET cc_start: 0.9199 (mmp) cc_final: 0.8941 (mmm) REVERT: F 141 HIS cc_start: 0.7828 (p-80) cc_final: 0.7181 (p-80) REVERT: F 195 LEU cc_start: 0.8742 (tt) cc_final: 0.8325 (mm) REVERT: F 208 LYS cc_start: 0.8901 (tptp) cc_final: 0.8700 (tppt) REVERT: F 237 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7937 (tm-30) REVERT: F 250 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8678 (ttpp) REVERT: G 141 HIS cc_start: 0.7233 (p-80) cc_final: 0.6943 (p-80) REVERT: G 195 LEU cc_start: 0.8708 (tt) cc_final: 0.8221 (mm) REVERT: H 187 MET cc_start: 0.9145 (mmp) cc_final: 0.8919 (mmm) REVERT: H 195 LEU cc_start: 0.8798 (tt) cc_final: 0.8267 (mm) REVERT: H 208 LYS cc_start: 0.8946 (tptp) cc_final: 0.8312 (mmtp) REVERT: H 229 ARG cc_start: 0.8245 (tpt90) cc_final: 0.7982 (tpp80) REVERT: H 234 GLN cc_start: 0.8626 (tt0) cc_final: 0.8404 (tt0) REVERT: H 258 SER cc_start: 0.8589 (m) cc_final: 0.8294 (t) REVERT: I 208 LYS cc_start: 0.9039 (tptp) cc_final: 0.8398 (mmtm) REVERT: I 237 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8087 (tm-30) REVERT: I 242 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8394 (mt) REVERT: J 14 ARG cc_start: 0.8191 (mtm110) cc_final: 0.7055 (ptm160) REVERT: J 104 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: J 155 GLU cc_start: 0.8337 (tp30) cc_final: 0.7923 (tm-30) REVERT: K 31 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8388 (tm-30) REVERT: K 104 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7222 (m-80) REVERT: K 258 SER cc_start: 0.8354 (m) cc_final: 0.7980 (t) REVERT: L 195 LEU cc_start: 0.8767 (tt) cc_final: 0.8389 (mm) REVERT: L 208 LYS cc_start: 0.9119 (tptp) cc_final: 0.8563 (mmtm) REVERT: L 242 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8238 (mt) REVERT: M 171 ILE cc_start: 0.8557 (pt) cc_final: 0.8114 (pt) REVERT: M 195 LEU cc_start: 0.8668 (tt) cc_final: 0.8250 (mm) REVERT: M 208 LYS cc_start: 0.8939 (tptp) cc_final: 0.8440 (mmtm) REVERT: N 195 LEU cc_start: 0.8624 (tt) cc_final: 0.8264 (mm) REVERT: N 208 LYS cc_start: 0.9012 (tptp) cc_final: 0.8712 (tppt) REVERT: N 258 SER cc_start: 0.8199 (m) cc_final: 0.7859 (t) REVERT: O 104 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: O 129 TYR cc_start: 0.9095 (t80) cc_final: 0.8641 (t80) REVERT: O 195 LEU cc_start: 0.8822 (tt) cc_final: 0.8308 (mm) REVERT: O 208 LYS cc_start: 0.8940 (tptp) cc_final: 0.8413 (mmtm) REVERT: P 229 ARG cc_start: 0.8064 (tpt90) cc_final: 0.7619 (tpp80) REVERT: P 237 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8156 (tm-30) REVERT: Q 96 GLU cc_start: 0.7724 (pt0) cc_final: 0.7474 (pt0) REVERT: Q 187 MET cc_start: 0.9180 (mmp) cc_final: 0.8667 (mmm) REVERT: Q 208 LYS cc_start: 0.8946 (tptp) cc_final: 0.8367 (mmtm) REVERT: Q 244 MET cc_start: 0.8432 (tpp) cc_final: 0.7944 (tpt) REVERT: Q 258 SER cc_start: 0.8205 (m) cc_final: 0.7962 (t) REVERT: R 104 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: R 141 HIS cc_start: 0.7572 (p-80) cc_final: 0.7150 (p-80) REVERT: S 187 MET cc_start: 0.9187 (mmp) cc_final: 0.8916 (mmm) REVERT: S 195 LEU cc_start: 0.9011 (tt) cc_final: 0.8412 (mm) REVERT: S 208 LYS cc_start: 0.8889 (tptp) cc_final: 0.8531 (mmtm) REVERT: T 104 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: T 141 HIS cc_start: 0.8017 (p-80) cc_final: 0.7479 (p-80) REVERT: T 187 MET cc_start: 0.9271 (mmp) cc_final: 0.9011 (mmp) REVERT: T 195 LEU cc_start: 0.8800 (tt) cc_final: 0.8292 (mm) REVERT: T 208 LYS cc_start: 0.8900 (tppt) cc_final: 0.8477 (mmtm) REVERT: T 250 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8669 (ttpp) REVERT: U 104 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: U 176 GLU cc_start: 0.8126 (tp30) cc_final: 0.7899 (tp30) REVERT: V 104 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: V 187 MET cc_start: 0.9124 (mmm) cc_final: 0.8573 (mmm) REVERT: V 195 LEU cc_start: 0.8757 (tt) cc_final: 0.8195 (mm) REVERT: V 229 ARG cc_start: 0.8252 (tpt90) cc_final: 0.7839 (tpp80) REVERT: V 242 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8237 (mt) outliers start: 146 outliers final: 107 residues processed: 824 average time/residue: 0.5903 time to fit residues: 796.8416 Evaluate side-chains 730 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 608 time to evaluate : 5.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain F residue 266 ILE Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 258 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain O residue 104 PHE Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 104 PHE Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 104 PHE Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 104 PHE Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Chi-restraints excluded: chain V residue 258 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 chunk 432 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 520 optimal weight: 10.0000 chunk 562 optimal weight: 6.9990 chunk 463 optimal weight: 2.9990 chunk 516 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 417 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 46838 Z= 0.190 Angle : 0.525 6.219 63602 Z= 0.286 Chirality : 0.038 0.131 7414 Planarity : 0.005 0.065 7898 Dihedral : 4.052 16.897 6270 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.07 % Allowed : 17.20 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.11), residues: 5786 helix: 2.36 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.24 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 221 HIS 0.002 0.000 HIS S 141 PHE 0.015 0.001 PHE O 232 TYR 0.019 0.001 TYR R 51 ARG 0.006 0.000 ARG F 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 706 time to evaluate : 5.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TYR cc_start: 0.9171 (t80) cc_final: 0.8807 (t80) REVERT: A 187 MET cc_start: 0.9109 (mmm) cc_final: 0.8831 (mmm) REVERT: A 195 LEU cc_start: 0.8692 (tt) cc_final: 0.8227 (mm) REVERT: A 244 MET cc_start: 0.7979 (tpp) cc_final: 0.7670 (tpt) REVERT: B 74 MET cc_start: 0.8387 (tmm) cc_final: 0.7498 (tmm) REVERT: B 104 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: B 116 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7926 (tp) REVERT: B 128 TYR cc_start: 0.8981 (m-10) cc_final: 0.8654 (m-10) REVERT: B 155 GLU cc_start: 0.8205 (tp30) cc_final: 0.7806 (tm-30) REVERT: B 195 LEU cc_start: 0.8751 (tt) cc_final: 0.8339 (mm) REVERT: B 244 MET cc_start: 0.8272 (tpp) cc_final: 0.7957 (tpt) REVERT: C 74 MET cc_start: 0.8553 (tpp) cc_final: 0.8139 (tpp) REVERT: C 104 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7428 (m-80) REVERT: C 187 MET cc_start: 0.9104 (mmp) cc_final: 0.8460 (mmm) REVERT: C 191 ILE cc_start: 0.9274 (mt) cc_final: 0.9021 (mt) REVERT: C 195 LEU cc_start: 0.8529 (tt) cc_final: 0.8269 (mm) REVERT: C 229 ARG cc_start: 0.8112 (tpt90) cc_final: 0.7725 (tpp80) REVERT: D 13 GLN cc_start: 0.8018 (tp40) cc_final: 0.7040 (tm-30) REVERT: D 19 ILE cc_start: 0.8850 (mm) cc_final: 0.8609 (mt) REVERT: D 31 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8412 (tm-30) REVERT: D 229 ARG cc_start: 0.8008 (tpp-160) cc_final: 0.7724 (tpp80) REVERT: D 231 LEU cc_start: 0.8973 (tp) cc_final: 0.8588 (mm) REVERT: D 237 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7988 (tm-30) REVERT: E 19 ILE cc_start: 0.8980 (mm) cc_final: 0.8738 (mt) REVERT: E 104 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: E 145 PHE cc_start: 0.7098 (m-80) cc_final: 0.6890 (m-80) REVERT: E 153 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7966 (tpp80) REVERT: E 175 ASP cc_start: 0.8132 (m-30) cc_final: 0.7898 (m-30) REVERT: E 187 MET cc_start: 0.9177 (mmp) cc_final: 0.8899 (mmm) REVERT: F 141 HIS cc_start: 0.7741 (p-80) cc_final: 0.7152 (p-80) REVERT: F 195 LEU cc_start: 0.8698 (tt) cc_final: 0.8283 (mm) REVERT: F 208 LYS cc_start: 0.8943 (tptp) cc_final: 0.8705 (tppt) REVERT: F 237 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7914 (tm-30) REVERT: F 242 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7698 (mm) REVERT: F 250 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8632 (ttpp) REVERT: G 51 TYR cc_start: 0.9174 (t80) cc_final: 0.8857 (t80) REVERT: G 104 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: G 129 TYR cc_start: 0.9144 (t80) cc_final: 0.8723 (t80) REVERT: G 130 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7663 (mt-10) REVERT: G 195 LEU cc_start: 0.8800 (tt) cc_final: 0.8269 (mm) REVERT: H 195 LEU cc_start: 0.8808 (tt) cc_final: 0.8223 (mm) REVERT: H 208 LYS cc_start: 0.8960 (tptp) cc_final: 0.8316 (mmtp) REVERT: H 229 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7694 (tpp80) REVERT: H 258 SER cc_start: 0.8320 (m) cc_final: 0.8111 (t) REVERT: I 208 LYS cc_start: 0.9044 (tptp) cc_final: 0.8368 (mmtm) REVERT: J 14 ARG cc_start: 0.8321 (mtm110) cc_final: 0.7219 (ptm160) REVERT: J 104 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: J 130 GLU cc_start: 0.8182 (pp20) cc_final: 0.7799 (tm-30) REVERT: J 155 GLU cc_start: 0.8326 (tp30) cc_final: 0.7976 (tm-30) REVERT: J 187 MET cc_start: 0.9021 (mmp) cc_final: 0.8523 (mmm) REVERT: J 229 ARG cc_start: 0.8101 (tpt90) cc_final: 0.7807 (tpp80) REVERT: J 244 MET cc_start: 0.8387 (tpp) cc_final: 0.8084 (tpt) REVERT: K 19 ILE cc_start: 0.9027 (mm) cc_final: 0.8693 (mt) REVERT: K 31 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8369 (tm-30) REVERT: K 51 TYR cc_start: 0.9252 (t80) cc_final: 0.9012 (t80) REVERT: K 104 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7123 (m-80) REVERT: K 258 SER cc_start: 0.8026 (m) cc_final: 0.7672 (t) REVERT: L 195 LEU cc_start: 0.8749 (tt) cc_final: 0.8357 (mm) REVERT: L 208 LYS cc_start: 0.9127 (tptp) cc_final: 0.8541 (mmtm) REVERT: L 237 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7936 (tm-30) REVERT: L 280 LEU cc_start: 0.7723 (mt) cc_final: 0.7522 (pp) REVERT: M 128 TYR cc_start: 0.9113 (m-10) cc_final: 0.8791 (m-10) REVERT: M 144 MET cc_start: 0.7899 (ptp) cc_final: 0.7558 (ptt) REVERT: M 195 LEU cc_start: 0.8608 (tt) cc_final: 0.8226 (mm) REVERT: M 208 LYS cc_start: 0.8972 (tptp) cc_final: 0.8349 (mmtm) REVERT: M 244 MET cc_start: 0.8284 (tpp) cc_final: 0.7980 (tpt) REVERT: N 195 LEU cc_start: 0.8628 (tt) cc_final: 0.8259 (mm) REVERT: N 208 LYS cc_start: 0.8974 (tptp) cc_final: 0.8642 (tppt) REVERT: N 237 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7960 (tm-30) REVERT: N 258 SER cc_start: 0.8024 (m) cc_final: 0.7679 (t) REVERT: O 195 LEU cc_start: 0.8733 (tt) cc_final: 0.8219 (mm) REVERT: O 208 LYS cc_start: 0.8951 (tptp) cc_final: 0.8399 (mmtm) REVERT: P 74 MET cc_start: 0.8393 (tpp) cc_final: 0.8143 (tpp) REVERT: P 104 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: P 160 PHE cc_start: 0.8182 (m-80) cc_final: 0.7916 (m-80) REVERT: P 230 GLU cc_start: 0.7853 (tp30) cc_final: 0.7573 (tp30) REVERT: Q 141 HIS cc_start: 0.7946 (p-80) cc_final: 0.7332 (p-80) REVERT: Q 187 MET cc_start: 0.9161 (mmp) cc_final: 0.8532 (mmm) REVERT: Q 191 ILE cc_start: 0.9310 (mt) cc_final: 0.9043 (mt) REVERT: Q 208 LYS cc_start: 0.8972 (tptp) cc_final: 0.8334 (mmtm) REVERT: Q 244 MET cc_start: 0.8397 (tpp) cc_final: 0.7877 (tpt) REVERT: Q 258 SER cc_start: 0.8088 (m) cc_final: 0.7849 (t) REVERT: R 141 HIS cc_start: 0.7477 (p-80) cc_final: 0.7050 (p-80) REVERT: S 51 TYR cc_start: 0.9187 (t80) cc_final: 0.8714 (t80) REVERT: S 187 MET cc_start: 0.9248 (mmp) cc_final: 0.8938 (mmm) REVERT: S 195 LEU cc_start: 0.9091 (tt) cc_final: 0.8481 (mm) REVERT: S 208 LYS cc_start: 0.8912 (tptp) cc_final: 0.8520 (mmtm) REVERT: S 234 GLN cc_start: 0.8420 (tt0) cc_final: 0.8124 (tt0) REVERT: S 237 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7867 (tm-30) REVERT: S 280 LEU cc_start: 0.7406 (mt) cc_final: 0.7164 (pp) REVERT: T 141 HIS cc_start: 0.8009 (p-80) cc_final: 0.7498 (p-80) REVERT: T 187 MET cc_start: 0.9247 (mmp) cc_final: 0.9047 (mmm) REVERT: T 195 LEU cc_start: 0.8793 (tt) cc_final: 0.8294 (mm) REVERT: T 237 GLU cc_start: 0.8237 (tm-30) cc_final: 0.8023 (tm-30) REVERT: T 242 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8227 (mt) REVERT: T 250 LYS cc_start: 0.8800 (ttmt) cc_final: 0.8439 (ttpp) REVERT: U 104 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: V 187 MET cc_start: 0.9127 (mmm) cc_final: 0.8500 (mmm) REVERT: V 195 LEU cc_start: 0.8731 (tt) cc_final: 0.8188 (mm) REVERT: V 208 LYS cc_start: 0.8938 (tppt) cc_final: 0.8554 (mmtp) REVERT: V 229 ARG cc_start: 0.8231 (tpt90) cc_final: 0.7688 (tpp80) outliers start: 156 outliers final: 123 residues processed: 812 average time/residue: 0.5486 time to fit residues: 735.5883 Evaluate side-chains 773 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 638 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 104 PHE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 258 SER Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain J residue 104 PHE Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 258 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 41 CYS Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 104 PHE Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 245 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 3.9990 chunk 391 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 349 optimal weight: 4.9990 chunk 522 optimal weight: 6.9990 chunk 552 optimal weight: 0.9990 chunk 272 optimal weight: 10.0000 chunk 494 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 20 ASN P 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 46838 Z= 0.260 Angle : 0.539 13.797 63602 Z= 0.292 Chirality : 0.039 0.134 7414 Planarity : 0.004 0.047 7898 Dihedral : 3.990 15.875 6270 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.92 % Allowed : 18.20 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.11), residues: 5786 helix: 2.55 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.19 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 221 HIS 0.003 0.001 HIS J 239 PHE 0.017 0.001 PHE O 232 TYR 0.011 0.001 TYR O 129 ARG 0.005 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 658 time to evaluate : 5.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 TYR cc_start: 0.9164 (t80) cc_final: 0.8710 (t80) REVERT: A 187 MET cc_start: 0.8976 (mmm) cc_final: 0.8682 (mmm) REVERT: A 195 LEU cc_start: 0.8685 (tt) cc_final: 0.8197 (mm) REVERT: A 231 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 242 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.7975 (mm) REVERT: B 74 MET cc_start: 0.8328 (tmm) cc_final: 0.7427 (tmm) REVERT: B 116 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8044 (tp) REVERT: B 128 TYR cc_start: 0.9042 (m-10) cc_final: 0.8662 (m-10) REVERT: B 155 GLU cc_start: 0.8234 (tp30) cc_final: 0.7839 (tm-30) REVERT: B 195 LEU cc_start: 0.8798 (tt) cc_final: 0.8360 (mm) REVERT: B 244 MET cc_start: 0.8215 (tpp) cc_final: 0.7891 (tpt) REVERT: C 187 MET cc_start: 0.9080 (mmp) cc_final: 0.8436 (mmm) REVERT: C 191 ILE cc_start: 0.9267 (mt) cc_final: 0.8976 (mt) REVERT: C 195 LEU cc_start: 0.8656 (tt) cc_final: 0.8327 (mm) REVERT: C 229 ARG cc_start: 0.8093 (tpt90) cc_final: 0.7738 (tpp80) REVERT: D 31 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8680 (tm-30) REVERT: D 229 ARG cc_start: 0.8037 (tpp-160) cc_final: 0.7800 (tpp80) REVERT: D 231 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8611 (mm) REVERT: D 237 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8008 (tm-30) REVERT: E 153 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7813 (tpp80) REVERT: E 175 ASP cc_start: 0.8055 (m-30) cc_final: 0.7811 (m-30) REVERT: E 187 MET cc_start: 0.9271 (mmp) cc_final: 0.8987 (mmm) REVERT: E 195 LEU cc_start: 0.8702 (tt) cc_final: 0.8175 (mm) REVERT: F 141 HIS cc_start: 0.7752 (p-80) cc_final: 0.7239 (p-80) REVERT: F 195 LEU cc_start: 0.8730 (tt) cc_final: 0.8308 (mm) REVERT: F 208 LYS cc_start: 0.8978 (tptp) cc_final: 0.8695 (tppt) REVERT: F 237 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7933 (tm-30) REVERT: F 242 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.7783 (mm) REVERT: F 250 LYS cc_start: 0.8994 (ttmt) cc_final: 0.8642 (ttpp) REVERT: G 104 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: G 129 TYR cc_start: 0.9138 (t80) cc_final: 0.8706 (t80) REVERT: G 195 LEU cc_start: 0.8799 (tt) cc_final: 0.8251 (mm) REVERT: H 155 GLU cc_start: 0.8459 (tp30) cc_final: 0.8235 (tm-30) REVERT: H 195 LEU cc_start: 0.8784 (tt) cc_final: 0.8223 (mm) REVERT: H 208 LYS cc_start: 0.8978 (tptp) cc_final: 0.8636 (tppt) REVERT: H 258 SER cc_start: 0.8271 (m) cc_final: 0.8057 (t) REVERT: I 208 LYS cc_start: 0.9038 (tptp) cc_final: 0.8658 (tppt) REVERT: I 237 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8016 (tm-30) REVERT: J 155 GLU cc_start: 0.8305 (tp30) cc_final: 0.7962 (tm-30) REVERT: J 229 ARG cc_start: 0.8119 (tpt90) cc_final: 0.7670 (tpp80) REVERT: K 19 ILE cc_start: 0.9027 (mm) cc_final: 0.8691 (mt) REVERT: K 31 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8419 (tm-30) REVERT: K 51 TYR cc_start: 0.9212 (t80) cc_final: 0.8961 (t80) REVERT: K 104 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: K 237 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7988 (tm-30) REVERT: K 258 SER cc_start: 0.7881 (m) cc_final: 0.7490 (t) REVERT: L 195 LEU cc_start: 0.8773 (tt) cc_final: 0.8361 (mm) REVERT: L 208 LYS cc_start: 0.9098 (tptp) cc_final: 0.8779 (tppt) REVERT: M 144 MET cc_start: 0.7980 (ptp) cc_final: 0.7666 (ptt) REVERT: M 195 LEU cc_start: 0.8690 (tt) cc_final: 0.8280 (mm) REVERT: M 208 LYS cc_start: 0.8971 (tptp) cc_final: 0.8341 (mmtm) REVERT: N 195 LEU cc_start: 0.8649 (tt) cc_final: 0.8274 (mm) REVERT: N 208 LYS cc_start: 0.9019 (tptp) cc_final: 0.8696 (tppt) REVERT: N 237 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7908 (tm-30) REVERT: N 258 SER cc_start: 0.7933 (m) cc_final: 0.7569 (t) REVERT: O 195 LEU cc_start: 0.8749 (tt) cc_final: 0.8237 (mm) REVERT: O 208 LYS cc_start: 0.8931 (tptp) cc_final: 0.8454 (mmtm) REVERT: O 242 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8012 (mm) REVERT: P 74 MET cc_start: 0.8563 (tpp) cc_final: 0.8250 (tpp) REVERT: P 104 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: P 160 PHE cc_start: 0.8290 (m-80) cc_final: 0.7967 (m-80) REVERT: Q 96 GLU cc_start: 0.7669 (pt0) cc_final: 0.7452 (pt0) REVERT: Q 141 HIS cc_start: 0.7967 (p-80) cc_final: 0.7325 (p-80) REVERT: Q 187 MET cc_start: 0.9115 (mmp) cc_final: 0.8462 (mmm) REVERT: Q 191 ILE cc_start: 0.9331 (mt) cc_final: 0.9079 (mt) REVERT: Q 208 LYS cc_start: 0.8953 (tptp) cc_final: 0.8321 (mmtm) REVERT: Q 242 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8281 (mm) REVERT: Q 244 MET cc_start: 0.8430 (tpp) cc_final: 0.7940 (tpt) REVERT: R 141 HIS cc_start: 0.7482 (p-80) cc_final: 0.7186 (p-80) REVERT: R 195 LEU cc_start: 0.8877 (tt) cc_final: 0.8409 (mm) REVERT: S 51 TYR cc_start: 0.9173 (t80) cc_final: 0.8813 (t80) REVERT: S 187 MET cc_start: 0.9243 (mmp) cc_final: 0.8944 (mmm) REVERT: S 195 LEU cc_start: 0.9053 (tt) cc_final: 0.8475 (mm) REVERT: S 208 LYS cc_start: 0.8874 (tptp) cc_final: 0.8506 (mmtm) REVERT: S 230 GLU cc_start: 0.7809 (tp30) cc_final: 0.7585 (tp30) REVERT: T 141 HIS cc_start: 0.7991 (p-80) cc_final: 0.7516 (p-80) REVERT: T 187 MET cc_start: 0.9227 (mmp) cc_final: 0.8963 (mmp) REVERT: T 195 LEU cc_start: 0.8819 (tt) cc_final: 0.8312 (mm) REVERT: T 237 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7976 (tm-30) REVERT: T 242 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.7687 (mm) REVERT: T 250 LYS cc_start: 0.8840 (ttmt) cc_final: 0.8466 (ttpp) REVERT: U 104 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: U 195 LEU cc_start: 0.8849 (tt) cc_final: 0.8315 (mm) REVERT: V 187 MET cc_start: 0.8971 (mmm) cc_final: 0.8454 (mmm) REVERT: V 195 LEU cc_start: 0.8770 (tt) cc_final: 0.8250 (mm) REVERT: V 229 ARG cc_start: 0.8228 (tpt90) cc_final: 0.7695 (tpp80) outliers start: 199 outliers final: 155 residues processed: 819 average time/residue: 0.5800 time to fit residues: 793.9249 Evaluate side-chains 786 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 618 time to evaluate : 5.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 258 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 231 LEU Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 104 PHE Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain V residue 245 MET Chi-restraints excluded: chain V residue 258 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 411 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 471 optimal weight: 1.9990 chunk 382 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 282 optimal weight: 0.7980 chunk 496 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 46838 Z= 0.172 Angle : 0.502 9.357 63602 Z= 0.271 Chirality : 0.037 0.228 7414 Planarity : 0.004 0.047 7898 Dihedral : 3.923 15.962 6270 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.27 % Allowed : 19.82 % Favored : 76.92 % 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: 2.81 (0.11), residues: 5786 helix: 2.81 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.11 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 221 HIS 0.002 0.000 HIS U 246 PHE 0.014 0.001 PHE E 232 TYR 0.014 0.001 TYR O 129 ARG 0.004 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 701 time to evaluate : 5.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.9150 (t80) cc_final: 0.8902 (t80) REVERT: A 107 ILE cc_start: 0.8232 (mm) cc_final: 0.7991 (mm) REVERT: A 187 MET cc_start: 0.8947 (mmm) cc_final: 0.8623 (mmm) REVERT: A 188 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9158 (tp) REVERT: A 195 LEU cc_start: 0.8662 (tt) cc_final: 0.8179 (mm) REVERT: A 242 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.7912 (mm) REVERT: A 244 MET cc_start: 0.7979 (tpp) cc_final: 0.7457 (tpp) REVERT: B 74 MET cc_start: 0.8265 (tmm) cc_final: 0.7469 (tmm) REVERT: B 116 LEU cc_start: 0.8195 (tp) cc_final: 0.7969 (tp) REVERT: B 128 TYR cc_start: 0.9022 (m-10) cc_final: 0.8648 (m-10) REVERT: B 155 GLU cc_start: 0.8242 (tp30) cc_final: 0.7758 (tm-30) REVERT: B 195 LEU cc_start: 0.8807 (tt) cc_final: 0.8326 (mm) REVERT: B 244 MET cc_start: 0.8199 (tpp) cc_final: 0.7776 (tpt) REVERT: C 104 PHE cc_start: 0.7912 (m-80) cc_final: 0.7652 (m-10) REVERT: C 144 MET cc_start: 0.7939 (ptp) cc_final: 0.7632 (ppp) REVERT: C 187 MET cc_start: 0.9063 (mmp) cc_final: 0.8359 (mmm) REVERT: C 191 ILE cc_start: 0.9238 (mt) cc_final: 0.8952 (mt) REVERT: C 195 LEU cc_start: 0.8621 (tt) cc_final: 0.8284 (mm) REVERT: C 229 ARG cc_start: 0.8029 (tpt90) cc_final: 0.7693 (tpp80) REVERT: D 13 GLN cc_start: 0.8049 (tp40) cc_final: 0.7221 (tm-30) REVERT: D 187 MET cc_start: 0.8955 (tpp) cc_final: 0.8499 (mmm) REVERT: D 195 LEU cc_start: 0.8932 (tt) cc_final: 0.8404 (mm) REVERT: D 229 ARG cc_start: 0.7945 (tpp-160) cc_final: 0.7728 (tpp80) REVERT: D 231 LEU cc_start: 0.8832 (tp) cc_final: 0.8616 (mm) REVERT: E 145 PHE cc_start: 0.7094 (m-80) cc_final: 0.6795 (m-80) REVERT: E 153 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7766 (tpp80) REVERT: E 175 ASP cc_start: 0.8003 (m-30) cc_final: 0.7739 (m-30) REVERT: E 187 MET cc_start: 0.9268 (mmp) cc_final: 0.8987 (mmm) REVERT: E 195 LEU cc_start: 0.8692 (tt) cc_final: 0.8189 (mm) REVERT: F 141 HIS cc_start: 0.7664 (p-80) cc_final: 0.7185 (p-80) REVERT: F 195 LEU cc_start: 0.8723 (tt) cc_final: 0.8319 (mm) REVERT: F 208 LYS cc_start: 0.9006 (tptp) cc_final: 0.8688 (tppt) REVERT: F 237 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7854 (tm-30) REVERT: F 242 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.7686 (mm) REVERT: F 250 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8602 (ttpp) REVERT: G 116 LEU cc_start: 0.8427 (tp) cc_final: 0.8139 (tp) REVERT: G 154 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7965 (mm-30) REVERT: G 195 LEU cc_start: 0.8873 (tt) cc_final: 0.8341 (mm) REVERT: H 195 LEU cc_start: 0.8790 (tt) cc_final: 0.8232 (mm) REVERT: H 208 LYS cc_start: 0.8928 (tptp) cc_final: 0.8667 (tppt) REVERT: I 141 HIS cc_start: 0.7456 (p90) cc_final: 0.7045 (p-80) REVERT: I 208 LYS cc_start: 0.9047 (tptp) cc_final: 0.8452 (mmtm) REVERT: J 130 GLU cc_start: 0.8253 (pp20) cc_final: 0.7907 (tm-30) REVERT: J 155 GLU cc_start: 0.8148 (tp30) cc_final: 0.7858 (tm-30) REVERT: J 187 MET cc_start: 0.9104 (mmm) cc_final: 0.8678 (mmm) REVERT: J 229 ARG cc_start: 0.8059 (tpt90) cc_final: 0.7709 (tpp80) REVERT: J 242 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8507 (mm) REVERT: K 19 ILE cc_start: 0.9006 (mm) cc_final: 0.8667 (mt) REVERT: K 31 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8457 (tm-30) REVERT: K 104 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7071 (m-80) REVERT: K 237 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7961 (tm-30) REVERT: K 258 SER cc_start: 0.7802 (m) cc_final: 0.7448 (t) REVERT: L 195 LEU cc_start: 0.8773 (tt) cc_final: 0.8366 (mm) REVERT: L 208 LYS cc_start: 0.9088 (tptp) cc_final: 0.8767 (tppt) REVERT: L 237 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7974 (tm-30) REVERT: M 144 MET cc_start: 0.7949 (ptp) cc_final: 0.7636 (ptt) REVERT: M 195 LEU cc_start: 0.8634 (tt) cc_final: 0.8254 (mm) REVERT: M 208 LYS cc_start: 0.8976 (tptp) cc_final: 0.8393 (mmtm) REVERT: M 280 LEU cc_start: 0.7286 (mt) cc_final: 0.6943 (pp) REVERT: N 195 LEU cc_start: 0.8591 (tt) cc_final: 0.8234 (mm) REVERT: N 208 LYS cc_start: 0.8977 (tptp) cc_final: 0.8623 (tppt) REVERT: N 237 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7949 (tm-30) REVERT: N 258 SER cc_start: 0.7623 (m) cc_final: 0.7245 (t) REVERT: O 195 LEU cc_start: 0.8730 (tt) cc_final: 0.8240 (mm) REVERT: O 208 LYS cc_start: 0.8998 (tptp) cc_final: 0.8511 (mmtm) REVERT: O 242 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8468 (mt) REVERT: O 244 MET cc_start: 0.7798 (tpp) cc_final: 0.7470 (tpp) REVERT: P 74 MET cc_start: 0.8538 (tpp) cc_final: 0.8227 (tpp) REVERT: P 104 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: P 195 LEU cc_start: 0.8782 (tt) cc_final: 0.8274 (mm) REVERT: P 234 GLN cc_start: 0.8469 (tt0) cc_final: 0.8259 (tt0) REVERT: Q 187 MET cc_start: 0.9112 (mmp) cc_final: 0.8457 (mmm) REVERT: Q 208 LYS cc_start: 0.8960 (tptp) cc_final: 0.8665 (tppt) REVERT: Q 242 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8166 (mm) REVERT: Q 244 MET cc_start: 0.8410 (tpp) cc_final: 0.7981 (tpt) REVERT: R 141 HIS cc_start: 0.7519 (p-80) cc_final: 0.7149 (p-80) REVERT: S 51 TYR cc_start: 0.9088 (t80) cc_final: 0.8736 (t80) REVERT: S 187 MET cc_start: 0.9238 (mmp) cc_final: 0.8920 (mmm) REVERT: S 195 LEU cc_start: 0.9031 (tt) cc_final: 0.8441 (mm) REVERT: S 208 LYS cc_start: 0.8879 (tptp) cc_final: 0.8535 (mmtm) REVERT: T 141 HIS cc_start: 0.8001 (p-80) cc_final: 0.7539 (p-80) REVERT: T 195 LEU cc_start: 0.8797 (tt) cc_final: 0.8275 (mm) REVERT: T 237 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7960 (tm-30) REVERT: T 242 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.7696 (mm) REVERT: T 250 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8496 (ttpp) REVERT: U 195 LEU cc_start: 0.8849 (tt) cc_final: 0.8317 (mm) REVERT: V 187 MET cc_start: 0.8972 (mmm) cc_final: 0.8465 (mmm) REVERT: V 195 LEU cc_start: 0.8774 (tt) cc_final: 0.8300 (mm) REVERT: V 229 ARG cc_start: 0.8146 (tpt90) cc_final: 0.7634 (tpp80) outliers start: 166 outliers final: 127 residues processed: 815 average time/residue: 0.5409 time to fit residues: 726.3863 Evaluate side-chains 778 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 641 time to evaluate : 5.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 258 SER Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 187 MET Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 104 PHE Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain V residue 245 MET Chi-restraints excluded: chain V residue 258 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 2.9990 chunk 497 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 324 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 553 optimal weight: 0.9980 chunk 459 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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: 0.8076 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 46838 Z= 0.220 Angle : 0.532 12.356 63602 Z= 0.286 Chirality : 0.038 0.177 7414 Planarity : 0.004 0.048 7898 Dihedral : 3.862 16.090 6270 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.88 % Allowed : 19.95 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.11), residues: 5786 helix: 2.84 (0.07), residues: 4554 sheet: None (None), residues: 0 loop : -2.17 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 221 HIS 0.002 0.000 HIS C 181 PHE 0.016 0.001 PHE F 232 TYR 0.013 0.001 TYR A 129 ARG 0.003 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 677 time to evaluate : 5.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.9096 (t80) cc_final: 0.8886 (t80) REVERT: A 187 MET cc_start: 0.8945 (mmm) cc_final: 0.8618 (mmm) REVERT: A 188 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9176 (tp) REVERT: A 195 LEU cc_start: 0.8667 (tt) cc_final: 0.8181 (mm) REVERT: A 231 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8474 (mm) REVERT: A 242 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.7926 (mm) REVERT: A 244 MET cc_start: 0.7996 (tpp) cc_final: 0.7669 (tpt) REVERT: B 74 MET cc_start: 0.8287 (tmm) cc_final: 0.7540 (tmm) REVERT: B 116 LEU cc_start: 0.8295 (tp) cc_final: 0.8010 (tp) REVERT: B 128 TYR cc_start: 0.9018 (m-10) cc_final: 0.8529 (m-10) REVERT: B 155 GLU cc_start: 0.8270 (tp30) cc_final: 0.7755 (tm-30) REVERT: B 195 LEU cc_start: 0.8800 (tt) cc_final: 0.8318 (mm) REVERT: B 244 MET cc_start: 0.8191 (tpp) cc_final: 0.7890 (tpt) REVERT: C 144 MET cc_start: 0.8179 (ptp) cc_final: 0.7838 (ppp) REVERT: C 187 MET cc_start: 0.9024 (mmp) cc_final: 0.8287 (mmm) REVERT: C 191 ILE cc_start: 0.9263 (mt) cc_final: 0.8946 (mt) REVERT: C 195 LEU cc_start: 0.8580 (tt) cc_final: 0.8235 (mm) REVERT: C 229 ARG cc_start: 0.8049 (tpt90) cc_final: 0.7711 (tpp80) REVERT: D 13 GLN cc_start: 0.8125 (tp40) cc_final: 0.7247 (tm-30) REVERT: D 116 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8267 (tp) REVERT: D 195 LEU cc_start: 0.8903 (tt) cc_final: 0.8369 (mm) REVERT: D 229 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7747 (tpp80) REVERT: D 231 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8645 (mm) REVERT: E 145 PHE cc_start: 0.7153 (m-80) cc_final: 0.6949 (m-80) REVERT: E 153 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7722 (tpp80) REVERT: E 175 ASP cc_start: 0.8036 (m-30) cc_final: 0.7747 (m-30) REVERT: E 187 MET cc_start: 0.9272 (mmp) cc_final: 0.8980 (mmm) REVERT: E 195 LEU cc_start: 0.8715 (tt) cc_final: 0.8194 (mm) REVERT: F 141 HIS cc_start: 0.7674 (p-80) cc_final: 0.7221 (p-80) REVERT: F 144 MET cc_start: 0.8035 (ptp) cc_final: 0.7705 (ptp) REVERT: F 195 LEU cc_start: 0.8818 (tt) cc_final: 0.8246 (mm) REVERT: F 208 LYS cc_start: 0.8984 (tptp) cc_final: 0.8385 (mmtm) REVERT: F 237 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7896 (tm-30) REVERT: F 242 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7735 (mm) REVERT: F 250 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8518 (ttpp) REVERT: G 116 LEU cc_start: 0.8457 (tp) cc_final: 0.8149 (tp) REVERT: G 195 LEU cc_start: 0.8895 (tt) cc_final: 0.8345 (mm) REVERT: H 176 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7784 (tm-30) REVERT: H 195 LEU cc_start: 0.8785 (tt) cc_final: 0.8236 (mm) REVERT: H 208 LYS cc_start: 0.8885 (tptp) cc_final: 0.8667 (tppt) REVERT: I 208 LYS cc_start: 0.9026 (tptp) cc_final: 0.8420 (mmtm) REVERT: I 242 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8319 (mt) REVERT: J 130 GLU cc_start: 0.8230 (pp20) cc_final: 0.7878 (tm-30) REVERT: J 155 GLU cc_start: 0.8134 (tp30) cc_final: 0.7853 (tm-30) REVERT: J 187 MET cc_start: 0.9102 (mmm) cc_final: 0.8718 (mmm) REVERT: J 229 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7624 (tpp80) REVERT: J 242 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8484 (mm) REVERT: K 19 ILE cc_start: 0.8986 (mm) cc_final: 0.8652 (mt) REVERT: K 31 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8461 (tm-30) REVERT: K 195 LEU cc_start: 0.8535 (tt) cc_final: 0.8150 (mm) REVERT: K 237 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7911 (tm-30) REVERT: K 258 SER cc_start: 0.7820 (m) cc_final: 0.7471 (t) REVERT: L 195 LEU cc_start: 0.8780 (tt) cc_final: 0.8363 (mm) REVERT: L 208 LYS cc_start: 0.9072 (tptp) cc_final: 0.8762 (tppt) REVERT: L 242 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7671 (mm) REVERT: M 195 LEU cc_start: 0.8647 (tt) cc_final: 0.8358 (mm) REVERT: M 208 LYS cc_start: 0.8971 (tptp) cc_final: 0.8389 (mmtm) REVERT: N 195 LEU cc_start: 0.8600 (tt) cc_final: 0.8238 (mm) REVERT: N 208 LYS cc_start: 0.9018 (tptp) cc_final: 0.8716 (tppt) REVERT: N 237 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7897 (tm-30) REVERT: N 258 SER cc_start: 0.7629 (m) cc_final: 0.7263 (t) REVERT: O 195 LEU cc_start: 0.8716 (tt) cc_final: 0.8191 (mm) REVERT: O 208 LYS cc_start: 0.8971 (tptp) cc_final: 0.8473 (mmtm) REVERT: O 242 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8013 (mm) REVERT: P 74 MET cc_start: 0.8590 (tpp) cc_final: 0.8233 (tpp) REVERT: P 195 LEU cc_start: 0.8792 (tt) cc_final: 0.8296 (mm) REVERT: P 234 GLN cc_start: 0.8461 (tt0) cc_final: 0.8207 (tt0) REVERT: Q 141 HIS cc_start: 0.7943 (p-80) cc_final: 0.7259 (p-80) REVERT: Q 187 MET cc_start: 0.9113 (mmp) cc_final: 0.8427 (mmm) REVERT: Q 191 ILE cc_start: 0.9272 (mt) cc_final: 0.9069 (mt) REVERT: Q 208 LYS cc_start: 0.8959 (tptp) cc_final: 0.8671 (tppt) REVERT: Q 242 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8290 (mm) REVERT: Q 244 MET cc_start: 0.8441 (tpp) cc_final: 0.7984 (tpt) REVERT: R 141 HIS cc_start: 0.7546 (p-80) cc_final: 0.7177 (p-80) REVERT: R 195 LEU cc_start: 0.8888 (tt) cc_final: 0.8404 (mm) REVERT: S 51 TYR cc_start: 0.9072 (t80) cc_final: 0.8839 (t80) REVERT: S 187 MET cc_start: 0.9238 (mmp) cc_final: 0.8952 (mmm) REVERT: S 195 LEU cc_start: 0.9004 (tt) cc_final: 0.8378 (mm) REVERT: S 208 LYS cc_start: 0.8891 (tptp) cc_final: 0.8562 (mmtm) REVERT: T 141 HIS cc_start: 0.7983 (p-80) cc_final: 0.7490 (p-80) REVERT: T 187 MET cc_start: 0.9132 (mmm) cc_final: 0.8866 (mmp) REVERT: T 195 LEU cc_start: 0.8822 (tt) cc_final: 0.8315 (mm) REVERT: T 242 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7633 (mm) REVERT: T 250 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8491 (ttpp) REVERT: U 116 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8120 (tp) REVERT: U 195 LEU cc_start: 0.8895 (tt) cc_final: 0.8356 (mm) REVERT: V 187 MET cc_start: 0.8979 (mmm) cc_final: 0.8470 (mmm) REVERT: V 195 LEU cc_start: 0.8787 (tt) cc_final: 0.8309 (mm) REVERT: V 229 ARG cc_start: 0.8149 (tpt90) cc_final: 0.7662 (tpp80) outliers start: 197 outliers final: 170 residues processed: 830 average time/residue: 0.5345 time to fit residues: 734.1997 Evaluate side-chains 823 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 639 time to evaluate : 5.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 258 SER Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain Q residue 255 ILE Chi-restraints excluded: chain Q residue 280 LEU Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 153 ARG Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 231 LEU Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Chi-restraints excluded: chain V residue 258 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 404 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 465 optimal weight: 5.9990 chunk 309 optimal weight: 0.7980 chunk 551 optimal weight: 0.6980 chunk 345 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 141 HIS I 227 ASN S 227 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 46838 Z= 0.169 Angle : 0.511 10.457 63602 Z= 0.273 Chirality : 0.037 0.142 7414 Planarity : 0.004 0.047 7898 Dihedral : 3.830 15.788 6270 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.66 % Allowed : 20.54 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.11), residues: 5786 helix: 2.96 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.16 (0.16), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 221 HIS 0.002 0.000 HIS E 181 PHE 0.017 0.001 PHE L 145 TYR 0.015 0.001 TYR A 129 ARG 0.003 0.000 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 690 time to evaluate : 5.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ILE cc_start: 0.8251 (mm) cc_final: 0.8029 (mm) REVERT: A 187 MET cc_start: 0.8934 (mmm) cc_final: 0.8590 (mmm) REVERT: A 188 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9185 (tp) REVERT: A 195 LEU cc_start: 0.8658 (tt) cc_final: 0.8181 (mm) REVERT: A 242 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7879 (mm) REVERT: A 244 MET cc_start: 0.8020 (tpp) cc_final: 0.7673 (tpt) REVERT: B 74 MET cc_start: 0.8210 (tmm) cc_final: 0.7478 (tmm) REVERT: B 116 LEU cc_start: 0.8264 (tp) cc_final: 0.8007 (tp) REVERT: B 128 TYR cc_start: 0.9002 (m-10) cc_final: 0.8579 (m-10) REVERT: B 155 GLU cc_start: 0.8197 (tp30) cc_final: 0.7670 (tm-30) REVERT: B 195 LEU cc_start: 0.8786 (tt) cc_final: 0.8317 (mm) REVERT: B 244 MET cc_start: 0.8212 (tpp) cc_final: 0.7805 (tpt) REVERT: C 144 MET cc_start: 0.8158 (ptp) cc_final: 0.7866 (ppp) REVERT: C 187 MET cc_start: 0.9021 (mmp) cc_final: 0.8281 (mmm) REVERT: C 191 ILE cc_start: 0.9264 (mt) cc_final: 0.8949 (mt) REVERT: C 195 LEU cc_start: 0.8572 (tt) cc_final: 0.8237 (mm) REVERT: C 229 ARG cc_start: 0.8001 (tpt90) cc_final: 0.7683 (tpp80) REVERT: D 13 GLN cc_start: 0.8117 (tp40) cc_final: 0.7109 (tm-30) REVERT: D 19 ILE cc_start: 0.8861 (mm) cc_final: 0.8598 (mt) REVERT: D 31 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8485 (tm-30) REVERT: D 155 GLU cc_start: 0.8315 (tp30) cc_final: 0.8007 (tm-30) REVERT: D 187 MET cc_start: 0.8942 (tpp) cc_final: 0.8470 (mmm) REVERT: D 195 LEU cc_start: 0.8889 (tt) cc_final: 0.8372 (mm) REVERT: D 229 ARG cc_start: 0.8008 (tpp-160) cc_final: 0.7741 (tpp80) REVERT: D 231 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8657 (mm) REVERT: E 145 PHE cc_start: 0.7133 (m-80) cc_final: 0.6883 (m-80) REVERT: E 153 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7736 (tpp80) REVERT: E 175 ASP cc_start: 0.8099 (m-30) cc_final: 0.7781 (m-30) REVERT: E 187 MET cc_start: 0.9264 (mmp) cc_final: 0.8970 (mmm) REVERT: E 195 LEU cc_start: 0.8753 (tt) cc_final: 0.8238 (mm) REVERT: F 141 HIS cc_start: 0.7617 (p-80) cc_final: 0.7161 (p-80) REVERT: F 144 MET cc_start: 0.8112 (ptp) cc_final: 0.7878 (ptp) REVERT: F 195 LEU cc_start: 0.8813 (tt) cc_final: 0.8237 (mm) REVERT: F 208 LYS cc_start: 0.8979 (tptp) cc_final: 0.8371 (mmtm) REVERT: F 242 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.7649 (mm) REVERT: F 250 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8520 (ttpp) REVERT: G 116 LEU cc_start: 0.8359 (tp) cc_final: 0.8095 (tp) REVERT: G 258 SER cc_start: 0.8143 (m) cc_final: 0.7918 (t) REVERT: H 195 LEU cc_start: 0.8799 (tt) cc_final: 0.8275 (mm) REVERT: H 208 LYS cc_start: 0.8941 (tptp) cc_final: 0.8649 (tppt) REVERT: I 116 LEU cc_start: 0.8203 (tp) cc_final: 0.7846 (tp) REVERT: I 208 LYS cc_start: 0.9030 (tptp) cc_final: 0.8414 (mmtm) REVERT: I 242 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8249 (mt) REVERT: J 130 GLU cc_start: 0.8186 (pp20) cc_final: 0.7839 (tm-30) REVERT: J 155 GLU cc_start: 0.8093 (tp30) cc_final: 0.7763 (tm-30) REVERT: J 187 MET cc_start: 0.9070 (mmm) cc_final: 0.8730 (mmm) REVERT: J 229 ARG cc_start: 0.8013 (tpt90) cc_final: 0.7568 (tpp80) REVERT: J 242 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8508 (mm) REVERT: K 19 ILE cc_start: 0.8977 (mm) cc_final: 0.8647 (mt) REVERT: K 195 LEU cc_start: 0.8533 (tt) cc_final: 0.8157 (mm) REVERT: K 258 SER cc_start: 0.7599 (m) cc_final: 0.7290 (t) REVERT: L 116 LEU cc_start: 0.8236 (tp) cc_final: 0.7892 (tp) REVERT: L 195 LEU cc_start: 0.8842 (tt) cc_final: 0.8407 (mm) REVERT: L 208 LYS cc_start: 0.9073 (tptp) cc_final: 0.8562 (mmtm) REVERT: L 237 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8033 (tm-30) REVERT: M 128 TYR cc_start: 0.8910 (m-10) cc_final: 0.8682 (m-10) REVERT: M 144 MET cc_start: 0.7850 (ptt) cc_final: 0.7581 (ptt) REVERT: M 195 LEU cc_start: 0.8597 (tt) cc_final: 0.8339 (mm) REVERT: M 208 LYS cc_start: 0.8971 (tptp) cc_final: 0.8380 (mmtm) REVERT: N 195 LEU cc_start: 0.8593 (tt) cc_final: 0.8235 (mm) REVERT: N 208 LYS cc_start: 0.8979 (tptp) cc_final: 0.8668 (tppt) REVERT: N 237 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7870 (tm-30) REVERT: N 258 SER cc_start: 0.7473 (m) cc_final: 0.7124 (t) REVERT: O 195 LEU cc_start: 0.8667 (tt) cc_final: 0.8147 (mm) REVERT: O 208 LYS cc_start: 0.8988 (tptp) cc_final: 0.8494 (mmtm) REVERT: O 242 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.7950 (mm) REVERT: O 244 MET cc_start: 0.7741 (tpp) cc_final: 0.7385 (tpp) REVERT: P 104 PHE cc_start: 0.7719 (m-80) cc_final: 0.7348 (m-10) REVERT: P 128 TYR cc_start: 0.8981 (m-10) cc_final: 0.8648 (m-10) REVERT: P 195 LEU cc_start: 0.8780 (tt) cc_final: 0.8292 (mm) REVERT: P 234 GLN cc_start: 0.8470 (tt0) cc_final: 0.8227 (tt0) REVERT: Q 141 HIS cc_start: 0.7916 (p-80) cc_final: 0.7241 (p-80) REVERT: Q 187 MET cc_start: 0.9085 (mmp) cc_final: 0.8342 (mmm) REVERT: Q 191 ILE cc_start: 0.9304 (mt) cc_final: 0.9079 (mt) REVERT: Q 208 LYS cc_start: 0.8958 (tptp) cc_final: 0.8657 (tppt) REVERT: Q 242 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8144 (mm) REVERT: Q 244 MET cc_start: 0.8422 (tpp) cc_final: 0.7967 (tpt) REVERT: R 141 HIS cc_start: 0.7490 (p-80) cc_final: 0.7119 (p-80) REVERT: S 187 MET cc_start: 0.9242 (mmp) cc_final: 0.8940 (mmm) REVERT: S 195 LEU cc_start: 0.8993 (tt) cc_final: 0.8381 (mm) REVERT: S 208 LYS cc_start: 0.8888 (tptp) cc_final: 0.8547 (mmtm) REVERT: T 129 TYR cc_start: 0.9313 (t80) cc_final: 0.8989 (t80) REVERT: T 141 HIS cc_start: 0.7981 (p-80) cc_final: 0.7507 (p-80) REVERT: T 187 MET cc_start: 0.9113 (mmm) cc_final: 0.8838 (mmp) REVERT: T 195 LEU cc_start: 0.8791 (tt) cc_final: 0.8207 (mm) REVERT: T 237 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7854 (tm-30) REVERT: T 242 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.7658 (mm) REVERT: T 250 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8521 (ttpp) REVERT: U 116 LEU cc_start: 0.8366 (tp) cc_final: 0.8063 (tp) REVERT: U 129 TYR cc_start: 0.9115 (t80) cc_final: 0.8708 (t80) REVERT: U 195 LEU cc_start: 0.8870 (tt) cc_final: 0.8332 (mm) REVERT: V 187 MET cc_start: 0.8972 (mmm) cc_final: 0.8476 (mmm) REVERT: V 195 LEU cc_start: 0.8777 (tt) cc_final: 0.8307 (mm) REVERT: V 229 ARG cc_start: 0.8105 (tpt90) cc_final: 0.7632 (tpp80) outliers start: 186 outliers final: 159 residues processed: 814 average time/residue: 0.5317 time to fit residues: 715.1359 Evaluate side-chains 826 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 657 time to evaluate : 5.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 258 SER Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 187 MET Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 258 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 231 LEU Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Chi-restraints excluded: chain V residue 258 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 329 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 chunk 272 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 433 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.8079 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 46838 Z= 0.238 Angle : 0.540 9.715 63602 Z= 0.290 Chirality : 0.038 0.171 7414 Planarity : 0.004 0.047 7898 Dihedral : 3.819 15.870 6270 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.82 % Allowed : 20.78 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.11), residues: 5786 helix: 2.91 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.24 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 221 HIS 0.002 0.001 HIS E 181 PHE 0.015 0.001 PHE F 232 TYR 0.015 0.001 TYR A 129 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 683 time to evaluate : 5.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9196 (tp) REVERT: A 195 LEU cc_start: 0.8675 (tt) cc_final: 0.8173 (mm) REVERT: A 242 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 244 MET cc_start: 0.8033 (tpp) cc_final: 0.7683 (tpt) REVERT: B 74 MET cc_start: 0.8264 (tmm) cc_final: 0.7562 (tmm) REVERT: B 116 LEU cc_start: 0.8285 (tp) cc_final: 0.7986 (tp) REVERT: B 128 TYR cc_start: 0.9008 (m-10) cc_final: 0.8513 (m-10) REVERT: B 155 GLU cc_start: 0.8164 (tp30) cc_final: 0.7929 (tm-30) REVERT: B 195 LEU cc_start: 0.8797 (tt) cc_final: 0.8321 (mm) REVERT: B 244 MET cc_start: 0.8202 (tpp) cc_final: 0.7763 (tpt) REVERT: C 144 MET cc_start: 0.8213 (ptp) cc_final: 0.7887 (ppp) REVERT: C 187 MET cc_start: 0.9023 (mmp) cc_final: 0.8293 (mmm) REVERT: C 191 ILE cc_start: 0.9291 (mt) cc_final: 0.8977 (mt) REVERT: C 195 LEU cc_start: 0.8585 (tt) cc_final: 0.8232 (mm) REVERT: C 229 ARG cc_start: 0.8043 (tpt90) cc_final: 0.7706 (tpp80) REVERT: D 13 GLN cc_start: 0.8064 (tp40) cc_final: 0.7622 (tm-30) REVERT: D 155 GLU cc_start: 0.8303 (tp30) cc_final: 0.8053 (tm-30) REVERT: D 195 LEU cc_start: 0.8902 (tt) cc_final: 0.8369 (mm) REVERT: D 231 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8666 (mm) REVERT: E 153 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7788 (tpp80) REVERT: E 175 ASP cc_start: 0.8105 (m-30) cc_final: 0.7777 (m-30) REVERT: E 187 MET cc_start: 0.9275 (mmp) cc_final: 0.8988 (mmm) REVERT: E 195 LEU cc_start: 0.8709 (tt) cc_final: 0.8169 (mm) REVERT: F 141 HIS cc_start: 0.7686 (p-80) cc_final: 0.7240 (p-80) REVERT: F 144 MET cc_start: 0.8141 (ptp) cc_final: 0.7907 (ptp) REVERT: F 195 LEU cc_start: 0.8827 (tt) cc_final: 0.8232 (mm) REVERT: F 208 LYS cc_start: 0.8978 (tptp) cc_final: 0.8374 (mmtm) REVERT: F 237 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7783 (tm-30) REVERT: F 242 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7732 (mm) REVERT: F 243 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8814 (tp) REVERT: F 250 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8548 (ttpp) REVERT: G 116 LEU cc_start: 0.8459 (tp) cc_final: 0.8146 (tp) REVERT: G 258 SER cc_start: 0.8158 (m) cc_final: 0.7923 (t) REVERT: H 176 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7722 (tm-30) REVERT: H 195 LEU cc_start: 0.8778 (tt) cc_final: 0.8251 (mm) REVERT: H 208 LYS cc_start: 0.8912 (tptp) cc_final: 0.8669 (tppt) REVERT: I 116 LEU cc_start: 0.8259 (tp) cc_final: 0.7894 (tp) REVERT: I 208 LYS cc_start: 0.9076 (tptp) cc_final: 0.8503 (mmtm) REVERT: I 242 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8311 (mt) REVERT: I 250 LYS cc_start: 0.8959 (ttmt) cc_final: 0.8389 (tttm) REVERT: J 130 GLU cc_start: 0.8207 (pp20) cc_final: 0.7855 (tm-30) REVERT: J 155 GLU cc_start: 0.8105 (tp30) cc_final: 0.7791 (tm-30) REVERT: J 187 MET cc_start: 0.9071 (mmm) cc_final: 0.8759 (mmm) REVERT: J 229 ARG cc_start: 0.8048 (tpt90) cc_final: 0.7591 (tpp80) REVERT: J 242 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8489 (mm) REVERT: K 19 ILE cc_start: 0.8985 (mm) cc_final: 0.8661 (mt) REVERT: K 195 LEU cc_start: 0.8549 (tt) cc_final: 0.8162 (mm) REVERT: K 258 SER cc_start: 0.7701 (m) cc_final: 0.7380 (t) REVERT: L 116 LEU cc_start: 0.8319 (tp) cc_final: 0.7933 (tp) REVERT: L 195 LEU cc_start: 0.8855 (tt) cc_final: 0.8418 (mm) REVERT: L 208 LYS cc_start: 0.9064 (tptp) cc_final: 0.8564 (mmtm) REVERT: L 242 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7804 (mm) REVERT: M 128 TYR cc_start: 0.8984 (m-10) cc_final: 0.8596 (m-10) REVERT: M 144 MET cc_start: 0.7898 (ptt) cc_final: 0.7634 (ptt) REVERT: M 195 LEU cc_start: 0.8647 (tt) cc_final: 0.8356 (mm) REVERT: M 208 LYS cc_start: 0.8971 (tptp) cc_final: 0.8379 (mmtm) REVERT: N 195 LEU cc_start: 0.8565 (tt) cc_final: 0.8182 (mm) REVERT: N 208 LYS cc_start: 0.8971 (tptp) cc_final: 0.8667 (tppt) REVERT: N 237 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7843 (tm-30) REVERT: N 258 SER cc_start: 0.7558 (m) cc_final: 0.7211 (t) REVERT: O 195 LEU cc_start: 0.8676 (tt) cc_final: 0.8141 (mm) REVERT: O 208 LYS cc_start: 0.8990 (tptp) cc_final: 0.8497 (mmtm) REVERT: O 242 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8025 (mm) REVERT: O 244 MET cc_start: 0.7748 (tpp) cc_final: 0.7383 (tpp) REVERT: P 74 MET cc_start: 0.8223 (tpp) cc_final: 0.7914 (tpp) REVERT: P 175 ASP cc_start: 0.7849 (m-30) cc_final: 0.7607 (m-30) REVERT: P 195 LEU cc_start: 0.8791 (tt) cc_final: 0.8285 (mm) REVERT: Q 141 HIS cc_start: 0.7894 (p-80) cc_final: 0.7221 (p-80) REVERT: Q 187 MET cc_start: 0.9081 (mmp) cc_final: 0.8405 (mmm) REVERT: Q 191 ILE cc_start: 0.9322 (mt) cc_final: 0.9096 (mt) REVERT: Q 208 LYS cc_start: 0.8945 (tptp) cc_final: 0.8640 (tppt) REVERT: Q 242 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8174 (mm) REVERT: Q 244 MET cc_start: 0.8450 (tpp) cc_final: 0.8019 (tpt) REVERT: R 141 HIS cc_start: 0.7491 (p-80) cc_final: 0.7102 (p-80) REVERT: R 195 LEU cc_start: 0.8885 (tt) cc_final: 0.8404 (mm) REVERT: S 51 TYR cc_start: 0.9058 (t80) cc_final: 0.8842 (t80) REVERT: S 187 MET cc_start: 0.9225 (mmp) cc_final: 0.8952 (mmm) REVERT: S 195 LEU cc_start: 0.9004 (tt) cc_final: 0.8381 (mm) REVERT: S 208 LYS cc_start: 0.8887 (tptp) cc_final: 0.8545 (mmtm) REVERT: T 141 HIS cc_start: 0.7959 (p-80) cc_final: 0.7479 (p-80) REVERT: T 187 MET cc_start: 0.9164 (mmm) cc_final: 0.8790 (mmp) REVERT: T 195 LEU cc_start: 0.8802 (tt) cc_final: 0.8216 (mm) REVERT: T 242 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7640 (mm) REVERT: T 250 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8517 (ttpp) REVERT: U 116 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8096 (tp) REVERT: U 195 LEU cc_start: 0.8881 (tt) cc_final: 0.8339 (mm) REVERT: V 187 MET cc_start: 0.8991 (mmm) cc_final: 0.8493 (mmm) REVERT: V 195 LEU cc_start: 0.8790 (tt) cc_final: 0.8312 (mm) REVERT: V 229 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7635 (tpp80) outliers start: 194 outliers final: 178 residues processed: 840 average time/residue: 0.5388 time to fit residues: 750.2889 Evaluate side-chains 835 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 644 time to evaluate : 5.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 240 SER Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 187 MET Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain O residue 248 ILE Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 231 LEU Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Chi-restraints excluded: chain V residue 258 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 4.9990 chunk 528 optimal weight: 0.0070 chunk 481 optimal weight: 5.9990 chunk 513 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 403 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 464 optimal weight: 5.9990 chunk 485 optimal weight: 4.9990 chunk 511 optimal weight: 3.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 46838 Z= 0.214 Angle : 0.543 9.863 63602 Z= 0.290 Chirality : 0.037 0.147 7414 Planarity : 0.004 0.047 7898 Dihedral : 3.822 15.737 6270 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.88 % Allowed : 20.94 % Favored : 75.19 % 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: 2.98 (0.11), residues: 5786 helix: 2.96 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.27 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 221 HIS 0.002 0.000 HIS E 181 PHE 0.015 0.001 PHE C 104 TYR 0.015 0.001 TYR A 129 ARG 0.004 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 672 time to evaluate : 5.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ILE cc_start: 0.8297 (mm) cc_final: 0.8060 (mm) REVERT: A 176 GLU cc_start: 0.7788 (tp30) cc_final: 0.7555 (tm-30) REVERT: A 188 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9220 (tp) REVERT: A 195 LEU cc_start: 0.8670 (tt) cc_final: 0.8167 (mm) REVERT: A 231 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8479 (mm) REVERT: A 242 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7894 (mm) REVERT: A 244 MET cc_start: 0.8037 (tpp) cc_final: 0.7673 (tpt) REVERT: B 74 MET cc_start: 0.8254 (tmm) cc_final: 0.7559 (tmm) REVERT: B 116 LEU cc_start: 0.8266 (tp) cc_final: 0.7975 (tp) REVERT: B 128 TYR cc_start: 0.8998 (m-10) cc_final: 0.8526 (m-10) REVERT: B 195 LEU cc_start: 0.8794 (tt) cc_final: 0.8323 (mm) REVERT: B 244 MET cc_start: 0.8194 (tpp) cc_final: 0.7778 (tpt) REVERT: C 144 MET cc_start: 0.8193 (ptp) cc_final: 0.7907 (ppp) REVERT: C 187 MET cc_start: 0.9005 (mmp) cc_final: 0.8260 (mmm) REVERT: C 191 ILE cc_start: 0.9290 (mt) cc_final: 0.8968 (mt) REVERT: C 195 LEU cc_start: 0.8583 (tt) cc_final: 0.8235 (mm) REVERT: C 229 ARG cc_start: 0.8029 (tpt90) cc_final: 0.7709 (tpp80) REVERT: D 13 GLN cc_start: 0.8045 (tp40) cc_final: 0.7116 (tm-30) REVERT: D 19 ILE cc_start: 0.8895 (mm) cc_final: 0.8653 (mt) REVERT: D 155 GLU cc_start: 0.8262 (tp30) cc_final: 0.7981 (tm-30) REVERT: D 195 LEU cc_start: 0.8896 (tt) cc_final: 0.8372 (mm) REVERT: D 231 LEU cc_start: 0.8879 (tp) cc_final: 0.8625 (mm) REVERT: E 153 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7857 (tpp80) REVERT: E 175 ASP cc_start: 0.8128 (m-30) cc_final: 0.7777 (m-30) REVERT: E 187 MET cc_start: 0.9259 (mmp) cc_final: 0.9010 (mmm) REVERT: E 195 LEU cc_start: 0.8717 (tt) cc_final: 0.8202 (mm) REVERT: E 208 LYS cc_start: 0.8714 (tppt) cc_final: 0.8380 (mmtm) REVERT: F 141 HIS cc_start: 0.7673 (p-80) cc_final: 0.7216 (p-80) REVERT: F 144 MET cc_start: 0.8065 (ptp) cc_final: 0.7848 (ptp) REVERT: F 195 LEU cc_start: 0.8797 (tt) cc_final: 0.8135 (mm) REVERT: F 208 LYS cc_start: 0.8976 (tptp) cc_final: 0.8370 (mmtm) REVERT: F 242 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.7683 (mm) REVERT: F 243 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8803 (tp) REVERT: F 250 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8522 (ttpp) REVERT: G 116 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8126 (tp) REVERT: G 258 SER cc_start: 0.8082 (m) cc_final: 0.7798 (t) REVERT: H 195 LEU cc_start: 0.8788 (tt) cc_final: 0.8294 (mm) REVERT: H 208 LYS cc_start: 0.8914 (tptp) cc_final: 0.8669 (tppt) REVERT: I 116 LEU cc_start: 0.8231 (tp) cc_final: 0.7847 (tp) REVERT: I 208 LYS cc_start: 0.9083 (tptp) cc_final: 0.8505 (mmtm) REVERT: I 242 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8297 (mt) REVERT: J 130 GLU cc_start: 0.8177 (pp20) cc_final: 0.7825 (tm-30) REVERT: J 155 GLU cc_start: 0.8083 (tp30) cc_final: 0.7783 (tm-30) REVERT: J 187 MET cc_start: 0.9055 (mmm) cc_final: 0.8740 (mmm) REVERT: J 229 ARG cc_start: 0.8016 (tpt90) cc_final: 0.7566 (tpp80) REVERT: J 242 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8468 (mm) REVERT: J 244 MET cc_start: 0.8249 (tpp) cc_final: 0.7926 (tpt) REVERT: K 19 ILE cc_start: 0.8978 (mm) cc_final: 0.8655 (mt) REVERT: K 195 LEU cc_start: 0.8547 (tt) cc_final: 0.8168 (mm) REVERT: K 258 SER cc_start: 0.7680 (m) cc_final: 0.7371 (t) REVERT: L 116 LEU cc_start: 0.8312 (tp) cc_final: 0.7922 (tp) REVERT: L 195 LEU cc_start: 0.8920 (tt) cc_final: 0.8450 (mm) REVERT: L 208 LYS cc_start: 0.9062 (tptp) cc_final: 0.8560 (mmtm) REVERT: L 237 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7959 (tm-30) REVERT: L 242 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.7771 (mm) REVERT: M 128 TYR cc_start: 0.8971 (m-10) cc_final: 0.8672 (m-10) REVERT: M 144 MET cc_start: 0.7895 (ptt) cc_final: 0.7639 (ptt) REVERT: M 195 LEU cc_start: 0.8643 (tt) cc_final: 0.8353 (mm) REVERT: M 208 LYS cc_start: 0.8966 (tptp) cc_final: 0.8374 (mmtm) REVERT: M 229 ARG cc_start: 0.8049 (tpt90) cc_final: 0.7696 (tpp80) REVERT: N 195 LEU cc_start: 0.8566 (tt) cc_final: 0.8179 (mm) REVERT: N 208 LYS cc_start: 0.8969 (tptp) cc_final: 0.8681 (tppt) REVERT: N 237 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7828 (tm-30) REVERT: N 258 SER cc_start: 0.7678 (m) cc_final: 0.7355 (t) REVERT: O 195 LEU cc_start: 0.8672 (tt) cc_final: 0.8143 (mm) REVERT: O 208 LYS cc_start: 0.8988 (tptp) cc_final: 0.8496 (mmtm) REVERT: O 242 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.7995 (mm) REVERT: P 74 MET cc_start: 0.7847 (tpp) cc_final: 0.7578 (tpp) REVERT: P 128 TYR cc_start: 0.9045 (m-10) cc_final: 0.8717 (m-10) REVERT: P 175 ASP cc_start: 0.7838 (m-30) cc_final: 0.7583 (m-30) REVERT: P 195 LEU cc_start: 0.8793 (tt) cc_final: 0.8325 (mm) REVERT: Q 141 HIS cc_start: 0.7917 (p-80) cc_final: 0.7249 (p-80) REVERT: Q 187 MET cc_start: 0.9069 (mmp) cc_final: 0.8370 (mmm) REVERT: Q 191 ILE cc_start: 0.9280 (mt) cc_final: 0.9040 (mt) REVERT: Q 208 LYS cc_start: 0.8937 (tptp) cc_final: 0.8614 (tppt) REVERT: Q 242 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8186 (mm) REVERT: Q 244 MET cc_start: 0.8468 (tpp) cc_final: 0.8007 (tpt) REVERT: R 141 HIS cc_start: 0.7473 (p-80) cc_final: 0.7116 (p-80) REVERT: S 51 TYR cc_start: 0.9047 (t80) cc_final: 0.8828 (t80) REVERT: S 187 MET cc_start: 0.9218 (mmp) cc_final: 0.8949 (mmm) REVERT: S 195 LEU cc_start: 0.9002 (tt) cc_final: 0.8385 (mm) REVERT: S 208 LYS cc_start: 0.8887 (tptp) cc_final: 0.8543 (mmtm) REVERT: S 237 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7878 (tm-30) REVERT: T 129 TYR cc_start: 0.9301 (t80) cc_final: 0.8943 (t80) REVERT: T 141 HIS cc_start: 0.7892 (p-80) cc_final: 0.7459 (p-80) REVERT: T 187 MET cc_start: 0.9144 (mmm) cc_final: 0.8843 (mmp) REVERT: T 195 LEU cc_start: 0.8803 (tt) cc_final: 0.8211 (mm) REVERT: T 237 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7791 (tm-30) REVERT: T 242 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.7726 (mm) REVERT: T 250 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8514 (ttpp) REVERT: U 116 LEU cc_start: 0.8393 (tp) cc_final: 0.8076 (tp) REVERT: U 195 LEU cc_start: 0.8878 (tt) cc_final: 0.8346 (mm) REVERT: V 187 MET cc_start: 0.8992 (mmm) cc_final: 0.8497 (mmm) REVERT: V 195 LEU cc_start: 0.8786 (tt) cc_final: 0.8311 (mm) REVERT: V 229 ARG cc_start: 0.8137 (tpt90) cc_final: 0.7665 (tpp80) outliers start: 197 outliers final: 180 residues processed: 825 average time/residue: 0.5596 time to fit residues: 765.7008 Evaluate side-chains 857 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 664 time to evaluate : 5.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 240 SER Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 170 VAL Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 280 LEU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 187 MET Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 131 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 231 LEU Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Chi-restraints excluded: chain V residue 258 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 5.9990 chunk 543 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 377 optimal weight: 5.9990 chunk 569 optimal weight: 0.9980 chunk 524 optimal weight: 0.9980 chunk 453 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 chunk 278 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 46838 Z= 0.244 Angle : 0.558 9.675 63602 Z= 0.298 Chirality : 0.038 0.153 7414 Planarity : 0.004 0.047 7898 Dihedral : 3.842 15.635 6270 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.94 % Allowed : 20.94 % Favored : 75.13 % 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: 2.91 (0.11), residues: 5786 helix: 2.92 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.32 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 221 HIS 0.002 0.000 HIS C 181 PHE 0.024 0.001 PHE P 104 TYR 0.015 0.001 TYR A 129 ARG 0.003 0.000 ARG K 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11572 Ramachandran restraints generated. 5786 Oldfield, 0 Emsley, 5786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 680 time to evaluate : 5.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.9041 (t80) cc_final: 0.8737 (t80) REVERT: A 176 GLU cc_start: 0.7800 (tp30) cc_final: 0.7587 (tm-30) REVERT: A 188 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9221 (tp) REVERT: A 195 LEU cc_start: 0.8699 (tt) cc_final: 0.8184 (mm) REVERT: A 231 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 242 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.7905 (mm) REVERT: A 244 MET cc_start: 0.8037 (tpp) cc_final: 0.7675 (tpt) REVERT: B 74 MET cc_start: 0.8261 (tmm) cc_final: 0.7574 (tmm) REVERT: B 116 LEU cc_start: 0.8303 (tp) cc_final: 0.7994 (tp) REVERT: B 128 TYR cc_start: 0.9005 (m-10) cc_final: 0.8499 (m-10) REVERT: B 195 LEU cc_start: 0.8797 (tt) cc_final: 0.8329 (mm) REVERT: B 244 MET cc_start: 0.8193 (tpp) cc_final: 0.7777 (tpt) REVERT: C 144 MET cc_start: 0.8198 (ptp) cc_final: 0.7896 (ppp) REVERT: C 187 MET cc_start: 0.9002 (mmp) cc_final: 0.8265 (mmm) REVERT: C 191 ILE cc_start: 0.9285 (mt) cc_final: 0.8949 (mt) REVERT: C 195 LEU cc_start: 0.8666 (tt) cc_final: 0.8266 (mm) REVERT: C 229 ARG cc_start: 0.8065 (tpt90) cc_final: 0.7715 (tpp80) REVERT: D 13 GLN cc_start: 0.8154 (tp40) cc_final: 0.7093 (tm-30) REVERT: D 19 ILE cc_start: 0.8929 (mm) cc_final: 0.8667 (mt) REVERT: D 155 GLU cc_start: 0.8248 (tp30) cc_final: 0.7979 (tm-30) REVERT: D 195 LEU cc_start: 0.8899 (tt) cc_final: 0.8374 (mm) REVERT: D 231 LEU cc_start: 0.8885 (tp) cc_final: 0.8633 (mm) REVERT: E 187 MET cc_start: 0.9235 (mmp) cc_final: 0.8910 (mmm) REVERT: E 195 LEU cc_start: 0.8727 (tt) cc_final: 0.8211 (mm) REVERT: E 208 LYS cc_start: 0.8734 (tppt) cc_final: 0.8398 (mmtm) REVERT: F 141 HIS cc_start: 0.7688 (p-80) cc_final: 0.7228 (p-80) REVERT: F 144 MET cc_start: 0.8026 (ptp) cc_final: 0.7794 (ptp) REVERT: F 195 LEU cc_start: 0.8788 (tt) cc_final: 0.8116 (mm) REVERT: F 208 LYS cc_start: 0.8973 (tptp) cc_final: 0.8374 (mmtm) REVERT: F 237 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7760 (tm-30) REVERT: F 242 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7724 (mm) REVERT: F 243 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8788 (tp) REVERT: F 250 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8538 (ttpp) REVERT: G 116 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8152 (tp) REVERT: H 176 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7686 (tm-30) REVERT: H 195 LEU cc_start: 0.8792 (tt) cc_final: 0.8301 (mm) REVERT: H 208 LYS cc_start: 0.8914 (tptp) cc_final: 0.8672 (tppt) REVERT: I 116 LEU cc_start: 0.8261 (tp) cc_final: 0.7899 (tp) REVERT: I 208 LYS cc_start: 0.9080 (tptp) cc_final: 0.8537 (mmtm) REVERT: I 242 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8298 (mt) REVERT: J 130 GLU cc_start: 0.8189 (pp20) cc_final: 0.7845 (tm-30) REVERT: J 155 GLU cc_start: 0.8093 (tp30) cc_final: 0.7794 (tm-30) REVERT: J 187 MET cc_start: 0.9065 (mmm) cc_final: 0.8724 (mmm) REVERT: J 229 ARG cc_start: 0.8036 (tpt90) cc_final: 0.7571 (tpp80) REVERT: J 242 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8491 (mm) REVERT: K 19 ILE cc_start: 0.8986 (mm) cc_final: 0.8671 (mt) REVERT: K 258 SER cc_start: 0.7766 (m) cc_final: 0.7440 (t) REVERT: L 116 LEU cc_start: 0.8332 (tp) cc_final: 0.7927 (tp) REVERT: L 195 LEU cc_start: 0.8923 (tt) cc_final: 0.8456 (mm) REVERT: L 208 LYS cc_start: 0.9060 (tptp) cc_final: 0.8569 (mmtm) REVERT: L 237 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7970 (tm-30) REVERT: L 242 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.7794 (mm) REVERT: M 128 TYR cc_start: 0.9005 (m-10) cc_final: 0.8594 (m-10) REVERT: M 144 MET cc_start: 0.8005 (ptt) cc_final: 0.7758 (ptt) REVERT: M 195 LEU cc_start: 0.8637 (tt) cc_final: 0.8250 (mm) REVERT: M 208 LYS cc_start: 0.8965 (tptp) cc_final: 0.8373 (mmtm) REVERT: M 229 ARG cc_start: 0.8068 (tpt90) cc_final: 0.7727 (tpp80) REVERT: N 195 LEU cc_start: 0.8568 (tt) cc_final: 0.8178 (mm) REVERT: N 208 LYS cc_start: 0.9009 (tptp) cc_final: 0.8723 (tppt) REVERT: N 237 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7828 (tm-30) REVERT: N 258 SER cc_start: 0.7615 (m) cc_final: 0.7255 (t) REVERT: O 51 TYR cc_start: 0.9172 (t80) cc_final: 0.8752 (t80) REVERT: O 195 LEU cc_start: 0.8721 (tt) cc_final: 0.8206 (mm) REVERT: O 208 LYS cc_start: 0.8987 (tptp) cc_final: 0.8498 (mmtm) REVERT: O 242 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.7994 (mm) REVERT: P 175 ASP cc_start: 0.7841 (m-30) cc_final: 0.7600 (m-30) REVERT: P 195 LEU cc_start: 0.8855 (tt) cc_final: 0.8334 (mm) REVERT: Q 96 GLU cc_start: 0.7735 (pt0) cc_final: 0.6757 (mm-30) REVERT: Q 141 HIS cc_start: 0.7935 (p-80) cc_final: 0.7278 (p-80) REVERT: Q 187 MET cc_start: 0.9059 (mmp) cc_final: 0.8376 (mmm) REVERT: Q 191 ILE cc_start: 0.9285 (mt) cc_final: 0.9047 (mt) REVERT: Q 208 LYS cc_start: 0.8961 (tptp) cc_final: 0.8634 (tppt) REVERT: Q 242 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8163 (mm) REVERT: Q 244 MET cc_start: 0.8467 (tpp) cc_final: 0.8035 (tpt) REVERT: R 141 HIS cc_start: 0.7600 (p-80) cc_final: 0.7243 (p-80) REVERT: S 51 TYR cc_start: 0.9042 (t80) cc_final: 0.8813 (t80) REVERT: S 187 MET cc_start: 0.9218 (mmp) cc_final: 0.8940 (mmm) REVERT: S 195 LEU cc_start: 0.9007 (tt) cc_final: 0.8386 (mm) REVERT: S 208 LYS cc_start: 0.8886 (tptp) cc_final: 0.8544 (mmtm) REVERT: S 237 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7861 (tm-30) REVERT: T 141 HIS cc_start: 0.7909 (p-80) cc_final: 0.7499 (p-80) REVERT: T 187 MET cc_start: 0.9167 (mmm) cc_final: 0.8834 (mmp) REVERT: T 195 LEU cc_start: 0.8805 (tt) cc_final: 0.8216 (mm) REVERT: T 242 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7772 (mm) REVERT: T 250 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8512 (ttpp) REVERT: U 116 LEU cc_start: 0.8395 (tp) cc_final: 0.8078 (tp) REVERT: U 195 LEU cc_start: 0.8879 (tt) cc_final: 0.8349 (mm) REVERT: V 187 MET cc_start: 0.8997 (mmm) cc_final: 0.8489 (mmm) REVERT: V 195 LEU cc_start: 0.8776 (tt) cc_final: 0.8271 (mm) REVERT: V 229 ARG cc_start: 0.8071 (tpt90) cc_final: 0.7660 (tpp80) REVERT: V 237 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7635 (tm-30) outliers start: 200 outliers final: 185 residues processed: 847 average time/residue: 0.5422 time to fit residues: 761.0458 Evaluate side-chains 866 residues out of total 5082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 669 time to evaluate : 5.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 MET Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 205 CYS Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 240 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 131 CYS Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 205 CYS Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 153 ARG Chi-restraints excluded: chain H residue 205 CYS Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 245 MET Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 240 SER Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 205 CYS Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 245 MET Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 131 CYS Chi-restraints excluded: chain L residue 205 CYS Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 240 SER Chi-restraints excluded: chain L residue 242 LEU Chi-restraints excluded: chain L residue 245 MET Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 280 LEU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 131 CYS Chi-restraints excluded: chain M residue 187 MET Chi-restraints excluded: chain M residue 205 CYS Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 240 SER Chi-restraints excluded: chain M residue 248 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 205 CYS Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 131 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain O residue 258 SER Chi-restraints excluded: chain P residue 65 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 131 CYS Chi-restraints excluded: chain P residue 205 CYS Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain Q residue 4 THR Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 195 LEU Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 205 CYS Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 242 LEU Chi-restraints excluded: chain Q residue 245 MET Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 205 CYS Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 258 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 205 CYS Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 205 CYS Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 231 LEU Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 245 MET Chi-restraints excluded: chain T residue 258 SER Chi-restraints excluded: chain U residue 112 VAL Chi-restraints excluded: chain U residue 153 ARG Chi-restraints excluded: chain U residue 205 CYS Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 205 CYS Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 231 LEU Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 242 LEU Chi-restraints excluded: chain V residue 245 MET Chi-restraints excluded: chain V residue 258 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 0.6980 chunk 483 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 418 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 chunk 126 optimal weight: 0.7980 chunk 454 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 466 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.152075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123889 restraints weight = 58524.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.126297 restraints weight = 40924.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127899 restraints weight = 32890.224| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46838 Z= 0.163 Angle : 0.533 9.596 63602 Z= 0.281 Chirality : 0.036 0.138 7414 Planarity : 0.004 0.046 7898 Dihedral : 3.785 15.655 6270 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.62 % Allowed : 22.37 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.11), residues: 5786 helix: 3.14 (0.07), residues: 4576 sheet: None (None), residues: 0 loop : -2.24 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 221 HIS 0.002 0.000 HIS E 181 PHE 0.014 0.001 PHE C 104 TYR 0.014 0.001 TYR A 129 ARG 0.004 0.000 ARG R 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11650.84 seconds wall clock time: 209 minutes 32.56 seconds (12572.56 seconds total)