Starting phenix.real_space_refine on Sat Jul 27 23:38:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yto_10920/07_2024/6yto_10920.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yto_10920/07_2024/6yto_10920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yto_10920/07_2024/6yto_10920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yto_10920/07_2024/6yto_10920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yto_10920/07_2024/6yto_10920.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yto_10920/07_2024/6yto_10920.cif" } resolution = 4.24 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= 0.005 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 400 5.16 5 C 26800 2.51 5 N 6980 2.21 5 O 7440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E GLU 176": "OE1" <-> "OE2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F ARG 174": "NH1" <-> "NH2" Residue "F GLU 176": "OE1" <-> "OE2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 174": "NH1" <-> "NH2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H ARG 164": "NH1" <-> "NH2" Residue "H ARG 174": "NH1" <-> "NH2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I ARG 174": "NH1" <-> "NH2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I ARG 247": "NH1" <-> "NH2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "J GLU 176": "OE1" <-> "OE2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K ARG 182": "NH1" <-> "NH2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 164": "NH1" <-> "NH2" Residue "L ARG 174": "NH1" <-> "NH2" Residue "L GLU 176": "OE1" <-> "OE2" Residue "L ARG 182": "NH1" <-> "NH2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M ARG 174": "NH1" <-> "NH2" Residue "M GLU 176": "OE1" <-> "OE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M ARG 247": "NH1" <-> "NH2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N GLU 135": "OE1" <-> "OE2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 164": "NH1" <-> "NH2" Residue "N ARG 174": "NH1" <-> "NH2" Residue "N GLU 176": "OE1" <-> "OE2" Residue "N ARG 182": "NH1" <-> "NH2" Residue "N ARG 247": "NH1" <-> "NH2" Residue "O GLU 96": "OE1" <-> "OE2" Residue "O GLU 135": "OE1" <-> "OE2" Residue "O GLU 155": "OE1" <-> "OE2" Residue "O PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O ARG 174": "NH1" <-> "NH2" Residue "O GLU 176": "OE1" <-> "OE2" Residue "O ARG 182": "NH1" <-> "NH2" Residue "O ARG 247": "NH1" <-> "NH2" Residue "P GLU 96": "OE1" <-> "OE2" Residue "P GLU 135": "OE1" <-> "OE2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 164": "NH1" <-> "NH2" Residue "P ARG 174": "NH1" <-> "NH2" Residue "P GLU 176": "OE1" <-> "OE2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P ARG 247": "NH1" <-> "NH2" Residue "Q GLU 96": "OE1" <-> "OE2" Residue "Q GLU 135": "OE1" <-> "OE2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "Q ARG 174": "NH1" <-> "NH2" Residue "Q GLU 176": "OE1" <-> "OE2" Residue "Q ARG 182": "NH1" <-> "NH2" Residue "Q ARG 247": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R GLU 155": "OE1" <-> "OE2" Residue "R PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 174": "NH1" <-> "NH2" Residue "R GLU 176": "OE1" <-> "OE2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R ARG 247": "NH1" <-> "NH2" Residue "S GLU 96": "OE1" <-> "OE2" Residue "S GLU 135": "OE1" <-> "OE2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "S PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S ARG 174": "NH1" <-> "NH2" Residue "S GLU 176": "OE1" <-> "OE2" Residue "S ARG 182": "NH1" <-> "NH2" Residue "S ARG 247": "NH1" <-> "NH2" Residue "T GLU 96": "OE1" <-> "OE2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "T GLU 155": "OE1" <-> "OE2" Residue "T PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 164": "NH1" <-> "NH2" Residue "T ARG 174": "NH1" <-> "NH2" Residue "T GLU 176": "OE1" <-> "OE2" Residue "T ARG 182": "NH1" <-> "NH2" Residue "T ARG 247": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 41620 Number of models: 1 Model: "" Number of chains: 20 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 Time building chain proxies: 20.46, per 1000 atoms: 0.49 Number of scatterers: 41620 At special positions: 0 Unit cell: (135.34, 135.34, 210.38, 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 400 16.00 O 7440 8.00 N 6980 7.00 C 26800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, 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=2.03 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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: 14.56 Conformation dependent library (CDL) restraints added in 6.8 seconds 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10160 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.574A pdb=" N ILE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 removed outlier: 3.904A 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: 3.755A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 112 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 167 through 210 Processing helix chain 'A' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 removed outlier: 3.904A 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: 3.755A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 112 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.815A pdb=" N CYS B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 167 through 210 Processing helix chain 'B' and resid 214 through 253 removed outlier: 3.582A pdb=" N HIS B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 removed outlier: 3.905A 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: 3.755A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 112 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.610A pdb=" N GLY C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS C 131 " --> pdb=" O THR C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 167 through 210 Processing helix chain 'C' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS C 218 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 3.905A 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: 3.755A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS D 131 " --> pdb=" O THR D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 159 Processing helix chain 'D' and resid 167 through 210 Processing helix chain 'D' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 15 through 38 removed outlier: 3.574A pdb=" N ILE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 removed outlier: 3.904A 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: 3.754A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 112 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 removed outlier: 3.815A pdb=" N CYS E 131 " --> pdb=" O THR E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 159 Processing helix chain 'E' and resid 167 through 210 Processing helix chain 'E' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 3.904A 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: 3.755A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 112 Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY F 126 " --> pdb=" O THR F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.815A pdb=" N CYS F 131 " --> pdb=" O THR F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 159 Processing helix chain 'F' and resid 167 through 210 Processing helix chain 'F' and resid 214 through 253 removed outlier: 3.582A pdb=" N HIS F 218 " --> pdb=" O THR F 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 15 through 38 removed outlier: 3.574A pdb=" N ILE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 70 removed outlier: 3.904A 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: 3.754A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 76 " --> pdb=" O SER G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 112 Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY G 126 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS G 131 " --> pdb=" O THR G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 159 Processing helix chain 'G' and resid 167 through 210 Processing helix chain 'G' and resid 214 through 253 removed outlier: 3.582A pdb=" N HIS G 218 " --> pdb=" O THR G 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS G 219 " --> pdb=" O SER G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 276 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 15 through 38 removed outlier: 3.574A pdb=" N ILE H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 removed outlier: 3.905A 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: 3.754A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR H 76 " --> pdb=" O SER H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 112 Processing helix chain 'H' and resid 112 through 126 removed outlier: 3.608A pdb=" N GLY H 126 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 133 removed outlier: 3.815A pdb=" N CYS H 131 " --> pdb=" O THR H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 167 through 210 Processing helix chain 'H' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS H 218 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS H 219 " --> pdb=" O SER H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 276 Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 removed outlier: 3.904A 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: 3.754A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 112 Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY I 126 " --> pdb=" O THR I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 167 through 210 Processing helix chain 'I' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS I 218 " --> pdb=" O THR I 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS I 219 " --> pdb=" O SER I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 276 Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 15 through 38 removed outlier: 3.575A pdb=" N ILE J 19 " --> pdb=" O ASN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 removed outlier: 3.904A 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: 3.755A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR J 76 " --> pdb=" O SER J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 112 Processing helix chain 'J' and resid 112 through 126 removed outlier: 3.609A pdb=" N GLY J 126 " --> pdb=" O THR J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 removed outlier: 3.816A pdb=" N CYS J 131 " --> pdb=" O THR J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 159 Processing helix chain 'J' and resid 167 through 210 Processing helix chain 'J' and resid 214 through 253 removed outlier: 3.581A pdb=" N HIS J 218 " --> pdb=" O THR J 214 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS J 219 " --> pdb=" O SER J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 276 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 removed outlier: 3.898A 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: 3.738A 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: 3.608A pdb=" N GLY K 126 " --> pdb=" O THR K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.831A pdb=" N CYS K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE K 160 " --> pdb=" O ILE K 156 " (cutoff:3.500A) Proline residue: K 161 - end of helix Processing helix chain 'K' and resid 167 through 210 Processing helix chain 'K' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS K 218 " --> pdb=" O THR K 214 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS K 219 " --> pdb=" O SER K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 276 Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 70 removed outlier: 3.898A 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: 3.737A 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: 3.608A pdb=" N GLY L 126 " --> pdb=" O THR L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS L 131 " --> pdb=" O THR L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 163 removed outlier: 3.704A pdb=" N PHE L 160 " --> pdb=" O ILE L 156 " (cutoff:3.500A) Proline residue: L 161 - end of helix Processing helix chain 'L' and resid 167 through 210 Processing helix chain 'L' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS L 218 " --> pdb=" O THR L 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS L 219 " --> pdb=" O SER L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 276 Processing helix chain 'M' and resid 5 through 15 Processing helix chain 'M' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 70 removed outlier: 3.899A 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: 3.738A 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: 3.608A pdb=" N GLY M 126 " --> pdb=" O THR M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS M 131 " --> pdb=" O THR M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 163 removed outlier: 3.704A pdb=" N PHE M 160 " --> pdb=" O ILE M 156 " (cutoff:3.500A) Proline residue: M 161 - end of helix Processing helix chain 'M' and resid 167 through 210 Processing helix chain 'M' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS M 218 " --> pdb=" O THR M 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS M 219 " --> pdb=" O SER M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 276 Processing helix chain 'N' and resid 5 through 15 Processing helix chain 'N' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE N 19 " --> pdb=" O ASN N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 70 removed outlier: 3.899A 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: 3.738A 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: 3.608A pdb=" N GLY N 126 " --> pdb=" O THR N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS N 131 " --> pdb=" O THR N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE N 160 " --> pdb=" O ILE N 156 " (cutoff:3.500A) Proline residue: N 161 - end of helix Processing helix chain 'N' and resid 167 through 210 Processing helix chain 'N' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS N 218 " --> pdb=" O THR N 214 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N CYS N 219 " --> pdb=" O SER N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 276 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 15 through 38 removed outlier: 3.686A pdb=" N ILE O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 70 removed outlier: 3.898A 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: 3.737A 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: 3.609A pdb=" N GLY O 126 " --> pdb=" O THR O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 133 removed outlier: 3.831A pdb=" N CYS O 131 " --> pdb=" O THR O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE O 160 " --> pdb=" O ILE O 156 " (cutoff:3.500A) Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 167 through 210 Processing helix chain 'O' and resid 214 through 253 removed outlier: 3.601A pdb=" N HIS O 218 " --> pdb=" O THR O 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS O 219 " --> pdb=" O SER O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'P' and resid 5 through 15 Processing helix chain 'P' and resid 15 through 38 removed outlier: 3.686A pdb=" N ILE P 19 " --> pdb=" O ASN P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 removed outlier: 3.899A 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: 3.737A 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: 3.608A pdb=" N GLY P 126 " --> pdb=" O THR P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS P 131 " --> pdb=" O THR P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 163 removed outlier: 3.704A pdb=" N PHE P 160 " --> pdb=" O ILE P 156 " (cutoff:3.500A) Proline residue: P 161 - end of helix Processing helix chain 'P' and resid 167 through 210 Processing helix chain 'P' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS P 218 " --> pdb=" O THR P 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS P 219 " --> pdb=" O SER P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 276 Processing helix chain 'Q' and resid 5 through 15 Processing helix chain 'Q' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 70 removed outlier: 3.898A 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: 3.738A 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: 3.607A pdb=" N GLY Q 126 " --> pdb=" O THR Q 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS Q 131 " --> pdb=" O THR Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 163 removed outlier: 3.704A pdb=" N PHE Q 160 " --> pdb=" O ILE Q 156 " (cutoff:3.500A) Proline residue: Q 161 - end of helix Processing helix chain 'Q' and resid 167 through 210 Processing helix chain 'Q' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS Q 218 " --> pdb=" O THR Q 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS Q 219 " --> pdb=" O SER Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 276 Processing helix chain 'R' and resid 5 through 15 Processing helix chain 'R' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE R 19 " --> pdb=" O ASN R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 70 removed outlier: 3.899A 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: 3.738A 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: 3.608A pdb=" N GLY R 126 " --> pdb=" O THR R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS R 131 " --> pdb=" O THR R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE R 160 " --> pdb=" O ILE R 156 " (cutoff:3.500A) Proline residue: R 161 - end of helix Processing helix chain 'R' and resid 167 through 210 Processing helix chain 'R' and resid 214 through 253 removed outlier: 3.601A pdb=" N HIS R 218 " --> pdb=" O THR R 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS R 219 " --> pdb=" O SER R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 276 Processing helix chain 'S' and resid 5 through 15 Processing helix chain 'S' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE S 19 " --> pdb=" O ASN S 15 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 70 removed outlier: 3.898A 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: 3.738A 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: 3.608A pdb=" N GLY S 126 " --> pdb=" O THR S 122 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 133 removed outlier: 3.832A pdb=" N CYS S 131 " --> pdb=" O THR S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE S 160 " --> pdb=" O ILE S 156 " (cutoff:3.500A) Proline residue: S 161 - end of helix Processing helix chain 'S' and resid 167 through 210 Processing helix chain 'S' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS S 218 " --> pdb=" O THR S 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS S 219 " --> pdb=" O SER S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 276 Processing helix chain 'T' and resid 5 through 15 Processing helix chain 'T' and resid 15 through 38 removed outlier: 3.685A pdb=" N ILE T 19 " --> pdb=" O ASN T 15 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 70 removed outlier: 3.899A 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: 3.737A 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: 3.608A pdb=" N GLY T 126 " --> pdb=" O THR T 122 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 133 removed outlier: 3.831A pdb=" N CYS T 131 " --> pdb=" O THR T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 163 removed outlier: 3.703A pdb=" N PHE T 160 " --> pdb=" O ILE T 156 " (cutoff:3.500A) Proline residue: T 161 - end of helix Processing helix chain 'T' and resid 167 through 210 Processing helix chain 'T' and resid 214 through 253 removed outlier: 3.600A pdb=" N HIS T 218 " --> pdb=" O THR T 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS T 219 " --> pdb=" O SER T 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 276 3171 hydrogen bonds defined for protein. 9513 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: 13.23 Time building geometry restraints manager: 16.16 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: 13125 1.34 - 1.46: 8828 1.46 - 1.58: 20127 1.58 - 1.70: 0 1.70 - 1.82: 500 Bond restraints: 42580 Sorted by residual: bond pdb=" CB CYS O 41 " pdb=" SG CYS O 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.41e+00 bond pdb=" CB CYS P 41 " pdb=" SG CYS P 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB CYS R 41 " pdb=" SG CYS R 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB CYS Q 41 " pdb=" SG CYS Q 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CB CYS N 41 " pdb=" SG CYS N 41 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.37e+00 ... (remaining 42575 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.76: 1225 106.76 - 113.59: 24515 113.59 - 120.42: 17404 120.42 - 127.26: 14210 127.26 - 134.09: 466 Bond angle restraints: 57820 Sorted by residual: angle pdb=" CA ARG M 164 " pdb=" CB ARG M 164 " pdb=" CG ARG M 164 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA ARG N 164 " pdb=" CB ARG N 164 " pdb=" CG ARG N 164 " ideal model delta sigma weight residual 114.10 121.09 -6.99 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ARG S 164 " pdb=" CB ARG S 164 " pdb=" CG ARG S 164 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ARG R 164 " pdb=" CB ARG R 164 " pdb=" CG ARG R 164 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA ARG L 164 " pdb=" CB ARG L 164 " pdb=" CG ARG L 164 " ideal model delta sigma weight residual 114.10 121.07 -6.97 2.00e+00 2.50e-01 1.22e+01 ... (remaining 57815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 22968 17.60 - 35.20: 2002 35.20 - 52.80: 390 52.80 - 70.40: 20 70.40 - 88.00: 60 Dihedral angle restraints: 25440 sinusoidal: 9820 harmonic: 15620 Sorted by residual: dihedral pdb=" CB CYS B 41 " pdb=" SG CYS B 41 " pdb=" SG CYS B 131 " pdb=" CB CYS B 131 " ideal model delta sinusoidal sigma weight residual -86.00 -174.00 88.00 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CB CYS A 41 " pdb=" SG CYS A 41 " pdb=" SG CYS A 131 " pdb=" CB CYS A 131 " ideal model delta sinusoidal sigma weight residual -86.00 -174.00 88.00 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS G 41 " pdb=" SG CYS G 41 " pdb=" SG CYS G 131 " pdb=" CB CYS G 131 " ideal model delta sinusoidal sigma weight residual -86.00 -173.99 87.99 1 1.00e+01 1.00e-02 9.26e+01 ... (remaining 25437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4161 0.036 - 0.071: 2017 0.071 - 0.107: 396 0.107 - 0.143: 134 0.143 - 0.178: 32 Chirality restraints: 6740 Sorted by residual: chirality pdb=" CA CYS A 43 " pdb=" N CYS A 43 " pdb=" C CYS A 43 " pdb=" CB CYS A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA CYS J 43 " pdb=" N CYS J 43 " pdb=" C CYS J 43 " pdb=" CB CYS J 43 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA CYS F 43 " pdb=" N CYS F 43 " pdb=" C CYS F 43 " pdb=" CB CYS F 43 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.70e-01 ... (remaining 6737 not shown) Planarity restraints: 7180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE S 160 " -0.019 2.00e-02 2.50e+03 1.74e-02 5.30e+00 pdb=" CG PHE S 160 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE S 160 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE S 160 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE S 160 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE S 160 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE S 160 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 160 " 0.019 2.00e-02 2.50e+03 1.74e-02 5.29e+00 pdb=" CG PHE P 160 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE P 160 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE P 160 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE P 160 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE P 160 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE P 160 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE T 160 " -0.019 2.00e-02 2.50e+03 1.74e-02 5.27e+00 pdb=" CG PHE T 160 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE T 160 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE T 160 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE T 160 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE T 160 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE T 160 " -0.000 2.00e-02 2.50e+03 ... (remaining 7177 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 11152 2.81 - 3.33: 44227 3.33 - 3.85: 66822 3.85 - 4.38: 67509 4.38 - 4.90: 121056 Nonbonded interactions: 310766 Sorted by model distance: nonbonded pdb=" OH TYR B 142 " pdb=" OE1 GLU B 176 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR G 142 " pdb=" OE1 GLU G 176 " model vdw 2.282 2.440 nonbonded pdb=" OH TYR I 142 " pdb=" OE1 GLU I 176 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR H 142 " pdb=" OE1 GLU H 176 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR A 142 " pdb=" OE1 GLU A 176 " model vdw 2.283 2.440 ... (remaining 310761 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' } 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: 0.540 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: 0.050 Extract box with map and model: 1.620 Check model and map are aligned: 0.300 Set scattering table: 0.400 Process input model: 94.640 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.039 42580 Z= 0.325 Angle : 0.704 7.985 57820 Z= 0.387 Chirality : 0.043 0.178 6740 Planarity : 0.005 0.054 7180 Dihedral : 13.409 80.955 15160 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5260 helix: 0.79 (0.08), residues: 4040 sheet: None (None), residues: 0 loop : -2.89 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 190 HIS 0.003 0.001 HIS C 218 PHE 0.040 0.002 PHE S 160 TYR 0.011 0.002 TYR K 81 ARG 0.005 0.001 ARG E 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1303 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 CYS cc_start: 0.6848 (m) cc_final: 0.6538 (p) REVERT: A 184 GLN cc_start: 0.8940 (mt0) cc_final: 0.8611 (tp40) REVERT: B 15 ASN cc_start: 0.8516 (t0) cc_final: 0.8220 (t0) REVERT: B 104 PHE cc_start: 0.7700 (t80) cc_final: 0.7480 (t80) REVERT: B 153 ARG cc_start: 0.9053 (ttp80) cc_final: 0.8756 (ttt180) REVERT: B 172 LEU cc_start: 0.8977 (tt) cc_final: 0.8680 (tp) REVERT: B 183 TYR cc_start: 0.9311 (t80) cc_final: 0.8915 (t80) REVERT: B 184 GLN cc_start: 0.8998 (mt0) cc_final: 0.8529 (tp40) REVERT: B 233 GLU cc_start: 0.8494 (tp30) cc_final: 0.8129 (tm-30) REVERT: B 237 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 245 MET cc_start: 0.8260 (ttm) cc_final: 0.7952 (mtm) REVERT: C 74 MET cc_start: 0.8050 (tmm) cc_final: 0.7443 (tmm) REVERT: C 153 ARG cc_start: 0.9162 (ttp80) cc_final: 0.8894 (ttt180) REVERT: C 162 CYS cc_start: 0.7512 (p) cc_final: 0.7160 (t) REVERT: C 183 TYR cc_start: 0.9198 (t80) cc_final: 0.8868 (t80) REVERT: C 184 GLN cc_start: 0.9037 (mt0) cc_final: 0.8475 (tp40) REVERT: D 154 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8803 (mm-30) REVERT: D 183 TYR cc_start: 0.9130 (t80) cc_final: 0.8714 (t80) REVERT: D 245 MET cc_start: 0.8143 (ttm) cc_final: 0.7861 (mtm) REVERT: D 249 LYS cc_start: 0.8728 (tttt) cc_final: 0.8300 (ttmm) REVERT: E 104 PHE cc_start: 0.7908 (t80) cc_final: 0.7367 (t80) REVERT: E 128 TYR cc_start: 0.8887 (m-10) cc_final: 0.8637 (m-80) REVERT: E 201 LEU cc_start: 0.9000 (tp) cc_final: 0.8791 (tt) REVERT: E 265 ARG cc_start: 0.7841 (ttt90) cc_final: 0.6780 (tpt170) REVERT: F 78 THR cc_start: 0.7689 (m) cc_final: 0.7262 (t) REVERT: F 153 ARG cc_start: 0.9067 (ttp80) cc_final: 0.8743 (ttt180) REVERT: F 162 CYS cc_start: 0.7786 (p) cc_final: 0.7348 (t) REVERT: F 174 ARG cc_start: 0.8733 (ttp80) cc_final: 0.8523 (ptm-80) REVERT: G 74 MET cc_start: 0.8412 (tmm) cc_final: 0.7919 (tmm) REVERT: G 153 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8792 (ttt180) REVERT: G 174 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8283 (ptm-80) REVERT: H 128 TYR cc_start: 0.8624 (m-10) cc_final: 0.8224 (m-80) REVERT: H 174 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8073 (ptm-80) REVERT: H 187 MET cc_start: 0.9151 (mmp) cc_final: 0.8808 (mmm) REVERT: H 192 LEU cc_start: 0.9170 (tp) cc_final: 0.8897 (tt) REVERT: H 237 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8431 (tm-30) REVERT: I 74 MET cc_start: 0.8171 (tmm) cc_final: 0.7258 (tmm) REVERT: I 107 ILE cc_start: 0.9214 (mm) cc_final: 0.8824 (tp) REVERT: I 146 ASP cc_start: 0.7776 (p0) cc_final: 0.7574 (p0) REVERT: I 153 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8811 (ttt180) REVERT: I 174 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8150 (ptm-80) REVERT: J 78 THR cc_start: 0.7826 (m) cc_final: 0.7496 (t) REVERT: J 184 GLN cc_start: 0.8914 (mt0) cc_final: 0.8619 (tp40) REVERT: J 244 MET cc_start: 0.9108 (tpt) cc_final: 0.8892 (tpt) REVERT: J 262 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8130 (mmmm) REVERT: K 26 LEU cc_start: 0.9146 (tp) cc_final: 0.8891 (tp) REVERT: K 74 MET cc_start: 0.8313 (tmm) cc_final: 0.7934 (tmm) REVERT: K 107 ILE cc_start: 0.9391 (mm) cc_final: 0.9086 (tp) REVERT: K 152 LYS cc_start: 0.9309 (tptt) cc_final: 0.9106 (tppp) REVERT: K 153 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8702 (ttt180) REVERT: K 221 TRP cc_start: 0.8954 (t60) cc_final: 0.8729 (t60) REVERT: K 245 MET cc_start: 0.8226 (ttm) cc_final: 0.7927 (mtm) REVERT: L 153 ARG cc_start: 0.8832 (ttp80) cc_final: 0.8495 (ttt180) REVERT: L 160 PHE cc_start: 0.8550 (m-80) cc_final: 0.8088 (m-80) REVERT: L 184 GLN cc_start: 0.8825 (mt0) cc_final: 0.8407 (tp40) REVERT: L 187 MET cc_start: 0.8923 (mmp) cc_final: 0.8713 (mmt) REVERT: L 255 ILE cc_start: 0.9439 (mm) cc_final: 0.9228 (mp) REVERT: M 153 ARG cc_start: 0.9085 (ttp80) cc_final: 0.8753 (ttt180) REVERT: M 160 PHE cc_start: 0.8307 (m-80) cc_final: 0.7425 (m-80) REVERT: M 245 MET cc_start: 0.8127 (ttm) cc_final: 0.7678 (mtm) REVERT: N 15 ASN cc_start: 0.8388 (t0) cc_final: 0.8074 (t0) REVERT: N 183 TYR cc_start: 0.8990 (t80) cc_final: 0.8644 (t80) REVERT: N 184 GLN cc_start: 0.8962 (mt0) cc_final: 0.8202 (mm-40) REVERT: O 237 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8663 (tm-30) REVERT: O 249 LYS cc_start: 0.8796 (tttt) cc_final: 0.8559 (ttpp) REVERT: P 74 MET cc_start: 0.7884 (tmm) cc_final: 0.7517 (tmm) REVERT: P 128 TYR cc_start: 0.8753 (m-10) cc_final: 0.8517 (m-80) REVERT: P 245 MET cc_start: 0.8353 (ttm) cc_final: 0.8056 (mtm) REVERT: Q 153 ARG cc_start: 0.9023 (ttp80) cc_final: 0.8784 (ttt180) REVERT: Q 160 PHE cc_start: 0.8278 (m-80) cc_final: 0.7826 (m-80) REVERT: Q 174 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8430 (ttp80) REVERT: Q 184 GLN cc_start: 0.9055 (mt0) cc_final: 0.8512 (tp40) REVERT: Q 245 MET cc_start: 0.8232 (ttm) cc_final: 0.7829 (mtm) REVERT: R 70 LEU cc_start: 0.9111 (mp) cc_final: 0.8829 (tt) REVERT: R 74 MET cc_start: 0.8194 (tmm) cc_final: 0.7382 (tmm) REVERT: R 146 ASP cc_start: 0.7893 (p0) cc_final: 0.7658 (p0) REVERT: R 153 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8604 (ttt180) REVERT: R 174 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8556 (ttp80) REVERT: R 201 LEU cc_start: 0.9011 (tp) cc_final: 0.8793 (tt) REVERT: R 233 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8437 (tm-30) REVERT: R 249 LYS cc_start: 0.8948 (tttt) cc_final: 0.8702 (ttmm) REVERT: S 61 LEU cc_start: 0.8573 (tt) cc_final: 0.8329 (mt) REVERT: S 245 MET cc_start: 0.8281 (ttm) cc_final: 0.8069 (mtm) REVERT: T 61 LEU cc_start: 0.8525 (tt) cc_final: 0.8207 (mt) REVERT: T 62 ILE cc_start: 0.9262 (mm) cc_final: 0.9031 (tp) REVERT: T 174 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8385 (ttp80) REVERT: T 237 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8602 (tm-30) REVERT: T 245 MET cc_start: 0.8241 (ttm) cc_final: 0.7991 (mtm) REVERT: T 249 LYS cc_start: 0.8735 (tttt) cc_final: 0.8509 (ttpp) outliers start: 0 outliers final: 0 residues processed: 1303 average time/residue: 0.5581 time to fit residues: 1139.8432 Evaluate side-chains 674 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 674 time to evaluate : 4.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 439 optimal weight: 5.9990 chunk 394 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 chunk 265 optimal weight: 0.0370 chunk 210 optimal weight: 0.8980 chunk 407 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 303 optimal weight: 0.8980 chunk 472 optimal weight: 3.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 A 227 ASN B 20 ASN B 48 ASN B 184 GLN B 217 GLN ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN C 184 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 184 GLN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN G 20 ASN G 184 GLN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN H 184 GLN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 20 ASN I 184 GLN ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 ASN J 184 GLN J 227 ASN K 184 GLN L 20 ASN L 184 GLN M 20 ASN M 184 GLN M 227 ASN N 20 ASN N 184 GLN O 20 ASN O 184 GLN P 184 GLN Q 20 ASN Q 48 ASN Q 184 GLN R 184 GLN R 227 ASN S 20 ASN S 184 GLN S 234 GLN T 20 ASN T 184 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 42580 Z= 0.182 Angle : 0.547 6.465 57820 Z= 0.287 Chirality : 0.039 0.150 6740 Planarity : 0.004 0.055 7180 Dihedral : 3.826 14.850 5700 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.12), residues: 5260 helix: 1.83 (0.08), residues: 4140 sheet: None (None), residues: 0 loop : -2.89 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 75 HIS 0.002 0.000 HIS G 224 PHE 0.019 0.001 PHE L 232 TYR 0.021 0.001 TYR R 51 ARG 0.006 0.001 ARG S 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1091 time to evaluate : 5.365 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 14 ARG cc_start: 0.8008 (ptt90) cc_final: 0.7434 (ptt90) REVERT: A 31 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8340 (tm-30) REVERT: A 184 GLN cc_start: 0.9010 (mt0) cc_final: 0.8576 (tp-100) REVERT: A 208 LYS cc_start: 0.8844 (tppt) cc_final: 0.8179 (tmmt) REVERT: B 41 CYS cc_start: 0.6010 (t) cc_final: 0.5732 (t) REVERT: B 51 TYR cc_start: 0.9191 (t80) cc_final: 0.8895 (t80) REVERT: B 104 PHE cc_start: 0.7688 (t80) cc_final: 0.7178 (t80) REVERT: B 183 TYR cc_start: 0.9151 (t80) cc_final: 0.8936 (t80) REVERT: B 233 GLU cc_start: 0.8376 (tp30) cc_final: 0.8096 (tm-30) REVERT: B 279 THR cc_start: 0.7623 (m) cc_final: 0.7281 (p) REVERT: C 14 ARG cc_start: 0.8012 (ptt90) cc_final: 0.7686 (ppt170) REVERT: C 41 CYS cc_start: 0.5812 (t) cc_final: 0.5352 (t) REVERT: C 77 ILE cc_start: 0.8764 (tp) cc_final: 0.8517 (mm) REVERT: C 184 GLN cc_start: 0.9011 (mt0) cc_final: 0.8494 (tp40) REVERT: D 128 TYR cc_start: 0.8909 (m-10) cc_final: 0.8674 (m-80) REVERT: D 153 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8487 (ttt180) REVERT: D 183 TYR cc_start: 0.8975 (t80) cc_final: 0.8519 (t80) REVERT: D 237 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 245 MET cc_start: 0.8152 (ttm) cc_final: 0.7779 (mtm) REVERT: E 104 PHE cc_start: 0.8015 (t80) cc_final: 0.7379 (t80) REVERT: E 128 TYR cc_start: 0.8965 (m-10) cc_final: 0.8691 (m-80) REVERT: E 152 LYS cc_start: 0.9156 (tptm) cc_final: 0.8829 (tppp) REVERT: E 155 GLU cc_start: 0.8938 (tp30) cc_final: 0.8588 (tm-30) REVERT: E 201 LEU cc_start: 0.9064 (tp) cc_final: 0.8824 (tt) REVERT: E 233 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8319 (tm-30) REVERT: E 249 LYS cc_start: 0.8258 (tttm) cc_final: 0.8022 (tttm) REVERT: E 265 ARG cc_start: 0.7581 (ttt90) cc_final: 0.6816 (tpt170) REVERT: F 128 TYR cc_start: 0.8818 (m-10) cc_final: 0.8246 (m-80) REVERT: F 153 ARG cc_start: 0.8826 (ttp80) cc_final: 0.8522 (ttt180) REVERT: F 174 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8430 (ptm-80) REVERT: F 184 GLN cc_start: 0.8967 (mt0) cc_final: 0.8521 (tp-100) REVERT: F 244 MET cc_start: 0.8954 (tpt) cc_final: 0.8626 (tpp) REVERT: G 146 ASP cc_start: 0.8051 (p0) cc_final: 0.7763 (p0) REVERT: G 228 GLU cc_start: 0.8936 (pp20) cc_final: 0.8666 (pp20) REVERT: G 245 MET cc_start: 0.8421 (ttm) cc_final: 0.8124 (mtm) REVERT: H 128 TYR cc_start: 0.8631 (m-10) cc_final: 0.8322 (m-80) REVERT: H 187 MET cc_start: 0.8986 (mmp) cc_final: 0.8742 (mmm) REVERT: H 237 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8458 (tm-30) REVERT: H 245 MET cc_start: 0.8377 (mtm) cc_final: 0.8126 (mtm) REVERT: I 153 ARG cc_start: 0.9096 (ttp80) cc_final: 0.8853 (ttt180) REVERT: I 249 LYS cc_start: 0.8770 (ttmm) cc_final: 0.8344 (ttmm) REVERT: J 184 GLN cc_start: 0.8914 (mt0) cc_final: 0.8485 (tp40) REVERT: J 208 LYS cc_start: 0.8783 (tppt) cc_final: 0.8289 (tmmt) REVERT: J 244 MET cc_start: 0.9131 (tpt) cc_final: 0.8924 (tpp) REVERT: J 262 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8059 (mmmm) REVERT: K 26 LEU cc_start: 0.9142 (tp) cc_final: 0.8909 (tp) REVERT: K 77 ILE cc_start: 0.8701 (tp) cc_final: 0.8441 (tp) REVERT: K 78 THR cc_start: 0.6596 (m) cc_final: 0.6247 (m) REVERT: K 107 ILE cc_start: 0.9375 (mm) cc_final: 0.8915 (tp) REVERT: K 160 PHE cc_start: 0.8483 (m-80) cc_final: 0.8061 (m-80) REVERT: K 221 TRP cc_start: 0.8800 (t60) cc_final: 0.8382 (t60) REVERT: K 245 MET cc_start: 0.8162 (ttm) cc_final: 0.7865 (mtm) REVERT: L 160 PHE cc_start: 0.8443 (m-80) cc_final: 0.7874 (m-80) REVERT: L 184 GLN cc_start: 0.8968 (mt0) cc_final: 0.8460 (tp40) REVERT: L 208 LYS cc_start: 0.8687 (tppt) cc_final: 0.8206 (tmmt) REVERT: M 160 PHE cc_start: 0.8258 (m-80) cc_final: 0.7531 (m-80) REVERT: M 184 GLN cc_start: 0.9148 (mt0) cc_final: 0.8656 (tp-100) REVERT: M 245 MET cc_start: 0.8006 (ttm) cc_final: 0.7748 (mtm) REVERT: N 41 CYS cc_start: 0.5035 (t) cc_final: 0.4733 (t) REVERT: N 116 LEU cc_start: 0.8719 (tt) cc_final: 0.8474 (tt) REVERT: N 152 LYS cc_start: 0.9187 (tppp) cc_final: 0.8932 (tppp) REVERT: N 153 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8533 (ptt90) REVERT: N 155 GLU cc_start: 0.8886 (tp30) cc_final: 0.8567 (tm-30) REVERT: N 183 TYR cc_start: 0.8925 (t80) cc_final: 0.8504 (t80) REVERT: N 184 GLN cc_start: 0.9032 (mt0) cc_final: 0.8268 (mm-40) REVERT: O 74 MET cc_start: 0.8441 (tpt) cc_final: 0.8210 (tpt) REVERT: O 160 PHE cc_start: 0.7945 (m-10) cc_final: 0.7725 (m-80) REVERT: O 234 GLN cc_start: 0.7946 (mt0) cc_final: 0.7650 (mt0) REVERT: P 103 ARG cc_start: 0.8810 (ttp-170) cc_final: 0.8537 (mtm-85) REVERT: P 128 TYR cc_start: 0.8765 (m-10) cc_final: 0.8434 (m-80) REVERT: P 154 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8586 (mm-30) REVERT: P 187 MET cc_start: 0.8969 (mmm) cc_final: 0.8730 (mmm) REVERT: P 245 MET cc_start: 0.8333 (ttm) cc_final: 0.8060 (mtm) REVERT: Q 160 PHE cc_start: 0.8313 (m-80) cc_final: 0.7644 (m-80) REVERT: Q 184 GLN cc_start: 0.9033 (mt0) cc_final: 0.8742 (tp40) REVERT: Q 187 MET cc_start: 0.9095 (mmp) cc_final: 0.8857 (mmt) REVERT: Q 230 GLU cc_start: 0.8337 (tp30) cc_final: 0.8125 (tp30) REVERT: R 146 ASP cc_start: 0.7699 (p0) cc_final: 0.7440 (p0) REVERT: R 187 MET cc_start: 0.8850 (mmm) cc_final: 0.8292 (mmm) REVERT: S 61 LEU cc_start: 0.8634 (tt) cc_final: 0.8362 (mt) REVERT: S 96 GLU cc_start: 0.6481 (pm20) cc_final: 0.4235 (tm-30) REVERT: T 61 LEU cc_start: 0.8570 (tt) cc_final: 0.8277 (mt) REVERT: T 74 MET cc_start: 0.8492 (tpt) cc_final: 0.8256 (tpt) REVERT: T 174 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8214 (ptm-80) REVERT: T 187 MET cc_start: 0.9213 (mmp) cc_final: 0.8980 (mmt) REVERT: T 249 LYS cc_start: 0.8559 (tttt) cc_final: 0.8356 (ttpp) outliers start: 2 outliers final: 0 residues processed: 1092 average time/residue: 0.4901 time to fit residues: 881.7009 Evaluate side-chains 716 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 716 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 262 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 393 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 473 optimal weight: 0.8980 chunk 511 optimal weight: 0.9990 chunk 421 optimal weight: 0.0370 chunk 469 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 379 optimal weight: 6.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN B 227 ASN D 227 ASN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN L 48 ASN M 48 ASN M 227 ASN N 227 ASN ** T 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 42580 Z= 0.165 Angle : 0.520 6.300 57820 Z= 0.273 Chirality : 0.038 0.149 6740 Planarity : 0.004 0.055 7180 Dihedral : 3.780 23.319 5700 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.34 % 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: 1.85 (0.12), residues: 5260 helix: 2.23 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.79 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 75 HIS 0.003 0.000 HIS M 246 PHE 0.024 0.001 PHE S 160 TYR 0.013 0.001 TYR O 81 ARG 0.007 0.001 ARG M 247 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1068 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8008 (ptt90) cc_final: 0.7550 (ptt90) REVERT: A 31 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8409 (tm-30) REVERT: A 184 GLN cc_start: 0.9025 (mt0) cc_final: 0.8660 (tp40) REVERT: A 208 LYS cc_start: 0.8835 (tppt) cc_final: 0.8191 (tmmt) REVERT: A 227 ASN cc_start: 0.8606 (t0) cc_final: 0.8383 (t0) REVERT: A 228 GLU cc_start: 0.8844 (pp20) cc_final: 0.8630 (tm-30) REVERT: B 39 PHE cc_start: 0.8934 (t80) cc_final: 0.8732 (t80) REVERT: B 41 CYS cc_start: 0.6167 (t) cc_final: 0.5913 (t) REVERT: B 51 TYR cc_start: 0.9144 (t80) cc_final: 0.8835 (t80) REVERT: B 74 MET cc_start: 0.8199 (tpt) cc_final: 0.7982 (tpp) REVERT: B 78 THR cc_start: 0.7343 (m) cc_final: 0.7037 (m) REVERT: B 233 GLU cc_start: 0.8386 (tp30) cc_final: 0.8182 (tm-30) REVERT: C 41 CYS cc_start: 0.5765 (t) cc_final: 0.5306 (t) REVERT: C 51 TYR cc_start: 0.9167 (t80) cc_final: 0.8846 (t80) REVERT: C 128 TYR cc_start: 0.9026 (m-10) cc_final: 0.8722 (m-80) REVERT: C 184 GLN cc_start: 0.8986 (mt0) cc_final: 0.8495 (tp40) REVERT: C 187 MET cc_start: 0.8874 (mmt) cc_final: 0.8232 (mmm) REVERT: D 128 TYR cc_start: 0.8881 (m-10) cc_final: 0.8637 (m-80) REVERT: D 183 TYR cc_start: 0.9045 (t80) cc_final: 0.8528 (t80) REVERT: D 237 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8386 (tm-30) REVERT: D 245 MET cc_start: 0.8032 (ttm) cc_final: 0.7635 (mtm) REVERT: E 155 GLU cc_start: 0.8941 (tp30) cc_final: 0.8568 (tm-30) REVERT: E 184 GLN cc_start: 0.9200 (mt0) cc_final: 0.8665 (mm-40) REVERT: E 249 LYS cc_start: 0.8077 (tttm) cc_final: 0.7767 (ttmm) REVERT: E 265 ARG cc_start: 0.7599 (ttt90) cc_final: 0.6839 (tpt170) REVERT: F 174 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8369 (ptm-80) REVERT: F 184 GLN cc_start: 0.8926 (mt0) cc_final: 0.8584 (tp-100) REVERT: F 244 MET cc_start: 0.9118 (tpt) cc_final: 0.8899 (tpt) REVERT: G 74 MET cc_start: 0.8443 (tpt) cc_final: 0.8169 (tpp) REVERT: G 146 ASP cc_start: 0.8002 (p0) cc_final: 0.7784 (p0) REVERT: G 228 GLU cc_start: 0.9026 (pp20) cc_final: 0.8731 (pp20) REVERT: G 233 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7979 (tm-30) REVERT: G 245 MET cc_start: 0.8356 (ttm) cc_final: 0.8140 (mtm) REVERT: H 61 LEU cc_start: 0.8359 (mt) cc_final: 0.8141 (tt) REVERT: H 128 TYR cc_start: 0.8616 (m-10) cc_final: 0.8289 (m-80) REVERT: H 221 TRP cc_start: 0.7871 (t60) cc_final: 0.7325 (t60) REVERT: H 237 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8390 (tm-30) REVERT: I 187 MET cc_start: 0.8893 (mmt) cc_final: 0.8687 (mmt) REVERT: J 183 TYR cc_start: 0.9005 (t80) cc_final: 0.8464 (t80) REVERT: J 184 GLN cc_start: 0.8914 (mt0) cc_final: 0.8501 (tp40) REVERT: J 208 LYS cc_start: 0.8802 (tppt) cc_final: 0.8298 (tmmt) REVERT: J 244 MET cc_start: 0.9107 (tpt) cc_final: 0.8884 (tpp) REVERT: J 249 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8061 (ttmm) REVERT: J 262 LYS cc_start: 0.8322 (mmmm) cc_final: 0.8111 (mmmm) REVERT: K 153 ARG cc_start: 0.9106 (ttp80) cc_final: 0.8766 (ptt180) REVERT: K 198 ILE cc_start: 0.8320 (mm) cc_final: 0.8057 (tp) REVERT: K 245 MET cc_start: 0.8154 (ttm) cc_final: 0.7927 (mtm) REVERT: L 153 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8532 (ttt180) REVERT: L 160 PHE cc_start: 0.8341 (m-80) cc_final: 0.8086 (m-80) REVERT: L 184 GLN cc_start: 0.8918 (mt0) cc_final: 0.8481 (tp40) REVERT: L 208 LYS cc_start: 0.8716 (tppt) cc_final: 0.8257 (tmmt) REVERT: M 153 ARG cc_start: 0.9086 (ttp80) cc_final: 0.8818 (ttt180) REVERT: M 160 PHE cc_start: 0.8204 (m-80) cc_final: 0.7877 (m-80) REVERT: M 184 GLN cc_start: 0.9147 (mt0) cc_final: 0.8687 (tp-100) REVERT: M 241 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8597 (tpp80) REVERT: M 245 MET cc_start: 0.7887 (ttm) cc_final: 0.7647 (mtm) REVERT: M 271 ASP cc_start: 0.9050 (m-30) cc_final: 0.8802 (m-30) REVERT: N 41 CYS cc_start: 0.5138 (t) cc_final: 0.4802 (t) REVERT: N 116 LEU cc_start: 0.8696 (tt) cc_final: 0.8447 (tt) REVERT: N 153 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8501 (ptt90) REVERT: N 155 GLU cc_start: 0.8855 (tp30) cc_final: 0.8548 (tm-30) REVERT: N 183 TYR cc_start: 0.8948 (t80) cc_final: 0.8662 (t80) REVERT: N 184 GLN cc_start: 0.9034 (mt0) cc_final: 0.8290 (mm-40) REVERT: N 249 LYS cc_start: 0.7929 (tttp) cc_final: 0.7674 (ttmm) REVERT: O 128 TYR cc_start: 0.8724 (m-10) cc_final: 0.8412 (m-80) REVERT: O 187 MET cc_start: 0.9052 (mmt) cc_final: 0.8691 (mmp) REVERT: O 249 LYS cc_start: 0.8564 (tttt) cc_final: 0.8319 (ttpp) REVERT: P 103 ARG cc_start: 0.8732 (ttp-170) cc_final: 0.8312 (mtm-85) REVERT: P 128 TYR cc_start: 0.8738 (m-10) cc_final: 0.8362 (m-80) REVERT: P 245 MET cc_start: 0.8291 (ttm) cc_final: 0.8047 (mtm) REVERT: Q 130 GLU cc_start: 0.8829 (pt0) cc_final: 0.8552 (pt0) REVERT: Q 160 PHE cc_start: 0.8060 (m-80) cc_final: 0.7673 (m-80) REVERT: Q 184 GLN cc_start: 0.9031 (mt0) cc_final: 0.8677 (tp40) REVERT: Q 244 MET cc_start: 0.8895 (tpt) cc_final: 0.8669 (tpt) REVERT: R 78 THR cc_start: 0.7307 (m) cc_final: 0.7048 (m) REVERT: R 153 ARG cc_start: 0.9106 (ttp80) cc_final: 0.8831 (ttt180) REVERT: R 187 MET cc_start: 0.8639 (mmm) cc_final: 0.8217 (mmm) REVERT: R 233 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8216 (tm-30) REVERT: S 96 GLU cc_start: 0.6512 (pm20) cc_final: 0.4332 (tm-30) REVERT: S 160 PHE cc_start: 0.8067 (m-80) cc_final: 0.7671 (m-80) REVERT: S 221 TRP cc_start: 0.8360 (t60) cc_final: 0.8089 (t60) REVERT: T 61 LEU cc_start: 0.8556 (tt) cc_final: 0.8249 (mt) REVERT: T 160 PHE cc_start: 0.7923 (m-80) cc_final: 0.7667 (m-80) outliers start: 4 outliers final: 3 residues processed: 1069 average time/residue: 0.5053 time to fit residues: 885.8159 Evaluate side-chains 728 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 725 time to evaluate : 4.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 467 optimal weight: 4.9990 chunk 355 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 317 optimal weight: 0.6980 chunk 474 optimal weight: 10.0000 chunk 502 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 449 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** C 48 ASN D 48 ASN ** E 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 ASN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN J 227 ASN M 227 ASN N 48 ASN R 44 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42580 Z= 0.170 Angle : 0.517 7.927 57820 Z= 0.272 Chirality : 0.038 0.154 6740 Planarity : 0.004 0.055 7180 Dihedral : 3.712 24.654 5700 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % 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: 2.17 (0.12), residues: 5260 helix: 2.46 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.69 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 221 HIS 0.002 0.000 HIS N 224 PHE 0.024 0.001 PHE R 160 TYR 0.012 0.001 TYR G 142 ARG 0.009 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1025 time to evaluate : 4.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.7991 (ptt90) cc_final: 0.7768 (ppt170) REVERT: A 31 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8405 (tm-30) REVERT: A 184 GLN cc_start: 0.9025 (mt0) cc_final: 0.8694 (tp40) REVERT: A 208 LYS cc_start: 0.8821 (tppt) cc_final: 0.8212 (tmmt) REVERT: B 41 CYS cc_start: 0.6131 (t) cc_final: 0.5904 (t) REVERT: B 51 TYR cc_start: 0.9125 (t80) cc_final: 0.8804 (t80) REVERT: B 74 MET cc_start: 0.8173 (tpt) cc_final: 0.7962 (tpp) REVERT: B 233 GLU cc_start: 0.8411 (tp30) cc_final: 0.8196 (tm-30) REVERT: C 41 CYS cc_start: 0.5556 (t) cc_final: 0.5250 (t) REVERT: C 48 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7597 (t0) REVERT: C 51 TYR cc_start: 0.9262 (t80) cc_final: 0.8880 (t80) REVERT: C 128 TYR cc_start: 0.8882 (m-10) cc_final: 0.8673 (m-80) REVERT: C 184 GLN cc_start: 0.8944 (mt0) cc_final: 0.8487 (tp40) REVERT: C 187 MET cc_start: 0.8754 (mmt) cc_final: 0.8233 (mmm) REVERT: D 41 CYS cc_start: 0.5841 (t) cc_final: 0.5620 (t) REVERT: D 128 TYR cc_start: 0.8901 (m-10) cc_final: 0.8639 (m-80) REVERT: D 233 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8364 (tm-30) REVERT: D 237 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8408 (tm-30) REVERT: D 244 MET cc_start: 0.9115 (tpt) cc_final: 0.8877 (tpp) REVERT: D 245 MET cc_start: 0.8097 (ttm) cc_final: 0.7724 (mtm) REVERT: D 249 LYS cc_start: 0.8141 (tttm) cc_final: 0.7896 (tttm) REVERT: E 155 GLU cc_start: 0.8895 (tp30) cc_final: 0.8513 (tm-30) REVERT: E 184 GLN cc_start: 0.9191 (mt0) cc_final: 0.8743 (mm-40) REVERT: E 265 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7056 (tpt170) REVERT: F 14 ARG cc_start: 0.7884 (ppt170) cc_final: 0.7452 (ppt170) REVERT: F 129 TYR cc_start: 0.9405 (t80) cc_final: 0.9178 (t80) REVERT: F 184 GLN cc_start: 0.8928 (mt0) cc_final: 0.8567 (tp-100) REVERT: F 233 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8246 (tm-30) REVERT: F 249 LYS cc_start: 0.7948 (tttm) cc_final: 0.7719 (ttpp) REVERT: G 233 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7952 (tm-30) REVERT: G 245 MET cc_start: 0.8378 (ttm) cc_final: 0.8125 (mtm) REVERT: G 271 ASP cc_start: 0.8431 (m-30) cc_final: 0.8208 (m-30) REVERT: H 61 LEU cc_start: 0.8350 (mt) cc_final: 0.8123 (tt) REVERT: H 128 TYR cc_start: 0.8582 (m-10) cc_final: 0.8309 (m-80) REVERT: H 135 GLU cc_start: 0.7996 (pp20) cc_final: 0.7660 (pp20) REVERT: H 221 TRP cc_start: 0.7901 (t60) cc_final: 0.7433 (t60) REVERT: H 237 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8387 (tm-30) REVERT: H 248 ILE cc_start: 0.8614 (mm) cc_final: 0.8149 (tp) REVERT: I 70 LEU cc_start: 0.9140 (mm) cc_final: 0.8903 (tt) REVERT: I 146 ASP cc_start: 0.8111 (p0) cc_final: 0.7707 (p0) REVERT: J 104 PHE cc_start: 0.6934 (t80) cc_final: 0.6716 (t80) REVERT: J 184 GLN cc_start: 0.9012 (mt0) cc_final: 0.8525 (tp40) REVERT: J 208 LYS cc_start: 0.8840 (tppt) cc_final: 0.8323 (tmmt) REVERT: J 244 MET cc_start: 0.8992 (tpt) cc_final: 0.8770 (tpp) REVERT: K 153 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8762 (ptt180) REVERT: K 198 ILE cc_start: 0.8342 (mm) cc_final: 0.8032 (tp) REVERT: K 221 TRP cc_start: 0.8527 (t60) cc_final: 0.8104 (t60) REVERT: L 153 ARG cc_start: 0.8930 (ttp80) cc_final: 0.8644 (ttt180) REVERT: L 184 GLN cc_start: 0.9010 (mt0) cc_final: 0.8534 (tp40) REVERT: L 208 LYS cc_start: 0.8691 (tppt) cc_final: 0.8280 (tmmt) REVERT: L 255 ILE cc_start: 0.9186 (mm) cc_final: 0.8869 (mm) REVERT: M 51 TYR cc_start: 0.9104 (t80) cc_final: 0.8767 (t80) REVERT: M 74 MET cc_start: 0.8465 (tpt) cc_final: 0.7991 (tpt) REVERT: M 184 GLN cc_start: 0.9105 (mt0) cc_final: 0.8660 (tp40) REVERT: M 241 ARG cc_start: 0.8936 (tpp80) cc_final: 0.8640 (tpp80) REVERT: M 271 ASP cc_start: 0.8934 (m-30) cc_final: 0.8686 (m-30) REVERT: N 116 LEU cc_start: 0.8731 (tt) cc_final: 0.8459 (tt) REVERT: N 153 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8575 (ptt90) REVERT: N 183 TYR cc_start: 0.8982 (t80) cc_final: 0.8571 (t80) REVERT: N 184 GLN cc_start: 0.9051 (mt0) cc_final: 0.8328 (mm-40) REVERT: N 226 GLN cc_start: 0.8133 (tt0) cc_final: 0.7787 (tm-30) REVERT: N 249 LYS cc_start: 0.7888 (tttp) cc_final: 0.7566 (ttmm) REVERT: O 128 TYR cc_start: 0.8687 (m-10) cc_final: 0.8378 (m-80) REVERT: O 241 ARG cc_start: 0.9220 (tpp80) cc_final: 0.8743 (tpp80) REVERT: P 74 MET cc_start: 0.8469 (tpp) cc_final: 0.8018 (tpt) REVERT: P 103 ARG cc_start: 0.8643 (ttp-170) cc_final: 0.8420 (ttp-170) REVERT: P 128 TYR cc_start: 0.8804 (m-10) cc_final: 0.8470 (m-80) REVERT: P 198 ILE cc_start: 0.8382 (mm) cc_final: 0.8105 (tp) REVERT: P 245 MET cc_start: 0.8280 (ttm) cc_final: 0.8043 (mtm) REVERT: Q 184 GLN cc_start: 0.9081 (mt0) cc_final: 0.8782 (tp40) REVERT: Q 241 ARG cc_start: 0.9182 (tpp80) cc_final: 0.8881 (tpp80) REVERT: Q 244 MET cc_start: 0.8966 (tpt) cc_final: 0.8657 (tpt) REVERT: R 153 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8846 (ttt180) REVERT: R 160 PHE cc_start: 0.7846 (m-80) cc_final: 0.7517 (m-80) REVERT: R 187 MET cc_start: 0.8776 (mmm) cc_final: 0.8530 (mmm) REVERT: R 241 ARG cc_start: 0.8938 (tpp80) cc_final: 0.8642 (tpp80) REVERT: S 129 TYR cc_start: 0.9182 (t80) cc_final: 0.8979 (t80) REVERT: S 160 PHE cc_start: 0.8146 (m-80) cc_final: 0.7935 (m-80) REVERT: S 221 TRP cc_start: 0.8214 (t60) cc_final: 0.7882 (t60) REVERT: T 128 TYR cc_start: 0.8638 (m-10) cc_final: 0.8317 (m-80) REVERT: T 160 PHE cc_start: 0.7996 (m-80) cc_final: 0.7754 (m-80) REVERT: T 187 MET cc_start: 0.9012 (mmt) cc_final: 0.8732 (mmp) REVERT: T 241 ARG cc_start: 0.9107 (tpp80) cc_final: 0.8724 (tpp80) REVERT: T 248 ILE cc_start: 0.8799 (mm) cc_final: 0.8554 (tp) outliers start: 5 outliers final: 0 residues processed: 1029 average time/residue: 0.4942 time to fit residues: 834.7165 Evaluate side-chains 712 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 711 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 418 optimal weight: 0.9990 chunk 285 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 374 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 428 optimal weight: 0.6980 chunk 347 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 256 optimal weight: 0.9990 chunk 451 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 227 ASN F 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN L 48 ASN ** L 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 ASN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 ASN R 227 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 42580 Z= 0.158 Angle : 0.516 8.256 57820 Z= 0.268 Chirality : 0.038 0.156 6740 Planarity : 0.004 0.068 7180 Dihedral : 3.696 23.873 5700 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.09 % Allowed : 2.58 % Favored : 97.34 % 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: 2.35 (0.12), residues: 5260 helix: 2.60 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.66 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 221 HIS 0.002 0.000 HIS E 246 PHE 0.025 0.001 PHE O 160 TYR 0.012 0.001 TYR L 81 ARG 0.010 0.000 ARG B 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 993 time to evaluate : 4.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8008 (ptt90) cc_final: 0.7772 (ppt170) REVERT: A 31 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8396 (tm-30) REVERT: A 184 GLN cc_start: 0.9035 (mt0) cc_final: 0.8690 (tp-100) REVERT: A 208 LYS cc_start: 0.8770 (tppt) cc_final: 0.8155 (tmmt) REVERT: A 244 MET cc_start: 0.9281 (tpt) cc_final: 0.8877 (tpt) REVERT: B 51 TYR cc_start: 0.9081 (t80) cc_final: 0.8844 (t80) REVERT: B 74 MET cc_start: 0.8141 (tpt) cc_final: 0.7872 (tpp) REVERT: C 41 CYS cc_start: 0.5625 (t) cc_final: 0.5263 (t) REVERT: C 51 TYR cc_start: 0.9245 (t80) cc_final: 0.8890 (t80) REVERT: C 128 TYR cc_start: 0.8902 (m-10) cc_final: 0.8626 (m-80) REVERT: C 184 GLN cc_start: 0.8936 (mt0) cc_final: 0.8395 (tp40) REVERT: C 187 MET cc_start: 0.8726 (mmt) cc_final: 0.8280 (mmm) REVERT: D 41 CYS cc_start: 0.5673 (t) cc_final: 0.5448 (t) REVERT: D 128 TYR cc_start: 0.8902 (m-10) cc_final: 0.8651 (m-80) REVERT: D 155 GLU cc_start: 0.8733 (tp30) cc_final: 0.8053 (tm-30) REVERT: D 184 GLN cc_start: 0.9147 (mt0) cc_final: 0.8546 (tp-100) REVERT: D 233 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8325 (tm-30) REVERT: D 244 MET cc_start: 0.8987 (tpt) cc_final: 0.8735 (tpp) REVERT: D 245 MET cc_start: 0.8105 (ttm) cc_final: 0.7679 (mtm) REVERT: E 155 GLU cc_start: 0.8958 (tp30) cc_final: 0.8539 (tm-30) REVERT: E 184 GLN cc_start: 0.9173 (mt0) cc_final: 0.8771 (mm-40) REVERT: E 249 LYS cc_start: 0.7945 (tttp) cc_final: 0.7740 (ttmm) REVERT: F 14 ARG cc_start: 0.7877 (ppt170) cc_final: 0.7582 (ppt170) REVERT: F 74 MET cc_start: 0.8312 (tpt) cc_final: 0.7951 (tpt) REVERT: F 184 GLN cc_start: 0.8917 (mt0) cc_final: 0.8559 (tp-100) REVERT: F 233 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8224 (tm-30) REVERT: G 245 MET cc_start: 0.8374 (ttm) cc_final: 0.8143 (mtm) REVERT: G 271 ASP cc_start: 0.8488 (m-30) cc_final: 0.8230 (m-30) REVERT: H 61 LEU cc_start: 0.8344 (mt) cc_final: 0.8115 (tt) REVERT: H 128 TYR cc_start: 0.8593 (m-10) cc_final: 0.8317 (m-80) REVERT: H 184 GLN cc_start: 0.8897 (mt0) cc_final: 0.8610 (tp40) REVERT: H 221 TRP cc_start: 0.7868 (t60) cc_final: 0.7410 (t60) REVERT: H 237 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8454 (tm-30) REVERT: H 245 MET cc_start: 0.8346 (mtm) cc_final: 0.7851 (mtm) REVERT: I 70 LEU cc_start: 0.9109 (mm) cc_final: 0.8894 (tt) REVERT: I 78 THR cc_start: 0.7063 (m) cc_final: 0.6620 (m) REVERT: I 146 ASP cc_start: 0.8023 (p0) cc_final: 0.7700 (p0) REVERT: J 184 GLN cc_start: 0.8963 (mt0) cc_final: 0.8487 (tp40) REVERT: J 208 LYS cc_start: 0.8894 (tppt) cc_final: 0.8327 (tmmt) REVERT: K 221 TRP cc_start: 0.8478 (t60) cc_final: 0.8069 (t60) REVERT: L 74 MET cc_start: 0.8345 (tpt) cc_final: 0.7987 (tpt) REVERT: L 183 TYR cc_start: 0.9087 (t80) cc_final: 0.8292 (t80) REVERT: L 184 GLN cc_start: 0.9009 (mt0) cc_final: 0.8606 (tp40) REVERT: L 208 LYS cc_start: 0.8736 (tppt) cc_final: 0.8239 (tmmt) REVERT: M 184 GLN cc_start: 0.9096 (mt0) cc_final: 0.8694 (tp-100) REVERT: M 216 LEU cc_start: 0.8726 (mt) cc_final: 0.8501 (mt) REVERT: M 271 ASP cc_start: 0.8899 (m-30) cc_final: 0.8519 (m-30) REVERT: N 31 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8580 (tm-30) REVERT: N 116 LEU cc_start: 0.8688 (tt) cc_final: 0.8434 (tt) REVERT: N 155 GLU cc_start: 0.8824 (tp30) cc_final: 0.8549 (tm-30) REVERT: N 183 TYR cc_start: 0.9002 (t80) cc_final: 0.8673 (t80) REVERT: N 184 GLN cc_start: 0.9087 (mt0) cc_final: 0.8386 (mm-40) REVERT: N 226 GLN cc_start: 0.8000 (tt0) cc_final: 0.7605 (tm-30) REVERT: O 128 TYR cc_start: 0.8611 (m-10) cc_final: 0.8302 (m-80) REVERT: O 152 LYS cc_start: 0.8785 (tptp) cc_final: 0.8515 (tppp) REVERT: O 154 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8560 (mm-30) REVERT: O 244 MET cc_start: 0.9116 (tpt) cc_final: 0.8781 (tpt) REVERT: O 248 ILE cc_start: 0.9064 (tp) cc_final: 0.8827 (tp) REVERT: P 103 ARG cc_start: 0.8657 (ttp-170) cc_final: 0.8381 (mtm-85) REVERT: P 128 TYR cc_start: 0.8808 (m-10) cc_final: 0.8542 (m-80) REVERT: P 198 ILE cc_start: 0.8241 (mm) cc_final: 0.7972 (tp) REVERT: Q 184 GLN cc_start: 0.9081 (mt0) cc_final: 0.8779 (tp40) REVERT: R 78 THR cc_start: 0.6475 (m) cc_final: 0.6214 (m) REVERT: R 153 ARG cc_start: 0.9131 (ttp80) cc_final: 0.8828 (ttt180) REVERT: R 160 PHE cc_start: 0.7946 (m-80) cc_final: 0.7619 (m-80) REVERT: R 187 MET cc_start: 0.8758 (mmm) cc_final: 0.8331 (mmm) REVERT: R 241 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8724 (tpp80) REVERT: S 152 LYS cc_start: 0.9164 (tptp) cc_final: 0.8931 (tppp) REVERT: S 160 PHE cc_start: 0.8055 (m-80) cc_final: 0.7824 (m-80) REVERT: S 221 TRP cc_start: 0.8103 (t60) cc_final: 0.7711 (t60) REVERT: T 128 TYR cc_start: 0.8587 (m-10) cc_final: 0.8295 (m-80) REVERT: T 154 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8573 (mm-30) REVERT: T 160 PHE cc_start: 0.7871 (m-80) cc_final: 0.7573 (m-10) REVERT: T 187 MET cc_start: 0.8970 (mmt) cc_final: 0.8711 (mmp) outliers start: 4 outliers final: 2 residues processed: 995 average time/residue: 0.4704 time to fit residues: 780.0491 Evaluate side-chains 696 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 694 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 169 optimal weight: 20.0000 chunk 452 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 503 optimal weight: 5.9990 chunk 417 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 166 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN B 227 ASN D 7 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 GLN N 48 ASN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 GLN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42580 Z= 0.195 Angle : 0.543 7.694 57820 Z= 0.283 Chirality : 0.039 0.146 6740 Planarity : 0.004 0.066 7180 Dihedral : 3.734 26.804 5700 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.02 % Allowed : 1.82 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.12), residues: 5260 helix: 2.66 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.35 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 221 HIS 0.002 0.001 HIS C 246 PHE 0.024 0.001 PHE L 160 TYR 0.009 0.001 TYR K 129 ARG 0.020 0.000 ARG J 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 982 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8066 (ptt90) cc_final: 0.7829 (ppt170) REVERT: A 184 GLN cc_start: 0.9026 (mt0) cc_final: 0.8604 (tp-100) REVERT: A 208 LYS cc_start: 0.8802 (tppt) cc_final: 0.8199 (tmmt) REVERT: A 244 MET cc_start: 0.9207 (tpt) cc_final: 0.8790 (tpt) REVERT: B 74 MET cc_start: 0.8220 (tpt) cc_final: 0.7932 (tpp) REVERT: B 233 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8299 (tm-30) REVERT: C 41 CYS cc_start: 0.5411 (t) cc_final: 0.5025 (t) REVERT: C 51 TYR cc_start: 0.9336 (t80) cc_final: 0.8988 (t80) REVERT: C 128 TYR cc_start: 0.8889 (m-10) cc_final: 0.8545 (m-80) REVERT: C 184 GLN cc_start: 0.8931 (mt0) cc_final: 0.8445 (tp40) REVERT: C 187 MET cc_start: 0.8761 (mmt) cc_final: 0.8325 (mmm) REVERT: D 41 CYS cc_start: 0.5627 (t) cc_final: 0.5400 (t) REVERT: D 128 TYR cc_start: 0.8905 (m-10) cc_final: 0.8630 (m-80) REVERT: D 152 LYS cc_start: 0.9280 (tppp) cc_final: 0.9003 (tppp) REVERT: D 184 GLN cc_start: 0.9136 (mt0) cc_final: 0.8688 (tp-100) REVERT: D 249 LYS cc_start: 0.8077 (tttm) cc_final: 0.7767 (tttm) REVERT: D 271 ASP cc_start: 0.8679 (m-30) cc_final: 0.8437 (m-30) REVERT: E 153 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8650 (ttt180) REVERT: E 155 GLU cc_start: 0.8922 (tp30) cc_final: 0.8533 (tm-30) REVERT: E 184 GLN cc_start: 0.9232 (mt0) cc_final: 0.8872 (mm-40) REVERT: E 198 ILE cc_start: 0.8459 (mm) cc_final: 0.7995 (tp) REVERT: F 74 MET cc_start: 0.8415 (tpt) cc_final: 0.8051 (tpt) REVERT: F 184 GLN cc_start: 0.8922 (mt0) cc_final: 0.8596 (tp-100) REVERT: F 244 MET cc_start: 0.9135 (tpt) cc_final: 0.8682 (tpt) REVERT: G 271 ASP cc_start: 0.8556 (m-30) cc_final: 0.8345 (m-30) REVERT: H 14 ARG cc_start: 0.8107 (ptt90) cc_final: 0.7722 (ppt170) REVERT: H 61 LEU cc_start: 0.8422 (mt) cc_final: 0.8116 (tt) REVERT: H 128 TYR cc_start: 0.8679 (m-10) cc_final: 0.8435 (m-80) REVERT: H 135 GLU cc_start: 0.8587 (pp20) cc_final: 0.8000 (pp20) REVERT: H 184 GLN cc_start: 0.8961 (mt0) cc_final: 0.8623 (tp40) REVERT: H 221 TRP cc_start: 0.8089 (t60) cc_final: 0.7604 (t60) REVERT: H 237 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8545 (tm-30) REVERT: H 245 MET cc_start: 0.8372 (mtm) cc_final: 0.7920 (mtm) REVERT: I 187 MET cc_start: 0.8880 (mmt) cc_final: 0.8452 (mmm) REVERT: J 142 TYR cc_start: 0.7070 (m-80) cc_final: 0.6850 (m-10) REVERT: J 153 ARG cc_start: 0.8928 (tmm-80) cc_final: 0.8640 (ttt180) REVERT: J 174 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8276 (ptt180) REVERT: J 184 GLN cc_start: 0.9047 (mt0) cc_final: 0.8591 (tp40) REVERT: J 192 LEU cc_start: 0.8947 (tt) cc_final: 0.8738 (tp) REVERT: J 208 LYS cc_start: 0.8924 (tppt) cc_final: 0.8412 (tmmt) REVERT: J 249 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8140 (ttmm) REVERT: K 22 LEU cc_start: 0.8944 (tp) cc_final: 0.8704 (tp) REVERT: K 152 LYS cc_start: 0.9201 (tppp) cc_final: 0.8973 (tppp) REVERT: K 221 TRP cc_start: 0.8463 (t60) cc_final: 0.8017 (t60) REVERT: L 31 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8734 (tm-30) REVERT: L 74 MET cc_start: 0.8358 (tpt) cc_final: 0.7999 (tpt) REVERT: L 157 LEU cc_start: 0.9102 (tp) cc_final: 0.8881 (tp) REVERT: L 184 GLN cc_start: 0.9006 (mt0) cc_final: 0.8550 (tp40) REVERT: L 208 LYS cc_start: 0.8756 (tppt) cc_final: 0.8249 (tmmt) REVERT: L 245 MET cc_start: 0.8550 (tpp) cc_final: 0.8059 (tpp) REVERT: M 184 GLN cc_start: 0.9142 (mt0) cc_final: 0.8725 (tp-100) REVERT: M 187 MET cc_start: 0.9122 (mmp) cc_final: 0.8901 (mmm) REVERT: M 216 LEU cc_start: 0.8748 (mt) cc_final: 0.8533 (mt) REVERT: M 271 ASP cc_start: 0.8892 (m-30) cc_final: 0.8451 (m-30) REVERT: N 183 TYR cc_start: 0.9142 (t80) cc_final: 0.8772 (t80) REVERT: N 184 GLN cc_start: 0.9116 (mt0) cc_final: 0.8435 (mm-40) REVERT: N 226 GLN cc_start: 0.8115 (tt0) cc_final: 0.7719 (tm-30) REVERT: O 154 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8537 (mm-30) REVERT: O 184 GLN cc_start: 0.8967 (mt0) cc_final: 0.8749 (tp-100) REVERT: O 187 MET cc_start: 0.9065 (mmt) cc_final: 0.8847 (mmp) REVERT: O 244 MET cc_start: 0.9150 (tpt) cc_final: 0.8854 (tpt) REVERT: O 248 ILE cc_start: 0.9082 (tp) cc_final: 0.8845 (tp) REVERT: P 74 MET cc_start: 0.8556 (tpp) cc_final: 0.8152 (tpp) REVERT: P 128 TYR cc_start: 0.8799 (m-10) cc_final: 0.8537 (m-80) REVERT: P 198 ILE cc_start: 0.8303 (mm) cc_final: 0.8014 (tp) REVERT: P 221 TRP cc_start: 0.8373 (t60) cc_final: 0.7957 (t60) REVERT: P 244 MET cc_start: 0.8733 (tpt) cc_final: 0.8371 (tpp) REVERT: P 245 MET cc_start: 0.8240 (mtm) cc_final: 0.7942 (mtp) REVERT: Q 184 GLN cc_start: 0.9072 (mt0) cc_final: 0.8810 (tp40) REVERT: Q 230 GLU cc_start: 0.8387 (tp30) cc_final: 0.8129 (tp30) REVERT: R 146 ASP cc_start: 0.7942 (p0) cc_final: 0.7660 (p0) REVERT: R 153 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8904 (ttt180) REVERT: R 160 PHE cc_start: 0.8117 (m-80) cc_final: 0.7913 (m-80) REVERT: R 187 MET cc_start: 0.8798 (mmm) cc_final: 0.8388 (mmm) REVERT: R 241 ARG cc_start: 0.8985 (tpp80) cc_final: 0.8725 (tpp80) REVERT: S 152 LYS cc_start: 0.9199 (tptp) cc_final: 0.8964 (tppp) REVERT: S 160 PHE cc_start: 0.8213 (m-80) cc_final: 0.8002 (m-80) REVERT: T 154 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8523 (mm-30) REVERT: T 184 GLN cc_start: 0.8956 (mt0) cc_final: 0.8734 (tp-100) REVERT: T 241 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8606 (tpp80) outliers start: 1 outliers final: 0 residues processed: 983 average time/residue: 0.4784 time to fit residues: 779.4377 Evaluate side-chains 679 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 679 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 485 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 286 optimal weight: 20.0000 chunk 367 optimal weight: 3.9990 chunk 284 optimal weight: 0.0370 chunk 423 optimal weight: 6.9990 chunk 280 optimal weight: 0.9990 chunk 501 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 305 optimal weight: 0.1980 chunk 231 optimal weight: 5.9990 overall best weight: 1.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN D 227 ASN F 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN M 227 ASN N 31 GLN N 48 ASN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 ASN R 227 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42580 Z= 0.180 Angle : 0.545 7.918 57820 Z= 0.282 Chirality : 0.039 0.145 6740 Planarity : 0.004 0.064 7180 Dihedral : 3.729 26.175 5700 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.11 % Allowed : 1.19 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.12), residues: 5260 helix: 2.75 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.34 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 221 HIS 0.005 0.001 HIS S 246 PHE 0.022 0.001 PHE Q 160 TYR 0.017 0.001 TYR R 81 ARG 0.015 0.000 ARG J 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 949 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 184 GLN cc_start: 0.8964 (mt0) cc_final: 0.8571 (tp-100) REVERT: A 208 LYS cc_start: 0.8810 (tppt) cc_final: 0.8206 (tmmt) REVERT: A 216 LEU cc_start: 0.8627 (mt) cc_final: 0.8400 (mt) REVERT: A 244 MET cc_start: 0.9261 (tpt) cc_final: 0.8874 (tpt) REVERT: B 74 MET cc_start: 0.8174 (tpt) cc_final: 0.7886 (tpp) REVERT: B 244 MET cc_start: 0.9044 (tpt) cc_final: 0.8839 (tpt) REVERT: B 255 ILE cc_start: 0.8924 (mm) cc_final: 0.8668 (mm) REVERT: C 41 CYS cc_start: 0.5314 (t) cc_final: 0.4999 (t) REVERT: C 48 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7401 (t0) REVERT: C 51 TYR cc_start: 0.9333 (t80) cc_final: 0.8965 (t80) REVERT: C 128 TYR cc_start: 0.8886 (m-10) cc_final: 0.8658 (m-80) REVERT: C 184 GLN cc_start: 0.8899 (mt0) cc_final: 0.8433 (tp40) REVERT: C 187 MET cc_start: 0.8717 (mmt) cc_final: 0.8304 (mmm) REVERT: D 184 GLN cc_start: 0.9117 (mt0) cc_final: 0.8693 (tp-100) REVERT: D 216 LEU cc_start: 0.8517 (mt) cc_final: 0.8279 (mt) REVERT: D 245 MET cc_start: 0.8580 (tpp) cc_final: 0.8100 (tpp) REVERT: D 249 LYS cc_start: 0.8003 (tttm) cc_final: 0.7662 (tttp) REVERT: D 271 ASP cc_start: 0.8723 (m-30) cc_final: 0.8420 (m-30) REVERT: E 155 GLU cc_start: 0.8892 (tp30) cc_final: 0.8505 (tm-30) REVERT: E 184 GLN cc_start: 0.9146 (mt0) cc_final: 0.8879 (mm-40) REVERT: E 187 MET cc_start: 0.8834 (mmt) cc_final: 0.8586 (mmp) REVERT: E 249 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7885 (ttmm) REVERT: F 74 MET cc_start: 0.8434 (tpt) cc_final: 0.8034 (tpt) REVERT: F 184 GLN cc_start: 0.8909 (mt0) cc_final: 0.8595 (tp-100) REVERT: F 244 MET cc_start: 0.9122 (tpt) cc_final: 0.8872 (tpt) REVERT: G 187 MET cc_start: 0.8799 (mmm) cc_final: 0.8541 (mmm) REVERT: G 271 ASP cc_start: 0.8705 (m-30) cc_final: 0.8430 (m-30) REVERT: H 14 ARG cc_start: 0.7967 (ptt90) cc_final: 0.7649 (ppt170) REVERT: H 128 TYR cc_start: 0.8716 (m-10) cc_final: 0.8480 (m-80) REVERT: H 184 GLN cc_start: 0.9063 (mt0) cc_final: 0.8632 (tp40) REVERT: H 221 TRP cc_start: 0.8142 (t60) cc_final: 0.7596 (t60) REVERT: H 237 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8555 (tm-30) REVERT: H 245 MET cc_start: 0.8232 (mtm) cc_final: 0.7918 (mtm) REVERT: I 74 MET cc_start: 0.8451 (tpt) cc_final: 0.8246 (tpt) REVERT: I 78 THR cc_start: 0.7243 (m) cc_final: 0.6967 (m) REVERT: I 187 MET cc_start: 0.8857 (mmt) cc_final: 0.8546 (mmm) REVERT: J 153 ARG cc_start: 0.8925 (tmm-80) cc_final: 0.8692 (ttt180) REVERT: J 174 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8270 (ptt180) REVERT: J 184 GLN cc_start: 0.9044 (mt0) cc_final: 0.8582 (tp40) REVERT: J 187 MET cc_start: 0.8565 (mmt) cc_final: 0.8305 (mmp) REVERT: J 208 LYS cc_start: 0.8927 (tppt) cc_final: 0.8435 (tmmt) REVERT: J 241 ARG cc_start: 0.9172 (tpp80) cc_final: 0.8806 (tpp80) REVERT: J 244 MET cc_start: 0.9041 (tpt) cc_final: 0.8543 (tpp) REVERT: J 249 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8019 (ttmm) REVERT: K 221 TRP cc_start: 0.8425 (t60) cc_final: 0.7941 (t60) REVERT: K 279 THR cc_start: 0.7621 (m) cc_final: 0.7138 (p) REVERT: L 31 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8739 (tm-30) REVERT: L 51 TYR cc_start: 0.9159 (t80) cc_final: 0.8931 (t80) REVERT: L 74 MET cc_start: 0.8321 (tpt) cc_final: 0.7936 (tpt) REVERT: L 157 LEU cc_start: 0.9116 (tp) cc_final: 0.8897 (tp) REVERT: L 184 GLN cc_start: 0.8981 (mt0) cc_final: 0.8539 (tp40) REVERT: L 187 MET cc_start: 0.8793 (mmt) cc_final: 0.7961 (mmm) REVERT: L 208 LYS cc_start: 0.8737 (tppt) cc_final: 0.8266 (tmmt) REVERT: L 245 MET cc_start: 0.8586 (tpp) cc_final: 0.8129 (tpp) REVERT: M 184 GLN cc_start: 0.9127 (mt0) cc_final: 0.8725 (tp-100) REVERT: M 187 MET cc_start: 0.9101 (mmp) cc_final: 0.8869 (mmm) REVERT: M 271 ASP cc_start: 0.8828 (m-30) cc_final: 0.8448 (m-30) REVERT: N 183 TYR cc_start: 0.9129 (t80) cc_final: 0.8733 (t80) REVERT: N 184 GLN cc_start: 0.9115 (mt0) cc_final: 0.8453 (mm-40) REVERT: O 154 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8516 (mm-30) REVERT: O 184 GLN cc_start: 0.8974 (mt0) cc_final: 0.8696 (tp-100) REVERT: O 187 MET cc_start: 0.9046 (mmt) cc_final: 0.8828 (mmp) REVERT: O 244 MET cc_start: 0.9125 (tpt) cc_final: 0.8817 (tpt) REVERT: O 248 ILE cc_start: 0.9072 (tp) cc_final: 0.8816 (tp) REVERT: P 128 TYR cc_start: 0.8811 (m-10) cc_final: 0.8559 (m-80) REVERT: P 198 ILE cc_start: 0.8222 (mm) cc_final: 0.7971 (tp) REVERT: P 221 TRP cc_start: 0.8458 (t60) cc_final: 0.8070 (t60) REVERT: P 279 THR cc_start: 0.7372 (m) cc_final: 0.6994 (p) REVERT: Q 184 GLN cc_start: 0.9117 (mt0) cc_final: 0.8677 (tp40) REVERT: R 51 TYR cc_start: 0.9004 (t80) cc_final: 0.8704 (t80) REVERT: R 146 ASP cc_start: 0.7854 (p0) cc_final: 0.7640 (p0) REVERT: R 187 MET cc_start: 0.8778 (mmm) cc_final: 0.8445 (mmm) REVERT: R 244 MET cc_start: 0.9024 (tpt) cc_final: 0.8562 (tpt) REVERT: S 74 MET cc_start: 0.8159 (tpt) cc_final: 0.7781 (tpp) REVERT: S 152 LYS cc_start: 0.9211 (tptp) cc_final: 0.8992 (tppp) REVERT: T 154 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8496 (mm-30) outliers start: 5 outliers final: 0 residues processed: 954 average time/residue: 0.4850 time to fit residues: 761.8169 Evaluate side-chains 673 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 672 time to evaluate : 4.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 310 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 299 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 318 optimal weight: 3.9990 chunk 341 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 393 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN D 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN L 48 ASN M 227 ASN N 31 GLN N 48 ASN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 184 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42580 Z= 0.187 Angle : 0.559 8.351 57820 Z= 0.288 Chirality : 0.039 0.143 6740 Planarity : 0.004 0.081 7180 Dihedral : 3.746 25.397 5700 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.06 % Allowed : 1.26 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.12), residues: 5260 helix: 2.79 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.33 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 221 HIS 0.004 0.000 HIS M 246 PHE 0.027 0.001 PHE R 160 TYR 0.016 0.001 TYR A 81 ARG 0.014 0.000 ARG J 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 932 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 184 GLN cc_start: 0.8981 (mt0) cc_final: 0.8575 (tp-100) REVERT: A 208 LYS cc_start: 0.8796 (tppt) cc_final: 0.8203 (tmmt) REVERT: A 216 LEU cc_start: 0.8514 (mt) cc_final: 0.8314 (mt) REVERT: A 244 MET cc_start: 0.9298 (tpt) cc_final: 0.8891 (tpt) REVERT: B 74 MET cc_start: 0.8170 (tpt) cc_final: 0.7886 (tpp) REVERT: B 255 ILE cc_start: 0.8964 (mm) cc_final: 0.8705 (mm) REVERT: C 51 TYR cc_start: 0.9341 (t80) cc_final: 0.8998 (t80) REVERT: C 184 GLN cc_start: 0.8901 (mt0) cc_final: 0.8430 (tp40) REVERT: C 187 MET cc_start: 0.8722 (mmt) cc_final: 0.8302 (mmm) REVERT: D 48 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7587 (t0) REVERT: D 155 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8486 (tp30) REVERT: D 184 GLN cc_start: 0.9096 (mt0) cc_final: 0.8702 (tp-100) REVERT: D 271 ASP cc_start: 0.8736 (m-30) cc_final: 0.8385 (m-30) REVERT: E 184 GLN cc_start: 0.9130 (mt0) cc_final: 0.8863 (mm-40) REVERT: E 249 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7917 (ttmm) REVERT: F 74 MET cc_start: 0.8374 (tpt) cc_final: 0.8025 (tpt) REVERT: F 184 GLN cc_start: 0.8889 (mt0) cc_final: 0.8595 (tp-100) REVERT: F 244 MET cc_start: 0.9116 (tpt) cc_final: 0.8867 (tpt) REVERT: G 187 MET cc_start: 0.8766 (mmm) cc_final: 0.8462 (mmm) REVERT: G 233 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7852 (tm-30) REVERT: G 245 MET cc_start: 0.8280 (mtm) cc_final: 0.8067 (mtp) REVERT: G 271 ASP cc_start: 0.8694 (m-30) cc_final: 0.8430 (m-30) REVERT: H 14 ARG cc_start: 0.8022 (ptt90) cc_final: 0.7752 (ppt170) REVERT: H 70 LEU cc_start: 0.9322 (mm) cc_final: 0.9079 (mp) REVERT: H 128 TYR cc_start: 0.8713 (m-10) cc_final: 0.8476 (m-80) REVERT: H 184 GLN cc_start: 0.9041 (mt0) cc_final: 0.8662 (tp40) REVERT: H 237 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8578 (tm-30) REVERT: H 245 MET cc_start: 0.8209 (mtm) cc_final: 0.7987 (mtm) REVERT: H 271 ASP cc_start: 0.8917 (m-30) cc_final: 0.8648 (m-30) REVERT: I 74 MET cc_start: 0.8444 (tpt) cc_final: 0.8152 (tpt) REVERT: I 187 MET cc_start: 0.8873 (mmt) cc_final: 0.8669 (mmm) REVERT: I 245 MET cc_start: 0.8299 (ttm) cc_final: 0.7957 (mtm) REVERT: J 153 ARG cc_start: 0.8961 (tmm-80) cc_final: 0.8724 (ttt180) REVERT: J 174 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8290 (ptt180) REVERT: J 184 GLN cc_start: 0.9079 (mt0) cc_final: 0.8620 (tp40) REVERT: J 208 LYS cc_start: 0.8949 (tppt) cc_final: 0.8474 (tmmt) REVERT: J 241 ARG cc_start: 0.9191 (tpp80) cc_final: 0.8812 (tpp80) REVERT: J 244 MET cc_start: 0.9002 (tpt) cc_final: 0.8535 (tpp) REVERT: J 249 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7980 (ttmm) REVERT: K 22 LEU cc_start: 0.8961 (tp) cc_final: 0.8710 (tp) REVERT: K 221 TRP cc_start: 0.8434 (t60) cc_final: 0.7968 (t60) REVERT: K 279 THR cc_start: 0.7456 (m) cc_final: 0.7029 (p) REVERT: L 31 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8763 (tm-30) REVERT: L 74 MET cc_start: 0.8320 (tpt) cc_final: 0.7756 (tpt) REVERT: L 184 GLN cc_start: 0.9105 (mt0) cc_final: 0.8495 (tp40) REVERT: L 208 LYS cc_start: 0.8716 (tppt) cc_final: 0.8228 (tmmt) REVERT: L 244 MET cc_start: 0.8996 (tpt) cc_final: 0.8744 (tpt) REVERT: L 245 MET cc_start: 0.8571 (tpp) cc_final: 0.8151 (tpp) REVERT: M 184 GLN cc_start: 0.9122 (mt0) cc_final: 0.8702 (tp-100) REVERT: M 187 MET cc_start: 0.9050 (mmp) cc_final: 0.8816 (mmm) REVERT: M 271 ASP cc_start: 0.8810 (m-30) cc_final: 0.8424 (m-30) REVERT: N 128 TYR cc_start: 0.9094 (m-10) cc_final: 0.8857 (m-80) REVERT: N 152 LYS cc_start: 0.9227 (tppp) cc_final: 0.9009 (tppp) REVERT: N 183 TYR cc_start: 0.9161 (t80) cc_final: 0.8636 (t80) REVERT: N 184 GLN cc_start: 0.9091 (mt0) cc_final: 0.8472 (mm-40) REVERT: O 128 TYR cc_start: 0.8737 (m-10) cc_final: 0.8402 (m-80) REVERT: O 154 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8520 (mm-30) REVERT: O 244 MET cc_start: 0.9127 (tpt) cc_final: 0.8856 (tpt) REVERT: O 248 ILE cc_start: 0.9043 (tp) cc_final: 0.8788 (tp) REVERT: P 74 MET cc_start: 0.8561 (tpp) cc_final: 0.8197 (tpp) REVERT: P 128 TYR cc_start: 0.8852 (m-10) cc_final: 0.8628 (m-80) REVERT: P 221 TRP cc_start: 0.8427 (t60) cc_final: 0.8033 (t60) REVERT: P 241 ARG cc_start: 0.9221 (tpp80) cc_final: 0.8637 (mmm-85) REVERT: P 249 LYS cc_start: 0.8239 (tttm) cc_final: 0.8019 (ttmt) REVERT: P 279 THR cc_start: 0.7345 (m) cc_final: 0.7001 (p) REVERT: Q 184 GLN cc_start: 0.9114 (mt0) cc_final: 0.8675 (tp40) REVERT: R 187 MET cc_start: 0.8767 (mmm) cc_final: 0.8456 (mmm) REVERT: R 241 ARG cc_start: 0.9008 (tpp80) cc_final: 0.8671 (tpp80) REVERT: R 271 ASP cc_start: 0.8602 (m-30) cc_final: 0.8342 (m-30) REVERT: S 74 MET cc_start: 0.8097 (tpt) cc_final: 0.7730 (tpp) REVERT: S 249 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7858 (ttmm) REVERT: T 154 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8492 (mm-30) outliers start: 3 outliers final: 0 residues processed: 935 average time/residue: 0.4950 time to fit residues: 764.4639 Evaluate side-chains 685 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 684 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 455 optimal weight: 6.9990 chunk 480 optimal weight: 0.7980 chunk 438 optimal weight: 0.0770 chunk 467 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 366 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 422 optimal weight: 0.0170 chunk 441 optimal weight: 2.9990 chunk 465 optimal weight: 2.9990 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN D 227 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN N 31 GLN N 48 ASN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 184 GLN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 42580 Z= 0.182 Angle : 0.562 8.891 57820 Z= 0.289 Chirality : 0.039 0.152 6740 Planarity : 0.004 0.088 7180 Dihedral : 3.742 26.808 5700 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.02 % Allowed : 0.63 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.12), residues: 5260 helix: 2.81 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.32 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 221 HIS 0.003 0.000 HIS E 246 PHE 0.024 0.001 PHE R 160 TYR 0.028 0.001 TYR Q 183 ARG 0.009 0.000 ARG M 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 922 time to evaluate : 4.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.8979 (mt0) cc_final: 0.8572 (tp-100) REVERT: A 208 LYS cc_start: 0.8786 (tppt) cc_final: 0.8216 (tmmt) REVERT: A 244 MET cc_start: 0.9266 (tpt) cc_final: 0.8898 (tpt) REVERT: B 255 ILE cc_start: 0.9036 (mm) cc_final: 0.8771 (mm) REVERT: C 51 TYR cc_start: 0.9359 (t80) cc_final: 0.9038 (t80) REVERT: C 74 MET cc_start: 0.8440 (tpt) cc_final: 0.8196 (tpt) REVERT: C 184 GLN cc_start: 0.8887 (mt0) cc_final: 0.8431 (tp40) REVERT: C 187 MET cc_start: 0.8738 (mmt) cc_final: 0.8338 (mmm) REVERT: D 184 GLN cc_start: 0.9079 (mt0) cc_final: 0.8703 (tp-100) REVERT: D 233 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 245 MET cc_start: 0.8382 (tpp) cc_final: 0.8161 (tpp) REVERT: D 271 ASP cc_start: 0.8693 (m-30) cc_final: 0.8367 (m-30) REVERT: E 184 GLN cc_start: 0.9169 (mt0) cc_final: 0.8904 (mm-40) REVERT: E 249 LYS cc_start: 0.8310 (ttmm) cc_final: 0.8044 (ttmm) REVERT: F 74 MET cc_start: 0.8383 (tpt) cc_final: 0.8079 (tpt) REVERT: F 184 GLN cc_start: 0.8902 (mt0) cc_final: 0.8590 (tp-100) REVERT: F 244 MET cc_start: 0.9092 (tpt) cc_final: 0.8844 (tpt) REVERT: F 279 THR cc_start: 0.7306 (m) cc_final: 0.7105 (p) REVERT: G 74 MET cc_start: 0.8229 (tpt) cc_final: 0.7887 (tpt) REVERT: G 187 MET cc_start: 0.8761 (mmm) cc_final: 0.8455 (mmm) REVERT: G 233 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7860 (tm-30) REVERT: G 245 MET cc_start: 0.8287 (mtm) cc_final: 0.8000 (mtp) REVERT: G 271 ASP cc_start: 0.8718 (m-30) cc_final: 0.8432 (m-30) REVERT: H 70 LEU cc_start: 0.9324 (mm) cc_final: 0.9069 (mp) REVERT: H 128 TYR cc_start: 0.8721 (m-10) cc_final: 0.8506 (m-80) REVERT: H 184 GLN cc_start: 0.9033 (mt0) cc_final: 0.8607 (tp40) REVERT: H 237 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8570 (tm-30) REVERT: H 271 ASP cc_start: 0.8885 (m-30) cc_final: 0.8593 (m-30) REVERT: I 74 MET cc_start: 0.8460 (tpt) cc_final: 0.8132 (tpt) REVERT: I 244 MET cc_start: 0.8802 (tpt) cc_final: 0.8280 (tpt) REVERT: J 184 GLN cc_start: 0.9098 (mt0) cc_final: 0.8567 (tp40) REVERT: J 208 LYS cc_start: 0.8991 (tppt) cc_final: 0.8492 (tmmt) REVERT: J 244 MET cc_start: 0.9122 (tpt) cc_final: 0.8828 (tpp) REVERT: K 22 LEU cc_start: 0.8959 (tp) cc_final: 0.8699 (tp) REVERT: K 221 TRP cc_start: 0.8414 (t60) cc_final: 0.7923 (t60) REVERT: K 279 THR cc_start: 0.7456 (m) cc_final: 0.7036 (p) REVERT: L 31 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8771 (tm-30) REVERT: L 184 GLN cc_start: 0.9021 (mt0) cc_final: 0.8537 (tp40) REVERT: L 208 LYS cc_start: 0.8677 (tppt) cc_final: 0.8159 (tmmt) REVERT: L 245 MET cc_start: 0.8589 (tpp) cc_final: 0.8203 (tpp) REVERT: M 184 GLN cc_start: 0.9117 (mt0) cc_final: 0.8699 (tp-100) REVERT: M 255 ILE cc_start: 0.9147 (mp) cc_final: 0.8932 (mp) REVERT: M 271 ASP cc_start: 0.8806 (m-30) cc_final: 0.8421 (m-30) REVERT: N 128 TYR cc_start: 0.9085 (m-10) cc_final: 0.8845 (m-80) REVERT: N 183 TYR cc_start: 0.9153 (t80) cc_final: 0.8634 (t80) REVERT: N 184 GLN cc_start: 0.9058 (mt0) cc_final: 0.8474 (mm-40) REVERT: O 128 TYR cc_start: 0.8777 (m-10) cc_final: 0.8460 (m-80) REVERT: O 154 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8491 (mm-30) REVERT: O 244 MET cc_start: 0.9108 (tpt) cc_final: 0.8777 (tpt) REVERT: O 248 ILE cc_start: 0.9073 (tp) cc_final: 0.8823 (tp) REVERT: P 221 TRP cc_start: 0.8386 (t60) cc_final: 0.8061 (t60) REVERT: P 241 ARG cc_start: 0.9205 (tpp80) cc_final: 0.8623 (mmm-85) REVERT: P 244 MET cc_start: 0.9076 (tpt) cc_final: 0.8553 (tpp) REVERT: P 279 THR cc_start: 0.7502 (m) cc_final: 0.7148 (p) REVERT: Q 170 VAL cc_start: 0.6817 (t) cc_final: 0.6534 (t) REVERT: Q 184 GLN cc_start: 0.9074 (mt0) cc_final: 0.8757 (tp40) REVERT: Q 230 GLU cc_start: 0.8508 (tp30) cc_final: 0.8222 (tp30) REVERT: R 157 LEU cc_start: 0.9005 (tp) cc_final: 0.8760 (tp) REVERT: R 187 MET cc_start: 0.8742 (mmm) cc_final: 0.8430 (mmm) REVERT: R 241 ARG cc_start: 0.9029 (tpp80) cc_final: 0.8447 (tpp80) REVERT: R 245 MET cc_start: 0.8166 (ttm) cc_final: 0.7945 (mtm) REVERT: R 271 ASP cc_start: 0.8620 (m-30) cc_final: 0.8320 (m-30) REVERT: S 74 MET cc_start: 0.8178 (tpt) cc_final: 0.7910 (tpp) REVERT: S 104 PHE cc_start: 0.7379 (t80) cc_final: 0.7073 (t80) REVERT: S 241 ARG cc_start: 0.9106 (tpp80) cc_final: 0.8883 (tpp80) REVERT: S 249 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7985 (ttmm) REVERT: T 128 TYR cc_start: 0.8609 (m-10) cc_final: 0.8362 (m-80) REVERT: T 154 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8503 (mm-30) REVERT: T 187 MET cc_start: 0.8983 (mmt) cc_final: 0.8531 (mmp) REVERT: T 258 SER cc_start: 0.8617 (p) cc_final: 0.8277 (p) outliers start: 1 outliers final: 0 residues processed: 923 average time/residue: 0.4815 time to fit residues: 738.9396 Evaluate side-chains 645 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 645 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 306 optimal weight: 0.0670 chunk 493 optimal weight: 5.9990 chunk 301 optimal weight: 0.0970 chunk 234 optimal weight: 8.9990 chunk 343 optimal weight: 0.0370 chunk 518 optimal weight: 0.0010 chunk 476 optimal weight: 10.0000 chunk 412 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 318 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 overall best weight: 0.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN G 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 ASN M 48 ASN M 227 ASN N 48 ASN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 GLN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 42580 Z= 0.159 Angle : 0.578 12.493 57820 Z= 0.293 Chirality : 0.039 0.180 6740 Planarity : 0.004 0.060 7180 Dihedral : 3.719 24.713 5700 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.57 % 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: 2.92 (0.12), residues: 5260 helix: 3.04 (0.08), residues: 3980 sheet: None (None), residues: 0 loop : -1.94 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 221 HIS 0.004 0.001 HIS R 246 PHE 0.023 0.001 PHE R 160 TYR 0.035 0.001 TYR J 183 ARG 0.009 0.000 ARG R 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10520 Ramachandran restraints generated. 5260 Oldfield, 0 Emsley, 5260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 950 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 184 GLN cc_start: 0.8960 (mt0) cc_final: 0.8520 (tp-100) REVERT: A 208 LYS cc_start: 0.8950 (tppt) cc_final: 0.8203 (tmmt) REVERT: A 244 MET cc_start: 0.9209 (tpt) cc_final: 0.8935 (tpt) REVERT: B 135 GLU cc_start: 0.8797 (pm20) cc_final: 0.8065 (pp20) REVERT: B 255 ILE cc_start: 0.8989 (mm) cc_final: 0.8693 (mm) REVERT: C 51 TYR cc_start: 0.9272 (t80) cc_final: 0.8916 (t80) REVERT: C 74 MET cc_start: 0.8334 (tpt) cc_final: 0.8119 (tpt) REVERT: C 184 GLN cc_start: 0.8814 (mt0) cc_final: 0.8395 (tp40) REVERT: D 108 THR cc_start: 0.8896 (m) cc_final: 0.8653 (t) REVERT: D 184 GLN cc_start: 0.9127 (mt0) cc_final: 0.8587 (tp40) REVERT: D 249 LYS cc_start: 0.7884 (tttm) cc_final: 0.7560 (tttp) REVERT: D 271 ASP cc_start: 0.8646 (m-30) cc_final: 0.8329 (m-30) REVERT: E 184 GLN cc_start: 0.9116 (mt0) cc_final: 0.8882 (mm-40) REVERT: E 187 MET cc_start: 0.8773 (mmt) cc_final: 0.8382 (mmp) REVERT: F 74 MET cc_start: 0.8485 (tpt) cc_final: 0.8181 (tpt) REVERT: F 184 GLN cc_start: 0.8840 (mt0) cc_final: 0.8543 (tp-100) REVERT: F 279 THR cc_start: 0.7340 (m) cc_final: 0.7071 (p) REVERT: G 74 MET cc_start: 0.8195 (tpt) cc_final: 0.7813 (tpt) REVERT: G 187 MET cc_start: 0.8695 (mmm) cc_final: 0.8370 (mmm) REVERT: G 231 LEU cc_start: 0.9065 (tt) cc_final: 0.8761 (mm) REVERT: G 233 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7887 (tm-30) REVERT: G 241 ARG cc_start: 0.9023 (tpp80) cc_final: 0.8647 (mmm-85) REVERT: G 245 MET cc_start: 0.8144 (mtm) cc_final: 0.7760 (mtp) REVERT: H 70 LEU cc_start: 0.9321 (mm) cc_final: 0.9093 (mp) REVERT: H 128 TYR cc_start: 0.8748 (m-10) cc_final: 0.8514 (m-80) REVERT: H 184 GLN cc_start: 0.8964 (mt0) cc_final: 0.8654 (tp40) REVERT: H 237 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8596 (tm-30) REVERT: H 255 ILE cc_start: 0.8885 (mm) cc_final: 0.8645 (mm) REVERT: H 271 ASP cc_start: 0.8845 (m-30) cc_final: 0.8510 (m-30) REVERT: I 74 MET cc_start: 0.8410 (tpt) cc_final: 0.8022 (tpt) REVERT: I 78 THR cc_start: 0.7215 (m) cc_final: 0.6896 (m) REVERT: I 130 GLU cc_start: 0.8504 (pt0) cc_final: 0.8290 (pt0) REVERT: I 187 MET cc_start: 0.8967 (mmm) cc_final: 0.8615 (mmm) REVERT: I 245 MET cc_start: 0.7999 (mtm) cc_final: 0.7626 (mtt) REVERT: J 184 GLN cc_start: 0.9036 (mt0) cc_final: 0.8728 (mm-40) REVERT: J 208 LYS cc_start: 0.8946 (tppt) cc_final: 0.8471 (tmmt) REVERT: J 233 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8383 (tm-30) REVERT: J 244 MET cc_start: 0.8991 (tpt) cc_final: 0.8760 (tpp) REVERT: K 221 TRP cc_start: 0.8243 (t60) cc_final: 0.7786 (t60) REVERT: K 279 THR cc_start: 0.7334 (m) cc_final: 0.6927 (p) REVERT: L 14 ARG cc_start: 0.7985 (ptt90) cc_final: 0.7664 (ppt170) REVERT: L 31 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8774 (tm-30) REVERT: L 74 MET cc_start: 0.8269 (tpt) cc_final: 0.7848 (tpt) REVERT: L 184 GLN cc_start: 0.8996 (mt0) cc_final: 0.8514 (tp40) REVERT: L 187 MET cc_start: 0.8767 (mmt) cc_final: 0.8104 (mmm) REVERT: L 208 LYS cc_start: 0.8683 (tppt) cc_final: 0.8220 (tmmt) REVERT: L 245 MET cc_start: 0.8529 (tpp) cc_final: 0.8095 (tpp) REVERT: M 152 LYS cc_start: 0.9151 (tppp) cc_final: 0.8930 (tppp) REVERT: M 184 GLN cc_start: 0.9133 (mt0) cc_final: 0.8544 (tp-100) REVERT: M 187 MET cc_start: 0.8982 (mmp) cc_final: 0.8765 (mmm) REVERT: M 271 ASP cc_start: 0.8790 (m-30) cc_final: 0.8455 (m-30) REVERT: N 183 TYR cc_start: 0.9096 (t80) cc_final: 0.8581 (t80) REVERT: N 184 GLN cc_start: 0.9081 (mt0) cc_final: 0.8468 (mm-40) REVERT: N 192 LEU cc_start: 0.9018 (tt) cc_final: 0.8691 (tp) REVERT: N 242 LEU cc_start: 0.9111 (mm) cc_final: 0.8733 (tp) REVERT: O 14 ARG cc_start: 0.8231 (ptt90) cc_final: 0.7945 (ppt170) REVERT: O 128 TYR cc_start: 0.8750 (m-10) cc_final: 0.8472 (m-80) REVERT: O 135 GLU cc_start: 0.9014 (pm20) cc_final: 0.8680 (pp20) REVERT: O 154 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8563 (mm-30) REVERT: O 160 PHE cc_start: 0.7684 (m-80) cc_final: 0.7163 (m-80) REVERT: O 244 MET cc_start: 0.9011 (tpt) cc_final: 0.8756 (tpt) REVERT: O 248 ILE cc_start: 0.9042 (tp) cc_final: 0.8760 (tp) REVERT: P 221 TRP cc_start: 0.8128 (t60) cc_final: 0.7847 (t60) REVERT: P 241 ARG cc_start: 0.9181 (tpp80) cc_final: 0.8563 (mmm-85) REVERT: P 244 MET cc_start: 0.9079 (tpt) cc_final: 0.8861 (tpt) REVERT: P 279 THR cc_start: 0.7436 (m) cc_final: 0.7109 (p) REVERT: Q 74 MET cc_start: 0.8478 (tpt) cc_final: 0.8128 (tpt) REVERT: Q 170 VAL cc_start: 0.6866 (t) cc_final: 0.6536 (t) REVERT: Q 184 GLN cc_start: 0.9037 (mt0) cc_final: 0.8593 (tp40) REVERT: Q 230 GLU cc_start: 0.8513 (tp30) cc_final: 0.8293 (tp30) REVERT: R 157 LEU cc_start: 0.9043 (tp) cc_final: 0.8750 (tp) REVERT: R 160 PHE cc_start: 0.8109 (m-80) cc_final: 0.7903 (m-80) REVERT: R 184 GLN cc_start: 0.9167 (mt0) cc_final: 0.8781 (tp-100) REVERT: R 271 ASP cc_start: 0.8604 (m-30) cc_final: 0.8319 (m-30) REVERT: S 152 LYS cc_start: 0.9070 (tptp) cc_final: 0.8838 (tppp) REVERT: S 249 LYS cc_start: 0.8276 (ttpp) cc_final: 0.8030 (ttmm) REVERT: T 128 TYR cc_start: 0.8575 (m-10) cc_final: 0.8365 (m-80) REVERT: T 187 MET cc_start: 0.8914 (mmt) cc_final: 0.8444 (mmp) outliers start: 4 outliers final: 0 residues processed: 954 average time/residue: 0.4856 time to fit residues: 768.2371 Evaluate side-chains 681 residues out of total 4620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 327 optimal weight: 3.9990 chunk 439 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 380 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 413 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 424 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 76 optimal weight: 0.0470 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** G 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN ** H 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN N 31 GLN N 48 ASN ** N 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 ASN ** R 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101561 restraints weight = 74309.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103610 restraints weight = 48016.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104815 restraints weight = 36259.851| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 42580 Z= 0.184 Angle : 0.585 9.556 57820 Z= 0.300 Chirality : 0.039 0.150 6740 Planarity : 0.004 0.058 7180 Dihedral : 3.678 25.763 5700 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.12), residues: 5260 helix: 2.84 (0.08), residues: 4120 sheet: None (None), residues: 0 loop : -2.23 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 221 HIS 0.004 0.001 HIS R 246 PHE 0.022 0.001 PHE R 160 TYR 0.020 0.001 TYR B 81 ARG 0.006 0.000 ARG G 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11962.02 seconds wall clock time: 211 minutes 28.41 seconds (12688.41 seconds total)