Starting phenix.real_space_refine on Wed Mar 20 23:13:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txi_26158/03_2024/7txi_26158.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txi_26158/03_2024/7txi_26158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txi_26158/03_2024/7txi_26158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txi_26158/03_2024/7txi_26158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txi_26158/03_2024/7txi_26158.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7txi_26158/03_2024/7txi_26158.pdb" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.034 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 120 5.16 5 C 18280 2.51 5 N 4580 2.21 5 O 5680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 11": "OE1" <-> "OE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ASP 72": "OD1" <-> "OD2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D ASP 72": "OD1" <-> "OD2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 170": "OE1" <-> "OE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F ASP 114": "OD1" <-> "OD2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G ASP 114": "OD1" <-> "OD2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 170": "OE1" <-> "OE2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 114": "OD1" <-> "OD2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "I GLU 11": "OE1" <-> "OE2" Residue "I PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I ASP 114": "OD1" <-> "OD2" Residue "I ASP 120": "OD1" <-> "OD2" Residue "I TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "J GLU 11": "OE1" <-> "OE2" Residue "J PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J ASP 114": "OD1" <-> "OD2" Residue "J ASP 120": "OD1" <-> "OD2" Residue "J TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 170": "OE1" <-> "OE2" Residue "J GLU 175": "OE1" <-> "OE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K ASP 114": "OD1" <-> "OD2" Residue "K ASP 120": "OD1" <-> "OD2" Residue "K TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 170": "OE1" <-> "OE2" Residue "K GLU 175": "OE1" <-> "OE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "L GLU 11": "OE1" <-> "OE2" Residue "L PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L ASP 72": "OD1" <-> "OD2" Residue "L ASP 114": "OD1" <-> "OD2" Residue "L ASP 120": "OD1" <-> "OD2" Residue "L TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 170": "OE1" <-> "OE2" Residue "L GLU 175": "OE1" <-> "OE2" Residue "M GLU 11": "OE1" <-> "OE2" Residue "M PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M ASP 72": "OD1" <-> "OD2" Residue "M ASP 114": "OD1" <-> "OD2" Residue "M ASP 120": "OD1" <-> "OD2" Residue "M TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 170": "OE1" <-> "OE2" Residue "M GLU 175": "OE1" <-> "OE2" Residue "N GLU 11": "OE1" <-> "OE2" Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N ASP 114": "OD1" <-> "OD2" Residue "N ASP 120": "OD1" <-> "OD2" Residue "N TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N GLU 175": "OE1" <-> "OE2" Residue "O GLU 11": "OE1" <-> "OE2" Residue "O PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O ASP 72": "OD1" <-> "OD2" Residue "O ASP 114": "OD1" <-> "OD2" Residue "O ASP 120": "OD1" <-> "OD2" Residue "O TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 170": "OE1" <-> "OE2" Residue "O GLU 175": "OE1" <-> "OE2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ASP 72": "OD1" <-> "OD2" Residue "P ASP 114": "OD1" <-> "OD2" Residue "P ASP 120": "OD1" <-> "OD2" Residue "P TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 170": "OE1" <-> "OE2" Residue "P GLU 175": "OE1" <-> "OE2" Residue "Q GLU 11": "OE1" <-> "OE2" Residue "Q PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 43": "OE1" <-> "OE2" Residue "Q ASP 72": "OD1" <-> "OD2" Residue "Q ASP 114": "OD1" <-> "OD2" Residue "Q ASP 120": "OD1" <-> "OD2" Residue "Q TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 170": "OE1" <-> "OE2" Residue "Q GLU 175": "OE1" <-> "OE2" Residue "R GLU 11": "OE1" <-> "OE2" Residue "R PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 43": "OE1" <-> "OE2" Residue "R ASP 72": "OD1" <-> "OD2" Residue "R ASP 114": "OD1" <-> "OD2" Residue "R ASP 120": "OD1" <-> "OD2" Residue "R TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 170": "OE1" <-> "OE2" Residue "R GLU 175": "OE1" <-> "OE2" Residue "S GLU 11": "OE1" <-> "OE2" Residue "S PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 43": "OE1" <-> "OE2" Residue "S ASP 72": "OD1" <-> "OD2" Residue "S ASP 114": "OD1" <-> "OD2" Residue "S ASP 120": "OD1" <-> "OD2" Residue "S TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 170": "OE1" <-> "OE2" Residue "S GLU 175": "OE1" <-> "OE2" Residue "T GLU 11": "OE1" <-> "OE2" Residue "T PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 43": "OE1" <-> "OE2" Residue "T ASP 72": "OD1" <-> "OD2" Residue "T ASP 114": "OD1" <-> "OD2" Residue "T ASP 120": "OD1" <-> "OD2" Residue "T TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 170": "OE1" <-> "OE2" Residue "T GLU 175": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28660 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "C" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "D" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "E" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "F" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "G" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "H" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "I" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "J" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "K" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "L" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "M" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "N" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "O" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "P" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "Q" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "R" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "S" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "T" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Time building chain proxies: 13.67, per 1000 atoms: 0.48 Number of scatterers: 28660 At special positions: 0 Unit cell: (111.24, 109.08, 219.24, 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 120 16.00 O 5680 8.00 N 4580 7.00 C 18280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 132 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 132 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 132 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 132 " distance=2.03 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 132 " distance=2.03 Simple disulfide: pdb=" SG CYS I 110 " - pdb=" SG CYS I 132 " distance=2.03 Simple disulfide: pdb=" SG CYS J 110 " - pdb=" SG CYS J 132 " distance=2.03 Simple disulfide: pdb=" SG CYS K 110 " - pdb=" SG CYS K 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS L 110 " - pdb=" SG CYS L 132 " distance=2.03 Simple disulfide: pdb=" SG CYS M 110 " - pdb=" SG CYS M 132 " distance=2.03 Simple disulfide: pdb=" SG CYS N 110 " - pdb=" SG CYS N 132 " distance=2.03 Simple disulfide: pdb=" SG CYS O 110 " - pdb=" SG CYS O 132 " distance=2.03 Simple disulfide: pdb=" SG CYS P 110 " - pdb=" SG CYS P 132 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 110 " - pdb=" SG CYS Q 132 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 132 " distance=2.03 Simple disulfide: pdb=" SG CYS S 110 " - pdb=" SG CYS S 132 " distance=2.03 Simple disulfide: pdb=" SG CYS T 110 " - pdb=" SG CYS T 132 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.15 Conformation dependent library (CDL) restraints added in 5.6 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7120 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 80 sheets defined 28.1% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'B' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA B 12 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'C' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA C 12 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 Processing helix chain 'D' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 130 Processing helix chain 'E' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'F' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 130 Processing helix chain 'G' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA G 12 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 130 Processing helix chain 'H' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA H 12 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 130 Processing helix chain 'I' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA I 12 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 130 Processing helix chain 'J' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA J 12 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 130 Processing helix chain 'K' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA K 12 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 130 Processing helix chain 'L' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA L 12 " --> pdb=" O VAL L 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 130 Processing helix chain 'M' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 130 Processing helix chain 'N' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA N 12 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 130 Processing helix chain 'O' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA O 12 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR O 53 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 130 Processing helix chain 'P' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA P 12 " --> pdb=" O VAL P 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 130 Processing helix chain 'Q' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'R' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA R 12 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 130 Processing helix chain 'S' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA S 12 " --> pdb=" O VAL S 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 130 Processing helix chain 'T' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA T 12 " --> pdb=" O VAL T 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 130 Processing sheet with id= 1, first strand: chain 'A' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU A 139 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 112 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 141 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP A 114 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN A 65 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A 74 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 63 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 87 through 88 Processing sheet with id= 4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG A 188 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU B 139 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 112 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 141 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP B 114 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN B 65 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE B 74 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 63 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 87 through 88 Processing sheet with id= 8, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG B 188 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU C 139 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL C 112 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE C 141 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP C 114 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN C 65 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE C 74 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 63 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 87 through 88 Processing sheet with id= 12, first strand: chain 'C' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG C 188 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU D 139 " --> pdb=" O CYS D 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL D 112 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE D 141 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP D 114 " --> pdb=" O ILE D 141 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN D 65 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE D 74 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 63 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 87 through 88 Processing sheet with id= 16, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG D 188 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU E 139 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL E 112 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE E 141 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP E 114 " --> pdb=" O ILE E 141 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN E 65 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE E 74 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE E 63 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 87 through 88 Processing sheet with id= 20, first strand: chain 'E' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG E 188 " --> pdb=" O PHE E 172 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU F 139 " --> pdb=" O CYS F 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL F 112 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE F 141 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP F 114 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN F 65 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 63 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 87 through 88 Processing sheet with id= 24, first strand: chain 'F' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG F 188 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU G 139 " --> pdb=" O CYS G 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL G 112 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE G 141 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP G 114 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'G' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN G 65 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE G 74 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE G 63 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'G' and resid 87 through 88 Processing sheet with id= 28, first strand: chain 'G' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG G 188 " --> pdb=" O PHE G 172 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'H' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU H 139 " --> pdb=" O CYS H 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL H 112 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE H 141 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP H 114 " --> pdb=" O ILE H 141 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN H 65 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE H 74 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE H 63 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'H' and resid 87 through 88 Processing sheet with id= 32, first strand: chain 'H' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG H 188 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'I' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU I 139 " --> pdb=" O CYS I 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL I 112 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE I 141 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP I 114 " --> pdb=" O ILE I 141 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'I' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN I 65 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE I 74 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 63 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'I' and resid 87 through 88 Processing sheet with id= 36, first strand: chain 'I' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG I 188 " --> pdb=" O PHE I 172 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'J' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU J 139 " --> pdb=" O CYS J 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL J 112 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE J 141 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP J 114 " --> pdb=" O ILE J 141 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'J' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN J 65 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE J 74 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE J 63 " --> pdb=" O ILE J 74 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'J' and resid 87 through 88 Processing sheet with id= 40, first strand: chain 'J' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG J 188 " --> pdb=" O PHE J 172 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'K' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU K 139 " --> pdb=" O CYS K 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL K 112 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE K 141 " --> pdb=" O VAL K 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP K 114 " --> pdb=" O ILE K 141 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'K' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN K 65 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE K 74 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE K 63 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'K' and resid 87 through 88 Processing sheet with id= 44, first strand: chain 'K' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG K 188 " --> pdb=" O PHE K 172 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'L' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU L 139 " --> pdb=" O CYS L 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL L 112 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE L 141 " --> pdb=" O VAL L 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP L 114 " --> pdb=" O ILE L 141 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'L' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN L 65 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE L 74 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE L 63 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'L' and resid 87 through 88 Processing sheet with id= 48, first strand: chain 'L' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG L 188 " --> pdb=" O PHE L 172 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'M' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU M 139 " --> pdb=" O CYS M 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL M 112 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE M 141 " --> pdb=" O VAL M 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP M 114 " --> pdb=" O ILE M 141 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'M' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN M 65 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE M 74 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE M 63 " --> pdb=" O ILE M 74 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'M' and resid 87 through 88 Processing sheet with id= 52, first strand: chain 'M' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG M 188 " --> pdb=" O PHE M 172 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'N' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU N 139 " --> pdb=" O CYS N 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL N 112 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE N 141 " --> pdb=" O VAL N 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP N 114 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'N' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN N 65 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE N 74 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE N 63 " --> pdb=" O ILE N 74 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'N' and resid 87 through 88 Processing sheet with id= 56, first strand: chain 'N' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG N 188 " --> pdb=" O PHE N 172 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'O' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU O 139 " --> pdb=" O CYS O 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL O 112 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE O 141 " --> pdb=" O VAL O 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP O 114 " --> pdb=" O ILE O 141 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'O' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN O 65 " --> pdb=" O ASP O 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE O 74 " --> pdb=" O ILE O 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE O 63 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'O' and resid 87 through 88 Processing sheet with id= 60, first strand: chain 'O' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG O 188 " --> pdb=" O PHE O 172 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'P' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU P 139 " --> pdb=" O CYS P 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL P 112 " --> pdb=" O LEU P 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE P 141 " --> pdb=" O VAL P 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP P 114 " --> pdb=" O ILE P 141 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'P' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN P 65 " --> pdb=" O ASP P 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE P 74 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE P 63 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'P' and resid 87 through 88 Processing sheet with id= 64, first strand: chain 'P' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG P 188 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Q' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU Q 139 " --> pdb=" O CYS Q 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL Q 112 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE Q 141 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP Q 114 " --> pdb=" O ILE Q 141 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Q' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN Q 65 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE Q 74 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE Q 63 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Q' and resid 87 through 88 Processing sheet with id= 68, first strand: chain 'Q' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG Q 188 " --> pdb=" O PHE Q 172 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'R' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU R 139 " --> pdb=" O CYS R 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL R 112 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE R 141 " --> pdb=" O VAL R 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP R 114 " --> pdb=" O ILE R 141 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'R' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN R 65 " --> pdb=" O ASP R 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE R 74 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE R 63 " --> pdb=" O ILE R 74 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'R' and resid 87 through 88 Processing sheet with id= 72, first strand: chain 'R' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG R 188 " --> pdb=" O PHE R 172 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'S' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU S 139 " --> pdb=" O CYS S 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL S 112 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE S 141 " --> pdb=" O VAL S 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP S 114 " --> pdb=" O ILE S 141 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'S' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN S 65 " --> pdb=" O ASP S 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE S 74 " --> pdb=" O ILE S 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE S 63 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'S' and resid 87 through 88 Processing sheet with id= 76, first strand: chain 'S' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG S 188 " --> pdb=" O PHE S 172 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'T' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU T 139 " --> pdb=" O CYS T 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL T 112 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE T 141 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP T 114 " --> pdb=" O ILE T 141 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'T' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN T 65 " --> pdb=" O ASP T 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE T 74 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE T 63 " --> pdb=" O ILE T 74 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'T' and resid 87 through 88 Processing sheet with id= 80, first strand: chain 'T' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG T 188 " --> pdb=" O PHE T 172 " (cutoff:3.500A) 1640 hydrogen bonds defined for protein. 4500 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: 10.85 Time building geometry restraints manager: 13.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9380 1.34 - 1.46: 5788 1.46 - 1.58: 13672 1.58 - 1.70: 20 1.70 - 1.81: 200 Bond restraints: 29060 Sorted by residual: bond pdb=" CG PRO T 165 " pdb=" CD PRO T 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.57e+01 bond pdb=" CG PRO F 165 " pdb=" CD PRO F 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.57e+01 bond pdb=" CG PRO K 165 " pdb=" CD PRO K 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.57e+01 bond pdb=" CG PRO O 165 " pdb=" CD PRO O 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.57e+01 bond pdb=" CG PRO R 165 " pdb=" CD PRO R 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.56e+01 ... (remaining 29055 not shown) Histogram of bond angle deviations from ideal: 90.78 - 99.41: 60 99.41 - 108.04: 940 108.04 - 116.67: 20420 116.67 - 125.31: 17880 125.31 - 133.94: 260 Bond angle restraints: 39560 Sorted by residual: angle pdb=" CA PRO L 165 " pdb=" N PRO L 165 " pdb=" CD PRO L 165 " ideal model delta sigma weight residual 112.00 98.22 13.78 1.40e+00 5.10e-01 9.69e+01 angle pdb=" CA PRO Q 165 " pdb=" N PRO Q 165 " pdb=" CD PRO Q 165 " ideal model delta sigma weight residual 112.00 98.22 13.78 1.40e+00 5.10e-01 9.69e+01 angle pdb=" CA PRO H 165 " pdb=" N PRO H 165 " pdb=" CD PRO H 165 " ideal model delta sigma weight residual 112.00 98.22 13.78 1.40e+00 5.10e-01 9.69e+01 angle pdb=" CA PRO C 165 " pdb=" N PRO C 165 " pdb=" CD PRO C 165 " ideal model delta sigma weight residual 112.00 98.22 13.78 1.40e+00 5.10e-01 9.69e+01 angle pdb=" CA PRO R 165 " pdb=" N PRO R 165 " pdb=" CD PRO R 165 " ideal model delta sigma weight residual 112.00 98.23 13.77 1.40e+00 5.10e-01 9.68e+01 ... (remaining 39555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.94: 15220 10.94 - 21.89: 1280 21.89 - 32.83: 620 32.83 - 43.78: 280 43.78 - 54.72: 120 Dihedral angle restraints: 17520 sinusoidal: 6420 harmonic: 11100 Sorted by residual: dihedral pdb=" CB CYS M 110 " pdb=" SG CYS M 110 " pdb=" SG CYS M 132 " pdb=" CB CYS M 132 " ideal model delta sinusoidal sigma weight residual 93.00 38.28 54.72 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CB CYS D 110 " pdb=" SG CYS D 110 " pdb=" SG CYS D 132 " pdb=" CB CYS D 132 " ideal model delta sinusoidal sigma weight residual 93.00 38.28 54.72 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 132 " pdb=" CB CYS R 132 " ideal model delta sinusoidal sigma weight residual 93.00 38.28 54.72 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 17517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2756 0.029 - 0.059: 1240 0.059 - 0.088: 564 0.088 - 0.118: 348 0.118 - 0.147: 52 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA TYR G 169 " pdb=" N TYR G 169 " pdb=" C TYR G 169 " pdb=" CB TYR G 169 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA TYR A 169 " pdb=" N TYR A 169 " pdb=" C TYR A 169 " pdb=" CB TYR A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA TYR B 169 " pdb=" N TYR B 169 " pdb=" C TYR B 169 " pdb=" CB TYR B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 4957 not shown) Planarity restraints: 5020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 164 " -0.146 5.00e-02 4.00e+02 2.07e-01 6.82e+01 pdb=" N PRO I 165 " 0.356 5.00e-02 4.00e+02 pdb=" CA PRO I 165 " -0.120 5.00e-02 4.00e+02 pdb=" CD PRO I 165 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 164 " 0.146 5.00e-02 4.00e+02 2.07e-01 6.82e+01 pdb=" N PRO M 165 " -0.356 5.00e-02 4.00e+02 pdb=" CA PRO M 165 " 0.120 5.00e-02 4.00e+02 pdb=" CD PRO M 165 " 0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 164 " -0.146 5.00e-02 4.00e+02 2.07e-01 6.82e+01 pdb=" N PRO R 165 " 0.356 5.00e-02 4.00e+02 pdb=" CA PRO R 165 " -0.120 5.00e-02 4.00e+02 pdb=" CD PRO R 165 " -0.090 5.00e-02 4.00e+02 ... (remaining 5017 not shown) Histogram of nonbonded interaction distances: 0.41 - 1.31: 51 1.31 - 2.21: 197 2.21 - 3.10: 21625 3.10 - 4.00: 72707 4.00 - 4.90: 128207 Warning: very small nonbonded interaction distances. Nonbonded interactions: 222787 Sorted by model distance: nonbonded pdb=" NH1 ARG L 84 " pdb=" CZ ARG O 47 " model vdw 0.409 3.350 nonbonded pdb=" NH1 ARG H 84 " pdb=" CZ ARG K 47 " model vdw 0.409 3.350 nonbonded pdb=" NH1 ARG Q 84 " pdb=" CZ ARG T 47 " model vdw 0.409 3.350 nonbonded pdb=" NH1 ARG C 84 " pdb=" CZ ARG F 47 " model vdw 0.409 3.350 nonbonded pdb=" NH1 ARG E 84 " pdb=" CZ ARG H 47 " model vdw 0.409 3.350 ... (remaining 222782 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: 4.040 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: 0.030 Extract box with map and model: 8.330 Check model and map are aligned: 0.400 Set scattering table: 0.270 Process input model: 76.200 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.260 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.230 29060 Z= 0.479 Angle : 0.991 17.041 39560 Z= 0.537 Chirality : 0.047 0.147 4960 Planarity : 0.014 0.207 5020 Dihedral : 12.090 50.273 10340 Min Nonbonded Distance : 0.409 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.67 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.39 (0.14), residues: 3880 helix: 3.50 (0.15), residues: 1040 sheet: 1.98 (0.18), residues: 900 loop : -1.18 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP T 136 PHE 0.021 0.002 PHE T 28 TYR 0.010 0.002 TYR I 138 ARG 0.008 0.001 ARG T 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1079 time to evaluate : 3.047 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LYS cc_start: 0.6243 (mttt) cc_final: 0.5711 (mmtp) REVERT: B 187 GLU cc_start: 0.7824 (tt0) cc_final: 0.7522 (tt0) REVERT: C 43 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7658 (tm-30) REVERT: C 93 LYS cc_start: 0.6947 (mttt) cc_final: 0.6140 (mmtm) REVERT: C 121 SER cc_start: 0.8160 (m) cc_final: 0.7081 (t) REVERT: D 95 THR cc_start: 0.9334 (m) cc_final: 0.9036 (p) REVERT: D 121 SER cc_start: 0.8701 (m) cc_final: 0.8424 (m) REVERT: D 138 TYR cc_start: 0.8580 (p90) cc_final: 0.7979 (p90) REVERT: E 46 GLN cc_start: 0.8925 (tt0) cc_final: 0.8549 (tm-30) REVERT: E 121 SER cc_start: 0.8904 (m) cc_final: 0.7911 (p) REVERT: E 138 TYR cc_start: 0.8916 (p90) cc_final: 0.8490 (p90) REVERT: F 43 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7961 (tm-30) REVERT: F 170 GLU cc_start: 0.8451 (pm20) cc_final: 0.8091 (pm20) REVERT: F 187 GLU cc_start: 0.7519 (tt0) cc_final: 0.6932 (tt0) REVERT: G 46 GLN cc_start: 0.9040 (tt0) cc_final: 0.8612 (tm-30) REVERT: G 92 ASP cc_start: 0.8611 (m-30) cc_final: 0.8410 (p0) REVERT: G 103 LYS cc_start: 0.7528 (mppt) cc_final: 0.7214 (mtmt) REVERT: H 19 PHE cc_start: 0.8434 (m-80) cc_final: 0.8215 (m-80) REVERT: H 93 LYS cc_start: 0.7076 (mttt) cc_final: 0.6049 (mmtp) REVERT: H 138 TYR cc_start: 0.8989 (p90) cc_final: 0.8759 (p90) REVERT: I 19 PHE cc_start: 0.8885 (m-80) cc_final: 0.8638 (m-80) REVERT: I 85 GLU cc_start: 0.7776 (tp30) cc_final: 0.7458 (tp30) REVERT: J 19 PHE cc_start: 0.8650 (m-80) cc_final: 0.8321 (m-80) REVERT: J 32 ASN cc_start: 0.9382 (t0) cc_final: 0.9173 (t0) REVERT: J 85 GLU cc_start: 0.7363 (tp30) cc_final: 0.6909 (tp30) REVERT: J 138 TYR cc_start: 0.8842 (p90) cc_final: 0.8263 (p90) REVERT: J 170 GLU cc_start: 0.8809 (pm20) cc_final: 0.8356 (pm20) REVERT: K 95 THR cc_start: 0.9479 (m) cc_final: 0.9241 (p) REVERT: K 105 TYR cc_start: 0.8956 (m-80) cc_final: 0.8649 (m-80) REVERT: K 138 TYR cc_start: 0.8470 (p90) cc_final: 0.8205 (p90) REVERT: K 173 LYS cc_start: 0.8658 (tttt) cc_final: 0.8359 (tttm) REVERT: L 11 GLU cc_start: 0.7944 (pm20) cc_final: 0.7709 (pm20) REVERT: M 85 GLU cc_start: 0.7897 (tp30) cc_final: 0.7537 (tp30) REVERT: M 171 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7989 (mt-10) REVERT: N 17 ILE cc_start: 0.9276 (mt) cc_final: 0.8960 (mt) REVERT: N 19 PHE cc_start: 0.8225 (m-80) cc_final: 0.7856 (m-80) REVERT: N 46 GLN cc_start: 0.9043 (tt0) cc_final: 0.8513 (tm-30) REVERT: N 85 GLU cc_start: 0.7974 (tp30) cc_final: 0.7467 (tp30) REVERT: N 173 LYS cc_start: 0.8749 (tttt) cc_final: 0.8442 (tttm) REVERT: O 173 LYS cc_start: 0.8462 (tttt) cc_final: 0.8209 (ttpt) REVERT: O 187 GLU cc_start: 0.7894 (tt0) cc_final: 0.7608 (tt0) REVERT: P 11 GLU cc_start: 0.7757 (pm20) cc_final: 0.7475 (pm20) REVERT: P 136 TRP cc_start: 0.7582 (m-90) cc_final: 0.7266 (m-10) REVERT: P 173 LYS cc_start: 0.8651 (tttt) cc_final: 0.8317 (tttm) REVERT: Q 28 PHE cc_start: 0.8929 (t80) cc_final: 0.8728 (t80) REVERT: Q 95 THR cc_start: 0.9186 (m) cc_final: 0.8898 (p) REVERT: Q 175 GLU cc_start: 0.8120 (tt0) cc_final: 0.7839 (tt0) REVERT: R 11 GLU cc_start: 0.8329 (pm20) cc_final: 0.8080 (pm20) REVERT: R 84 ARG cc_start: 0.7845 (mpt180) cc_final: 0.7041 (mpt180) REVERT: R 122 LYS cc_start: 0.7544 (mmmm) cc_final: 0.7199 (mmtt) REVERT: R 155 LYS cc_start: 0.8239 (mmtm) cc_final: 0.6975 (mmmt) REVERT: S 11 GLU cc_start: 0.7980 (pm20) cc_final: 0.7574 (pm20) REVERT: S 17 ILE cc_start: 0.9371 (mt) cc_final: 0.9169 (mt) REVERT: S 19 PHE cc_start: 0.8596 (m-80) cc_final: 0.8015 (m-80) REVERT: S 42 LYS cc_start: 0.9273 (tttt) cc_final: 0.8716 (tptt) REVERT: S 51 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8214 (tp30) REVERT: S 122 LYS cc_start: 0.8422 (mmmm) cc_final: 0.7373 (mmtt) REVERT: S 170 GLU cc_start: 0.8614 (pm20) cc_final: 0.8360 (pm20) REVERT: T 85 GLU cc_start: 0.8118 (tp30) cc_final: 0.7540 (tp30) REVERT: T 121 SER cc_start: 0.8597 (m) cc_final: 0.7858 (t) REVERT: T 122 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8037 (mmtt) REVERT: T 138 TYR cc_start: 0.8616 (p90) cc_final: 0.8216 (p90) REVERT: T 187 GLU cc_start: 0.7622 (tt0) cc_final: 0.7118 (tt0) outliers start: 0 outliers final: 0 residues processed: 1079 average time/residue: 0.4025 time to fit residues: 673.1064 Evaluate side-chains 724 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 724 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 0.8980 chunk 288 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 297 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 345 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN D 143 ASN E 180 GLN F 143 ASN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 ASN ** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 180 GLN A 180 GLN ** M 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 180 GLN Q 180 GLN R 180 GLN S 46 GLN T 180 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29060 Z= 0.253 Angle : 0.699 8.682 39560 Z= 0.356 Chirality : 0.047 0.169 4960 Planarity : 0.009 0.135 5020 Dihedral : 4.696 30.711 4080 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 1.03 % Allowed : 5.62 % Favored : 93.35 % Rotamer: Outliers : 1.99 % Allowed : 9.43 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.88 % 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: 1.31 (0.14), residues: 3880 helix: 3.46 (0.15), residues: 1040 sheet: 1.46 (0.16), residues: 1160 loop : -1.39 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 136 PHE 0.021 0.002 PHE A 28 TYR 0.014 0.002 TYR K 169 ARG 0.009 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 822 time to evaluate : 3.189 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: B 93 LYS cc_start: 0.6061 (mttt) cc_final: 0.5445 (mmtp) REVERT: C 93 LYS cc_start: 0.6736 (mttt) cc_final: 0.6016 (mmtm) REVERT: C 121 SER cc_start: 0.8211 (m) cc_final: 0.7239 (t) REVERT: C 172 PHE cc_start: 0.8380 (p90) cc_final: 0.8129 (p90) REVERT: D 95 THR cc_start: 0.9263 (m) cc_final: 0.8820 (p) REVERT: D 138 TYR cc_start: 0.8552 (p90) cc_final: 0.8078 (p90) REVERT: E 46 GLN cc_start: 0.8941 (tt0) cc_final: 0.8586 (tm-30) REVERT: E 76 ILE cc_start: 0.9470 (mt) cc_final: 0.9036 (tt) REVERT: E 122 LYS cc_start: 0.8871 (tppt) cc_final: 0.8543 (tptp) REVERT: E 173 LYS cc_start: 0.8915 (tttt) cc_final: 0.8656 (tttm) REVERT: F 59 ASP cc_start: 0.8073 (t0) cc_final: 0.7785 (t0) REVERT: F 84 ARG cc_start: 0.7563 (mpt180) cc_final: 0.7279 (mmt-90) REVERT: F 120 ASP cc_start: 0.7095 (t0) cc_final: 0.6858 (p0) REVERT: G 19 PHE cc_start: 0.8538 (m-80) cc_final: 0.8287 (m-80) REVERT: G 46 GLN cc_start: 0.8956 (tt0) cc_final: 0.8674 (tm-30) REVERT: G 92 ASP cc_start: 0.8714 (m-30) cc_final: 0.8496 (p0) REVERT: G 103 LYS cc_start: 0.7691 (mppt) cc_final: 0.7220 (mtmt) REVERT: H 19 PHE cc_start: 0.8567 (m-80) cc_final: 0.8329 (m-80) REVERT: H 93 LYS cc_start: 0.6753 (mttt) cc_final: 0.5806 (mmtp) REVERT: H 121 SER cc_start: 0.7771 (OUTLIER) cc_final: 0.6759 (t) REVERT: I 19 PHE cc_start: 0.8927 (m-80) cc_final: 0.8663 (m-80) REVERT: I 39 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8227 (mm110) REVERT: I 47 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6912 (mpp80) REVERT: I 138 TYR cc_start: 0.8324 (p90) cc_final: 0.8091 (p90) REVERT: J 19 PHE cc_start: 0.8738 (m-80) cc_final: 0.8435 (m-80) REVERT: J 50 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7532 (tm-30) REVERT: J 122 LYS cc_start: 0.7888 (tppp) cc_final: 0.7377 (tptt) REVERT: J 148 ASN cc_start: 0.8092 (m-40) cc_final: 0.7821 (t0) REVERT: K 138 TYR cc_start: 0.8403 (p90) cc_final: 0.8093 (p90) REVERT: K 173 LYS cc_start: 0.8821 (tttt) cc_final: 0.8473 (tttm) REVERT: L 85 GLU cc_start: 0.7432 (tp30) cc_final: 0.7216 (mm-30) REVERT: L 106 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7677 (tm-30) REVERT: L 172 PHE cc_start: 0.8478 (p90) cc_final: 0.8258 (p90) REVERT: M 171 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8143 (mt-10) REVERT: N 19 PHE cc_start: 0.8297 (m-80) cc_final: 0.7957 (m-80) REVERT: N 173 LYS cc_start: 0.8999 (tttt) cc_final: 0.8699 (tttm) REVERT: O 173 LYS cc_start: 0.8700 (tttt) cc_final: 0.8474 (ttpt) REVERT: P 19 PHE cc_start: 0.8595 (m-80) cc_final: 0.8370 (m-80) REVERT: P 84 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7524 (mtm110) REVERT: P 173 LYS cc_start: 0.8917 (tttt) cc_final: 0.8625 (tttm) REVERT: Q 95 THR cc_start: 0.9220 (m) cc_final: 0.8745 (p) REVERT: R 84 ARG cc_start: 0.7902 (mpt180) cc_final: 0.7103 (mpt180) REVERT: R 122 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7303 (mmtt) REVERT: R 148 ASN cc_start: 0.8000 (m-40) cc_final: 0.7784 (m-40) REVERT: R 155 LYS cc_start: 0.8899 (mmtm) cc_final: 0.7029 (tptm) REVERT: S 11 GLU cc_start: 0.8067 (pm20) cc_final: 0.7631 (pm20) REVERT: S 19 PHE cc_start: 0.8604 (m-80) cc_final: 0.8082 (m-80) REVERT: S 42 LYS cc_start: 0.9327 (tttt) cc_final: 0.8682 (tptt) REVERT: S 51 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8132 (tm-30) REVERT: S 122 LYS cc_start: 0.8545 (mmmm) cc_final: 0.7442 (mmtt) REVERT: S 155 LYS cc_start: 0.8866 (mmtm) cc_final: 0.7582 (mmmt) REVERT: T 39 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8838 (mm-40) REVERT: T 121 SER cc_start: 0.8703 (m) cc_final: 0.7920 (t) REVERT: T 122 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8104 (mmtt) REVERT: T 138 TYR cc_start: 0.8727 (p90) cc_final: 0.8322 (p90) REVERT: T 171 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7062 (tt0) REVERT: T 173 LYS cc_start: 0.8560 (tttt) cc_final: 0.8171 (tttp) outliers start: 63 outliers final: 42 residues processed: 845 average time/residue: 0.4272 time to fit residues: 551.2903 Evaluate side-chains 738 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 694 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 47 ARG Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 180 GLN Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 136 TRP Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 129 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 345 optimal weight: 2.9990 chunk 373 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 342 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 277 optimal weight: 0.0050 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN J 39 GLN J 143 ASN M 180 GLN Q 180 GLN S 180 GLN T 180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29060 Z= 0.194 Angle : 0.634 14.239 39560 Z= 0.325 Chirality : 0.046 0.180 4960 Planarity : 0.006 0.084 5020 Dihedral : 4.431 29.061 4080 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.57 % Favored : 92.91 % Rotamer: Outliers : 3.10 % Allowed : 12.34 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.14), residues: 3880 helix: 3.43 (0.15), residues: 1040 sheet: 1.43 (0.16), residues: 1160 loop : -1.39 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 136 PHE 0.025 0.001 PHE M 28 TYR 0.011 0.001 TYR A 105 ARG 0.005 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 802 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8201 (p0) REVERT: C 93 LYS cc_start: 0.6668 (mttt) cc_final: 0.5934 (mmtm) REVERT: C 121 SER cc_start: 0.8106 (m) cc_final: 0.7139 (t) REVERT: D 95 THR cc_start: 0.9170 (m) cc_final: 0.8671 (p) REVERT: D 138 TYR cc_start: 0.8401 (p90) cc_final: 0.8000 (p90) REVERT: E 46 GLN cc_start: 0.8944 (tt0) cc_final: 0.8607 (tm-30) REVERT: E 76 ILE cc_start: 0.9384 (mt) cc_final: 0.8985 (tt) REVERT: E 170 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: E 173 LYS cc_start: 0.8869 (tttt) cc_final: 0.8647 (tttm) REVERT: F 59 ASP cc_start: 0.8052 (t0) cc_final: 0.7812 (t0) REVERT: F 84 ARG cc_start: 0.7544 (mpt180) cc_final: 0.7313 (mmt180) REVERT: F 138 TYR cc_start: 0.8388 (p90) cc_final: 0.8174 (p90) REVERT: G 19 PHE cc_start: 0.8483 (m-80) cc_final: 0.8256 (m-80) REVERT: G 46 GLN cc_start: 0.8935 (tt0) cc_final: 0.8119 (tm-30) REVERT: G 103 LYS cc_start: 0.7446 (mppt) cc_final: 0.7029 (mtmt) REVERT: G 106 GLU cc_start: 0.8210 (tp30) cc_final: 0.7988 (tp30) REVERT: G 138 TYR cc_start: 0.8555 (p90) cc_final: 0.8347 (p90) REVERT: H 50 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7131 (tm-30) REVERT: H 84 ARG cc_start: 0.7089 (ptp90) cc_final: 0.6745 (ptp90) REVERT: H 93 LYS cc_start: 0.6686 (mttt) cc_final: 0.5791 (mmtp) REVERT: H 121 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.6777 (t) REVERT: I 19 PHE cc_start: 0.8872 (m-80) cc_final: 0.8652 (m-80) REVERT: I 39 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8240 (mm110) REVERT: J 19 PHE cc_start: 0.8718 (m-80) cc_final: 0.8421 (m-80) REVERT: J 28 PHE cc_start: 0.9093 (t80) cc_final: 0.8885 (t80) REVERT: J 50 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7314 (tm-30) REVERT: J 85 GLU cc_start: 0.7582 (tp30) cc_final: 0.7299 (tp30) REVERT: J 103 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7779 (mmmt) REVERT: J 148 ASN cc_start: 0.7977 (m-40) cc_final: 0.7775 (t0) REVERT: K 47 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6868 (mtp180) REVERT: K 173 LYS cc_start: 0.8787 (tttt) cc_final: 0.8474 (tttm) REVERT: A 11 GLU cc_start: 0.8050 (pm20) cc_final: 0.7848 (pm20) REVERT: L 50 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7860 (mm-30) REVERT: L 84 ARG cc_start: 0.6581 (mmt180) cc_final: 0.5741 (mmt180) REVERT: L 106 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7559 (tm-30) REVERT: L 172 PHE cc_start: 0.8590 (p90) cc_final: 0.8356 (p90) REVERT: M 28 PHE cc_start: 0.8991 (t80) cc_final: 0.8748 (t80) REVERT: M 43 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7550 (tm-30) REVERT: M 106 GLU cc_start: 0.7744 (tp30) cc_final: 0.7487 (tp30) REVERT: M 171 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8069 (mt-10) REVERT: N 19 PHE cc_start: 0.8161 (m-80) cc_final: 0.7844 (m-80) REVERT: N 50 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7015 (mm-30) REVERT: N 85 GLU cc_start: 0.8100 (tp30) cc_final: 0.7531 (tp30) REVERT: N 122 LYS cc_start: 0.8505 (mmtp) cc_final: 0.8203 (tptp) REVERT: N 173 LYS cc_start: 0.8959 (tttt) cc_final: 0.8653 (tttm) REVERT: O 43 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7409 (tm-30) REVERT: O 120 ASP cc_start: 0.7159 (t0) cc_final: 0.6523 (p0) REVERT: O 173 LYS cc_start: 0.8625 (tttt) cc_final: 0.8358 (ttpt) REVERT: P 19 PHE cc_start: 0.8559 (m-80) cc_final: 0.8356 (m-80) REVERT: P 136 TRP cc_start: 0.7718 (m-90) cc_final: 0.7337 (m-10) REVERT: P 173 LYS cc_start: 0.8993 (tttt) cc_final: 0.8709 (tttm) REVERT: Q 39 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8515 (mm110) REVERT: Q 95 THR cc_start: 0.9236 (m) cc_final: 0.8739 (p) REVERT: R 84 ARG cc_start: 0.7647 (mpt180) cc_final: 0.7054 (mpt180) REVERT: R 122 LYS cc_start: 0.7723 (mmmm) cc_final: 0.7356 (mptt) REVERT: R 155 LYS cc_start: 0.8948 (mmtm) cc_final: 0.7058 (tttt) REVERT: S 11 GLU cc_start: 0.8088 (pm20) cc_final: 0.7672 (pm20) REVERT: S 19 PHE cc_start: 0.8501 (m-80) cc_final: 0.7971 (m-80) REVERT: S 42 LYS cc_start: 0.9293 (tttt) cc_final: 0.8566 (tptt) REVERT: S 43 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7990 (tm-30) REVERT: S 51 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8141 (tm-30) REVERT: S 120 ASP cc_start: 0.6900 (t0) cc_final: 0.6380 (p0) REVERT: S 122 LYS cc_start: 0.8442 (mmmm) cc_final: 0.6894 (mmtt) REVERT: S 138 TYR cc_start: 0.8146 (p90) cc_final: 0.7086 (p90) REVERT: S 155 LYS cc_start: 0.8929 (mmtm) cc_final: 0.7637 (mtpt) REVERT: T 39 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8828 (mm-40) REVERT: T 121 SER cc_start: 0.8694 (m) cc_final: 0.7913 (t) REVERT: T 122 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8038 (mmtt) REVERT: T 173 LYS cc_start: 0.8534 (tttt) cc_final: 0.8305 (tttt) outliers start: 98 outliers final: 57 residues processed: 855 average time/residue: 0.4130 time to fit residues: 545.5437 Evaluate side-chains 769 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 709 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 169 TYR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 171 GLU Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 TRP Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 129 SER Chi-restraints excluded: chain T residue 180 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 6.9990 chunk 259 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 367 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN G 180 GLN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN K 180 GLN M 143 ASN O 180 GLN S 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29060 Z= 0.296 Angle : 0.681 14.378 39560 Z= 0.349 Chirality : 0.047 0.171 4960 Planarity : 0.007 0.089 5020 Dihedral : 4.459 28.031 4080 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.65 % Favored : 92.84 % Rotamer: Outliers : 3.54 % Allowed : 14.46 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.14), residues: 3880 helix: 3.30 (0.15), residues: 1040 sheet: 1.21 (0.16), residues: 1160 loop : -1.55 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 136 PHE 0.023 0.002 PHE F 28 TYR 0.009 0.001 TYR A 105 ARG 0.009 0.001 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 750 time to evaluate : 3.271 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: C 93 LYS cc_start: 0.6725 (mttt) cc_final: 0.5942 (mmtm) REVERT: C 180 GLN cc_start: 0.8395 (pm20) cc_final: 0.8121 (pm20) REVERT: D 95 THR cc_start: 0.9140 (m) cc_final: 0.8644 (p) REVERT: D 138 TYR cc_start: 0.8502 (p90) cc_final: 0.8038 (p90) REVERT: E 46 GLN cc_start: 0.8985 (tt0) cc_final: 0.8607 (tm-30) REVERT: E 170 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: E 173 LYS cc_start: 0.8850 (tttt) cc_final: 0.8599 (tttm) REVERT: F 84 ARG cc_start: 0.7653 (mpt180) cc_final: 0.7347 (mmt-90) REVERT: G 103 LYS cc_start: 0.7698 (mppt) cc_final: 0.7435 (mttt) REVERT: G 106 GLU cc_start: 0.8052 (tp30) cc_final: 0.7770 (tp30) REVERT: G 138 TYR cc_start: 0.8766 (p90) cc_final: 0.8484 (p90) REVERT: H 50 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7296 (tm-30) REVERT: H 93 LYS cc_start: 0.6941 (mttt) cc_final: 0.5971 (mmtp) REVERT: I 19 PHE cc_start: 0.8890 (m-80) cc_final: 0.8628 (m-80) REVERT: I 39 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8307 (mm110) REVERT: I 99 MET cc_start: 0.8433 (tmm) cc_final: 0.8053 (tmm) REVERT: I 122 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7848 (mmtt) REVERT: I 138 TYR cc_start: 0.8273 (p90) cc_final: 0.7262 (p90) REVERT: J 19 PHE cc_start: 0.8802 (m-80) cc_final: 0.8450 (m-80) REVERT: J 47 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7819 (mtp85) REVERT: J 50 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7375 (tm-30) REVERT: J 85 GLU cc_start: 0.7736 (tp30) cc_final: 0.7289 (tp30) REVERT: K 47 ARG cc_start: 0.7148 (mtp180) cc_final: 0.6750 (mtp85) REVERT: K 173 LYS cc_start: 0.8852 (tttt) cc_final: 0.8494 (tttm) REVERT: A 36 PHE cc_start: 0.8448 (t80) cc_final: 0.8138 (t80) REVERT: L 172 PHE cc_start: 0.8712 (p90) cc_final: 0.8463 (p90) REVERT: M 33 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8706 (tpt) REVERT: M 106 GLU cc_start: 0.7912 (tp30) cc_final: 0.7670 (tp30) REVERT: M 171 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8104 (mt-10) REVERT: N 19 PHE cc_start: 0.8424 (m-80) cc_final: 0.8106 (m-80) REVERT: N 50 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7425 (tp30) REVERT: N 85 GLU cc_start: 0.8257 (tp30) cc_final: 0.7314 (tp30) REVERT: N 173 LYS cc_start: 0.8986 (tttt) cc_final: 0.8620 (tttm) REVERT: O 92 ASP cc_start: 0.8786 (p0) cc_final: 0.8543 (p0) REVERT: O 173 LYS cc_start: 0.8673 (tttt) cc_final: 0.8436 (tmtt) REVERT: P 19 PHE cc_start: 0.8612 (m-80) cc_final: 0.8375 (m-80) REVERT: P 84 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7371 (mtm-85) REVERT: P 92 ASP cc_start: 0.8365 (p0) cc_final: 0.8014 (p0) REVERT: P 121 SER cc_start: 0.8489 (m) cc_final: 0.7403 (t) REVERT: P 173 LYS cc_start: 0.8975 (tttt) cc_final: 0.8629 (tttm) REVERT: Q 95 THR cc_start: 0.9243 (m) cc_final: 0.8782 (p) REVERT: Q 103 LYS cc_start: 0.7826 (mppt) cc_final: 0.7403 (mtmt) REVERT: R 84 ARG cc_start: 0.7847 (mpt180) cc_final: 0.7311 (mpt180) REVERT: R 92 ASP cc_start: 0.8604 (p0) cc_final: 0.7950 (p0) REVERT: R 122 LYS cc_start: 0.7892 (mmmm) cc_final: 0.7570 (mptt) REVERT: R 148 ASN cc_start: 0.8159 (m-40) cc_final: 0.7953 (m-40) REVERT: R 155 LYS cc_start: 0.9012 (mmtm) cc_final: 0.7141 (tptt) REVERT: S 11 GLU cc_start: 0.8346 (pm20) cc_final: 0.8110 (pm20) REVERT: S 19 PHE cc_start: 0.8548 (m-80) cc_final: 0.8020 (m-80) REVERT: S 42 LYS cc_start: 0.9288 (tttt) cc_final: 0.8511 (tptt) REVERT: S 43 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7991 (tm-30) REVERT: S 50 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7614 (mm-30) REVERT: S 51 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8062 (tm-30) REVERT: S 84 ARG cc_start: 0.8060 (mpt180) cc_final: 0.7594 (mtt90) REVERT: S 85 GLU cc_start: 0.7244 (tp30) cc_final: 0.6368 (tp30) REVERT: S 120 ASP cc_start: 0.7005 (t0) cc_final: 0.6554 (p0) REVERT: S 122 LYS cc_start: 0.8762 (mmmm) cc_final: 0.7321 (mmtt) REVERT: S 155 LYS cc_start: 0.8858 (mmtm) cc_final: 0.7635 (mtpt) REVERT: T 39 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8881 (mm-40) REVERT: T 45 MET cc_start: 0.8622 (ptm) cc_final: 0.8248 (ptm) REVERT: T 121 SER cc_start: 0.8787 (m) cc_final: 0.8022 (t) REVERT: T 122 LYS cc_start: 0.8422 (mmmm) cc_final: 0.8024 (mmtt) REVERT: T 171 GLU cc_start: 0.7729 (tt0) cc_final: 0.7513 (tt0) outliers start: 112 outliers final: 67 residues processed: 818 average time/residue: 0.4176 time to fit residues: 526.0817 Evaluate side-chains 747 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 678 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 169 TYR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 180 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 169 TYR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 129 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 273 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 313 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 329 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN O 180 GLN S 180 GLN T 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29060 Z= 0.343 Angle : 0.723 14.060 39560 Z= 0.371 Chirality : 0.047 0.166 4960 Planarity : 0.006 0.092 5020 Dihedral : 4.532 24.290 4080 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.86 % Favored : 92.63 % Rotamer: Outliers : 3.01 % Allowed : 16.39 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3880 helix: 3.14 (0.15), residues: 1040 sheet: 0.78 (0.16), residues: 1180 loop : -1.66 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 136 PHE 0.023 0.002 PHE S 172 TYR 0.009 0.001 TYR B 105 ARG 0.008 0.001 ARG G 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 731 time to evaluate : 3.145 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: D 50 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8356 (mm-30) REVERT: D 95 THR cc_start: 0.9149 (m) cc_final: 0.8645 (p) REVERT: D 138 TYR cc_start: 0.8522 (p90) cc_final: 0.8009 (p90) REVERT: E 46 GLN cc_start: 0.9001 (tt0) cc_final: 0.8630 (tm-30) REVERT: E 170 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: E 173 LYS cc_start: 0.8927 (tttt) cc_final: 0.8625 (tttm) REVERT: G 19 PHE cc_start: 0.8681 (m-80) cc_final: 0.8373 (m-80) REVERT: G 46 GLN cc_start: 0.9023 (tt0) cc_final: 0.8698 (tm-30) REVERT: G 47 ARG cc_start: 0.8253 (tpp80) cc_final: 0.7592 (tpp80) REVERT: G 103 LYS cc_start: 0.7917 (mppt) cc_final: 0.7323 (mtmt) REVERT: G 106 GLU cc_start: 0.8030 (tp30) cc_final: 0.7733 (tp30) REVERT: G 122 LYS cc_start: 0.8353 (mmmm) cc_final: 0.8142 (tptp) REVERT: G 138 TYR cc_start: 0.8848 (p90) cc_final: 0.8524 (p90) REVERT: H 50 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: H 93 LYS cc_start: 0.7080 (mttt) cc_final: 0.6148 (mmtp) REVERT: H 106 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7902 (tm-30) REVERT: I 19 PHE cc_start: 0.8904 (m-80) cc_final: 0.8642 (m-80) REVERT: I 99 MET cc_start: 0.8445 (tmm) cc_final: 0.8099 (tmm) REVERT: I 138 TYR cc_start: 0.8357 (p90) cc_final: 0.7504 (p90) REVERT: J 19 PHE cc_start: 0.8858 (m-80) cc_final: 0.8464 (m-80) REVERT: J 47 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7735 (mtp85) REVERT: J 103 LYS cc_start: 0.8681 (mmtt) cc_final: 0.8412 (mmtt) REVERT: J 148 ASN cc_start: 0.7821 (m-40) cc_final: 0.7573 (t0) REVERT: K 47 ARG cc_start: 0.7225 (mtp180) cc_final: 0.6768 (mtp180) REVERT: K 138 TYR cc_start: 0.8507 (p90) cc_final: 0.8091 (p90) REVERT: K 173 LYS cc_start: 0.8885 (tttt) cc_final: 0.8558 (tttm) REVERT: A 50 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 170 GLU cc_start: 0.8235 (pm20) cc_final: 0.8006 (pm20) REVERT: L 88 ASP cc_start: 0.8856 (t0) cc_final: 0.8624 (t0) REVERT: L 103 LYS cc_start: 0.8298 (mppt) cc_final: 0.7807 (mttt) REVERT: L 172 PHE cc_start: 0.8774 (p90) cc_final: 0.8545 (p90) REVERT: M 106 GLU cc_start: 0.8072 (tp30) cc_final: 0.7807 (tp30) REVERT: M 136 TRP cc_start: 0.8292 (m-90) cc_final: 0.7930 (m-90) REVERT: N 19 PHE cc_start: 0.8562 (m-80) cc_final: 0.8152 (m-80) REVERT: N 50 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7598 (mm-30) REVERT: N 173 LYS cc_start: 0.9037 (tttt) cc_final: 0.8631 (tttm) REVERT: O 89 MET cc_start: 0.7689 (mmm) cc_final: 0.7419 (mmm) REVERT: O 92 ASP cc_start: 0.8869 (p0) cc_final: 0.8601 (p0) REVERT: P 19 PHE cc_start: 0.8688 (m-80) cc_final: 0.8428 (m-80) REVERT: P 46 GLN cc_start: 0.8998 (tt0) cc_final: 0.8782 (tm-30) REVERT: P 84 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7437 (mtm-85) REVERT: P 92 ASP cc_start: 0.8464 (p0) cc_final: 0.8178 (p0) REVERT: P 121 SER cc_start: 0.8499 (m) cc_final: 0.7437 (t) REVERT: P 173 LYS cc_start: 0.8951 (tttt) cc_final: 0.8629 (tttm) REVERT: Q 47 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7303 (mmm-85) REVERT: Q 95 THR cc_start: 0.9236 (m) cc_final: 0.8784 (p) REVERT: R 84 ARG cc_start: 0.7860 (mpt180) cc_final: 0.7304 (mpt180) REVERT: R 92 ASP cc_start: 0.8945 (p0) cc_final: 0.8672 (p0) REVERT: R 122 LYS cc_start: 0.8033 (mmmm) cc_final: 0.7718 (mptt) REVERT: R 155 LYS cc_start: 0.9033 (mmtm) cc_final: 0.7145 (tptt) REVERT: S 19 PHE cc_start: 0.8582 (m-80) cc_final: 0.8002 (m-80) REVERT: S 42 LYS cc_start: 0.9274 (tttt) cc_final: 0.8509 (tptt) REVERT: S 51 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8079 (tm-30) REVERT: S 84 ARG cc_start: 0.8122 (mpt180) cc_final: 0.7650 (mtt90) REVERT: S 120 ASP cc_start: 0.7132 (t0) cc_final: 0.6673 (p0) REVERT: S 122 LYS cc_start: 0.8961 (mmmm) cc_final: 0.7416 (mmtt) REVERT: S 155 LYS cc_start: 0.8900 (mmtm) cc_final: 0.7754 (mmmt) REVERT: T 45 MET cc_start: 0.8633 (ptm) cc_final: 0.8268 (ptm) REVERT: T 121 SER cc_start: 0.8828 (m) cc_final: 0.8072 (t) REVERT: T 122 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8058 (mmtt) outliers start: 95 outliers final: 66 residues processed: 789 average time/residue: 0.4168 time to fit residues: 503.4316 Evaluate side-chains 739 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 671 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 169 TYR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 129 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 367 optimal weight: 7.9990 chunk 305 optimal weight: 0.5980 chunk 170 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 39 GLN K 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29060 Z= 0.179 Angle : 0.665 15.889 39560 Z= 0.335 Chirality : 0.046 0.191 4960 Planarity : 0.006 0.087 5020 Dihedral : 4.267 25.676 4080 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.60 % Favored : 92.89 % Rotamer: Outliers : 2.66 % Allowed : 17.75 % Favored : 79.59 % 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: 0.88 (0.14), residues: 3880 helix: 3.31 (0.15), residues: 1040 sheet: 0.88 (0.16), residues: 1180 loop : -1.54 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 136 PHE 0.029 0.001 PHE N 28 TYR 0.008 0.001 TYR A 105 ARG 0.010 0.001 ARG R 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 755 time to evaluate : 3.189 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: C 93 LYS cc_start: 0.6617 (mttt) cc_final: 0.5860 (mmtm) REVERT: C 180 GLN cc_start: 0.8518 (pm20) cc_final: 0.8198 (pm20) REVERT: D 50 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8280 (mm-30) REVERT: D 138 TYR cc_start: 0.8321 (p90) cc_final: 0.7822 (p90) REVERT: E 46 GLN cc_start: 0.8958 (tt0) cc_final: 0.8621 (tm-30) REVERT: E 170 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: E 173 LYS cc_start: 0.8909 (tttt) cc_final: 0.8641 (tttm) REVERT: G 19 PHE cc_start: 0.8561 (m-80) cc_final: 0.8263 (m-80) REVERT: G 46 GLN cc_start: 0.8987 (tt0) cc_final: 0.8670 (tm-30) REVERT: G 47 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7953 (tpp80) REVERT: G 138 TYR cc_start: 0.8604 (p90) cc_final: 0.8267 (p90) REVERT: H 93 LYS cc_start: 0.7039 (mttt) cc_final: 0.6133 (mmtp) REVERT: H 106 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7804 (tm-30) REVERT: H 121 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.6876 (t) REVERT: I 16 LEU cc_start: 0.9232 (tp) cc_final: 0.8987 (tp) REVERT: I 19 PHE cc_start: 0.8879 (m-80) cc_final: 0.8582 (m-80) REVERT: I 39 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8340 (mm-40) REVERT: I 99 MET cc_start: 0.8407 (tmm) cc_final: 0.8097 (tmm) REVERT: I 105 TYR cc_start: 0.8771 (m-80) cc_final: 0.8428 (m-80) REVERT: J 19 PHE cc_start: 0.8765 (m-80) cc_final: 0.8338 (m-80) REVERT: J 103 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8210 (mptt) REVERT: K 173 LYS cc_start: 0.8864 (tttt) cc_final: 0.8545 (tttm) REVERT: K 189 ILE cc_start: 0.8917 (tt) cc_final: 0.8624 (pt) REVERT: L 172 PHE cc_start: 0.8635 (p90) cc_final: 0.8394 (p90) REVERT: M 33 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8635 (tpt) REVERT: N 19 PHE cc_start: 0.8468 (m-80) cc_final: 0.8086 (m-80) REVERT: N 28 PHE cc_start: 0.9018 (t80) cc_final: 0.8761 (t80) REVERT: N 85 GLU cc_start: 0.8132 (tp30) cc_final: 0.7200 (tp30) REVERT: N 173 LYS cc_start: 0.9010 (tttt) cc_final: 0.8623 (tttm) REVERT: O 92 ASP cc_start: 0.8842 (p0) cc_final: 0.8436 (p0) REVERT: O 105 TYR cc_start: 0.9013 (m-80) cc_final: 0.8790 (m-80) REVERT: O 120 ASP cc_start: 0.7180 (t0) cc_final: 0.6537 (p0) REVERT: P 19 PHE cc_start: 0.8549 (m-80) cc_final: 0.8297 (m-80) REVERT: P 84 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.7198 (mtm-85) REVERT: P 92 ASP cc_start: 0.8383 (p0) cc_final: 0.8066 (p0) REVERT: P 121 SER cc_start: 0.8501 (m) cc_final: 0.7465 (t) REVERT: P 173 LYS cc_start: 0.8978 (tttt) cc_final: 0.8624 (tttm) REVERT: Q 95 THR cc_start: 0.9220 (m) cc_final: 0.8724 (p) REVERT: R 19 PHE cc_start: 0.8556 (m-80) cc_final: 0.8277 (m-80) REVERT: R 84 ARG cc_start: 0.7818 (mpt180) cc_final: 0.7376 (mpt180) REVERT: R 92 ASP cc_start: 0.8915 (p0) cc_final: 0.8627 (p0) REVERT: R 122 LYS cc_start: 0.8024 (mmmm) cc_final: 0.7676 (mptt) REVERT: R 155 LYS cc_start: 0.8992 (mmtm) cc_final: 0.7210 (tttt) REVERT: R 180 GLN cc_start: 0.8066 (tt0) cc_final: 0.7811 (tt0) REVERT: S 19 PHE cc_start: 0.8531 (m-80) cc_final: 0.7950 (m-80) REVERT: S 42 LYS cc_start: 0.9223 (tttt) cc_final: 0.8428 (tptt) REVERT: S 84 ARG cc_start: 0.7935 (mpt180) cc_final: 0.7634 (mtt90) REVERT: S 120 ASP cc_start: 0.6918 (t0) cc_final: 0.6637 (p0) REVERT: S 122 LYS cc_start: 0.8899 (mmmm) cc_final: 0.7569 (mmtt) REVERT: S 155 LYS cc_start: 0.8919 (mmtm) cc_final: 0.7763 (mtpt) REVERT: T 39 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8911 (mm-40) REVERT: T 121 SER cc_start: 0.8768 (m) cc_final: 0.7986 (t) REVERT: T 122 LYS cc_start: 0.8410 (mmmm) cc_final: 0.7955 (mmtt) outliers start: 84 outliers final: 60 residues processed: 799 average time/residue: 0.4176 time to fit residues: 511.4191 Evaluate side-chains 739 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 676 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 169 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 169 TYR Chi-restraints excluded: chain K residue 180 GLN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 85 GLU Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 208 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 143 ASN Q 180 GLN S 180 GLN T 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29060 Z= 0.187 Angle : 0.691 15.573 39560 Z= 0.345 Chirality : 0.046 0.199 4960 Planarity : 0.006 0.092 5020 Dihedral : 4.161 25.220 4080 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.55 % Favored : 92.94 % Rotamer: Outliers : 2.91 % Allowed : 19.43 % Favored : 77.66 % 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: 0.87 (0.14), residues: 3880 helix: 3.29 (0.15), residues: 1040 sheet: 0.87 (0.16), residues: 1180 loop : -1.55 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 136 PHE 0.026 0.001 PHE N 28 TYR 0.008 0.001 TYR A 138 ARG 0.011 0.001 ARG R 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 717 time to evaluate : 3.168 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: C 93 LYS cc_start: 0.6599 (mttt) cc_final: 0.5894 (mmtm) REVERT: C 180 GLN cc_start: 0.8565 (pm20) cc_final: 0.8263 (pm20) REVERT: D 50 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8183 (mm-30) REVERT: D 138 TYR cc_start: 0.8301 (p90) cc_final: 0.7861 (p90) REVERT: E 46 GLN cc_start: 0.8955 (tt0) cc_final: 0.8642 (tm-30) REVERT: E 76 ILE cc_start: 0.9308 (mt) cc_final: 0.8951 (tt) REVERT: E 170 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: E 173 LYS cc_start: 0.8906 (tttt) cc_final: 0.8632 (tttm) REVERT: G 19 PHE cc_start: 0.8467 (m-80) cc_final: 0.8149 (m-80) REVERT: G 46 GLN cc_start: 0.8986 (tt0) cc_final: 0.8700 (tm-30) REVERT: G 47 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7715 (tpp80) REVERT: G 103 LYS cc_start: 0.7407 (mppt) cc_final: 0.6886 (mtmt) REVERT: G 138 TYR cc_start: 0.8579 (p90) cc_final: 0.8206 (p90) REVERT: H 50 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: H 59 ASP cc_start: 0.8323 (t0) cc_final: 0.8046 (t0) REVERT: H 93 LYS cc_start: 0.7083 (mttt) cc_final: 0.6054 (mmtp) REVERT: H 106 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7825 (tm-30) REVERT: I 16 LEU cc_start: 0.9242 (tp) cc_final: 0.8992 (tp) REVERT: I 19 PHE cc_start: 0.8811 (m-80) cc_final: 0.8578 (m-80) REVERT: I 39 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8356 (mm-40) REVERT: I 99 MET cc_start: 0.8385 (tmm) cc_final: 0.8060 (tmm) REVERT: J 19 PHE cc_start: 0.8726 (m-80) cc_final: 0.8293 (m-80) REVERT: K 173 LYS cc_start: 0.8851 (tttt) cc_final: 0.8511 (tttm) REVERT: K 189 ILE cc_start: 0.8853 (tt) cc_final: 0.8648 (pt) REVERT: L 120 ASP cc_start: 0.7131 (t0) cc_final: 0.6278 (p0) REVERT: L 172 PHE cc_start: 0.8625 (p90) cc_final: 0.8390 (p90) REVERT: M 50 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7568 (mm-30) REVERT: N 19 PHE cc_start: 0.8342 (m-80) cc_final: 0.8002 (m-80) REVERT: N 46 GLN cc_start: 0.9037 (tt0) cc_final: 0.8716 (tm-30) REVERT: N 173 LYS cc_start: 0.8998 (tttt) cc_final: 0.8650 (tttm) REVERT: O 89 MET cc_start: 0.7527 (mmm) cc_final: 0.7290 (mmm) REVERT: O 92 ASP cc_start: 0.8860 (p0) cc_final: 0.8434 (p0) REVERT: O 120 ASP cc_start: 0.7120 (t0) cc_final: 0.6571 (p0) REVERT: P 19 PHE cc_start: 0.8484 (m-80) cc_final: 0.8213 (m-80) REVERT: P 84 ARG cc_start: 0.7498 (mtm-85) cc_final: 0.7243 (mtm-85) REVERT: P 136 TRP cc_start: 0.7827 (m-90) cc_final: 0.7546 (m-10) REVERT: P 173 LYS cc_start: 0.8979 (tttt) cc_final: 0.8620 (tttm) REVERT: Q 39 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8595 (mm110) REVERT: Q 95 THR cc_start: 0.9218 (m) cc_final: 0.8744 (p) REVERT: R 19 PHE cc_start: 0.8559 (m-80) cc_final: 0.8262 (m-80) REVERT: R 84 ARG cc_start: 0.7847 (mpt180) cc_final: 0.7447 (mpt180) REVERT: R 122 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7397 (mptt) REVERT: R 155 LYS cc_start: 0.8952 (mmtm) cc_final: 0.7181 (tttt) REVERT: S 19 PHE cc_start: 0.8518 (m-80) cc_final: 0.7961 (m-80) REVERT: S 42 LYS cc_start: 0.9227 (tttt) cc_final: 0.8441 (tptt) REVERT: S 84 ARG cc_start: 0.7914 (mpt180) cc_final: 0.7635 (mtt90) REVERT: S 122 LYS cc_start: 0.8903 (mmmm) cc_final: 0.7432 (mmtt) REVERT: S 155 LYS cc_start: 0.8924 (mmtm) cc_final: 0.7763 (mtpt) REVERT: T 39 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8889 (mm-40) REVERT: T 45 MET cc_start: 0.8531 (ptm) cc_final: 0.8144 (ptm) REVERT: T 121 SER cc_start: 0.8729 (m) cc_final: 0.7916 (t) REVERT: T 122 LYS cc_start: 0.8401 (mmmm) cc_final: 0.7928 (mmtt) outliers start: 92 outliers final: 68 residues processed: 764 average time/residue: 0.4084 time to fit residues: 482.3156 Evaluate side-chains 736 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 666 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 39 GLN S 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29060 Z= 0.198 Angle : 0.697 15.748 39560 Z= 0.347 Chirality : 0.046 0.191 4960 Planarity : 0.007 0.098 5020 Dihedral : 4.131 25.258 4080 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.52 % Favored : 92.96 % Rotamer: Outliers : 2.82 % Allowed : 19.97 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.14), residues: 3880 helix: 3.29 (0.15), residues: 1040 sheet: 0.86 (0.16), residues: 1180 loop : -1.56 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 136 PHE 0.024 0.001 PHE N 28 TYR 0.017 0.001 TYR F 138 ARG 0.011 0.001 ARG R 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 702 time to evaluate : 3.765 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: C 93 LYS cc_start: 0.6665 (mttt) cc_final: 0.5915 (mmtm) REVERT: C 180 GLN cc_start: 0.8579 (pm20) cc_final: 0.8273 (pm20) REVERT: D 50 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8176 (mm-30) REVERT: E 46 GLN cc_start: 0.8961 (tt0) cc_final: 0.8643 (tm-30) REVERT: E 76 ILE cc_start: 0.9318 (mt) cc_final: 0.8963 (tt) REVERT: E 170 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: E 173 LYS cc_start: 0.8828 (tttt) cc_final: 0.8562 (tttm) REVERT: G 19 PHE cc_start: 0.8361 (m-80) cc_final: 0.8013 (m-80) REVERT: G 46 GLN cc_start: 0.8993 (tt0) cc_final: 0.8727 (tm-30) REVERT: G 47 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7907 (tpp80) REVERT: G 138 TYR cc_start: 0.8571 (p90) cc_final: 0.8213 (p90) REVERT: H 50 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: H 93 LYS cc_start: 0.6989 (mttt) cc_final: 0.6053 (mmtp) REVERT: H 106 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7827 (tm-30) REVERT: H 121 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.6840 (t) REVERT: I 16 LEU cc_start: 0.9259 (tp) cc_final: 0.9015 (tp) REVERT: I 19 PHE cc_start: 0.8752 (m-80) cc_final: 0.8515 (m-80) REVERT: I 39 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8392 (mm-40) REVERT: I 99 MET cc_start: 0.8401 (tmm) cc_final: 0.8055 (tmm) REVERT: I 105 TYR cc_start: 0.8662 (m-80) cc_final: 0.8403 (m-80) REVERT: I 138 TYR cc_start: 0.8002 (p90) cc_final: 0.7070 (p90) REVERT: J 19 PHE cc_start: 0.8706 (m-80) cc_final: 0.8282 (m-80) REVERT: J 103 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8288 (mmtt) REVERT: K 173 LYS cc_start: 0.8848 (tttt) cc_final: 0.8519 (tttm) REVERT: L 103 LYS cc_start: 0.8031 (mppt) cc_final: 0.7466 (mttt) REVERT: L 172 PHE cc_start: 0.8677 (p90) cc_final: 0.8428 (p90) REVERT: M 50 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7462 (mm-30) REVERT: M 85 GLU cc_start: 0.7194 (pt0) cc_final: 0.6772 (pt0) REVERT: N 19 PHE cc_start: 0.8301 (m-80) cc_final: 0.8011 (m-80) REVERT: N 46 GLN cc_start: 0.9037 (tt0) cc_final: 0.8713 (tm-30) REVERT: N 84 ARG cc_start: 0.6805 (mmt90) cc_final: 0.6392 (mmt90) REVERT: N 170 GLU cc_start: 0.8119 (pm20) cc_final: 0.7889 (pm20) REVERT: N 173 LYS cc_start: 0.8953 (tttt) cc_final: 0.8589 (tttm) REVERT: O 89 MET cc_start: 0.7577 (mmm) cc_final: 0.7304 (mmm) REVERT: O 92 ASP cc_start: 0.8867 (p0) cc_final: 0.8464 (p0) REVERT: O 120 ASP cc_start: 0.7138 (t0) cc_final: 0.6629 (p0) REVERT: P 19 PHE cc_start: 0.8430 (m-80) cc_final: 0.8165 (m-80) REVERT: P 84 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7304 (mtm-85) REVERT: P 136 TRP cc_start: 0.7814 (m-90) cc_final: 0.7531 (m-10) REVERT: P 173 LYS cc_start: 0.8972 (tttt) cc_final: 0.8615 (tttm) REVERT: Q 47 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7010 (mmm-85) REVERT: Q 95 THR cc_start: 0.9221 (m) cc_final: 0.8748 (p) REVERT: R 19 PHE cc_start: 0.8552 (m-80) cc_final: 0.8252 (m-80) REVERT: R 84 ARG cc_start: 0.7826 (mpt180) cc_final: 0.7473 (mpt180) REVERT: R 122 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7668 (mptt) REVERT: R 155 LYS cc_start: 0.8961 (mmtm) cc_final: 0.7182 (tttt) REVERT: S 19 PHE cc_start: 0.8473 (m-80) cc_final: 0.7889 (m-80) REVERT: S 42 LYS cc_start: 0.9232 (tttt) cc_final: 0.8439 (tptt) REVERT: S 84 ARG cc_start: 0.7917 (mpt180) cc_final: 0.7583 (mtm-85) REVERT: S 122 LYS cc_start: 0.8910 (mmmm) cc_final: 0.7558 (mmtt) REVERT: S 155 LYS cc_start: 0.8935 (mmtm) cc_final: 0.7769 (mtpt) REVERT: T 45 MET cc_start: 0.8539 (ptm) cc_final: 0.8181 (ptm) REVERT: T 121 SER cc_start: 0.8729 (m) cc_final: 0.7909 (t) REVERT: T 122 LYS cc_start: 0.8404 (mmmm) cc_final: 0.7921 (mmtt) outliers start: 89 outliers final: 73 residues processed: 747 average time/residue: 0.4201 time to fit residues: 483.8988 Evaluate side-chains 741 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 665 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 169 TYR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain L residue 169 TYR Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 4.9990 chunk 350 optimal weight: 9.9990 chunk 320 optimal weight: 4.9990 chunk 341 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 308 optimal weight: 6.9990 chunk 322 optimal weight: 0.6980 chunk 340 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29060 Z= 0.257 Angle : 0.743 16.883 39560 Z= 0.369 Chirality : 0.047 0.236 4960 Planarity : 0.007 0.105 5020 Dihedral : 4.231 25.293 4080 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.68 % Favored : 92.81 % Rotamer: Outliers : 3.01 % Allowed : 20.38 % Favored : 76.61 % 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: 0.72 (0.14), residues: 3880 helix: 3.22 (0.15), residues: 1040 sheet: 0.75 (0.16), residues: 1180 loop : -1.64 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 136 PHE 0.027 0.002 PHE A 28 TYR 0.016 0.001 TYR F 138 ARG 0.012 0.001 ARG T 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 687 time to evaluate : 3.312 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: C 180 GLN cc_start: 0.8655 (pm20) cc_final: 0.8384 (pm20) REVERT: D 50 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8212 (mm-30) REVERT: D 138 TYR cc_start: 0.8358 (p90) cc_final: 0.7916 (p90) REVERT: E 46 GLN cc_start: 0.8971 (tt0) cc_final: 0.8626 (tm-30) REVERT: E 76 ILE cc_start: 0.9308 (mt) cc_final: 0.8927 (tt) REVERT: E 122 LYS cc_start: 0.8631 (tptp) cc_final: 0.8230 (tppt) REVERT: E 170 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: E 173 LYS cc_start: 0.8851 (tttt) cc_final: 0.8588 (tttm) REVERT: F 122 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7852 (mmmt) REVERT: G 19 PHE cc_start: 0.8421 (m-80) cc_final: 0.8073 (m-80) REVERT: G 46 GLN cc_start: 0.9016 (tt0) cc_final: 0.8642 (tm-30) REVERT: G 47 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7923 (tpp80) REVERT: G 138 TYR cc_start: 0.8745 (p90) cc_final: 0.8410 (p90) REVERT: H 50 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7476 (tm-30) REVERT: H 59 ASP cc_start: 0.8294 (t0) cc_final: 0.8027 (t0) REVERT: H 93 LYS cc_start: 0.7042 (mttt) cc_final: 0.6141 (mmtp) REVERT: H 106 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7935 (tm-30) REVERT: I 16 LEU cc_start: 0.9279 (tp) cc_final: 0.9056 (tp) REVERT: I 19 PHE cc_start: 0.8790 (m-80) cc_final: 0.8546 (m-80) REVERT: I 99 MET cc_start: 0.8436 (tmm) cc_final: 0.8080 (tmm) REVERT: I 138 TYR cc_start: 0.8121 (p90) cc_final: 0.7079 (p90) REVERT: J 19 PHE cc_start: 0.8761 (m-80) cc_final: 0.8403 (m-80) REVERT: J 47 ARG cc_start: 0.8015 (mmm160) cc_final: 0.7748 (mtp85) REVERT: J 103 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8529 (mmtt) REVERT: J 148 ASN cc_start: 0.7701 (m-40) cc_final: 0.7423 (t0) REVERT: K 173 LYS cc_start: 0.8891 (tttt) cc_final: 0.8548 (tttm) REVERT: L 103 LYS cc_start: 0.8229 (mppt) cc_final: 0.7665 (mttt) REVERT: N 19 PHE cc_start: 0.8352 (m-80) cc_final: 0.8052 (m-80) REVERT: N 46 GLN cc_start: 0.9030 (tt0) cc_final: 0.8685 (tm-30) REVERT: N 170 GLU cc_start: 0.8200 (pm20) cc_final: 0.7953 (pm20) REVERT: N 173 LYS cc_start: 0.9022 (tttt) cc_final: 0.8598 (tttm) REVERT: O 89 MET cc_start: 0.7674 (mmm) cc_final: 0.7368 (mmm) REVERT: O 92 ASP cc_start: 0.8905 (p0) cc_final: 0.8524 (p0) REVERT: O 120 ASP cc_start: 0.7120 (t0) cc_final: 0.6598 (p0) REVERT: P 19 PHE cc_start: 0.8509 (m-80) cc_final: 0.8217 (m-80) REVERT: P 84 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7204 (mtm-85) REVERT: P 173 LYS cc_start: 0.8979 (tttt) cc_final: 0.8641 (tttm) REVERT: Q 95 THR cc_start: 0.9268 (m) cc_final: 0.8787 (p) REVERT: R 84 ARG cc_start: 0.7890 (mpt180) cc_final: 0.7512 (mpt180) REVERT: R 122 LYS cc_start: 0.8102 (mmmm) cc_final: 0.7671 (mptt) REVERT: R 155 LYS cc_start: 0.8961 (mmtm) cc_final: 0.7215 (tttt) REVERT: S 19 PHE cc_start: 0.8596 (m-80) cc_final: 0.7987 (m-80) REVERT: S 42 LYS cc_start: 0.9263 (tttt) cc_final: 0.8478 (tptt) REVERT: S 84 ARG cc_start: 0.8045 (mpt180) cc_final: 0.7708 (mpp-170) REVERT: S 122 LYS cc_start: 0.9002 (mmmm) cc_final: 0.7726 (mmtt) REVERT: S 152 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8532 (tt) REVERT: S 155 LYS cc_start: 0.8949 (mmtm) cc_final: 0.7834 (mtpt) REVERT: T 45 MET cc_start: 0.8563 (ptm) cc_final: 0.8173 (ptm) REVERT: T 121 SER cc_start: 0.8746 (m) cc_final: 0.7947 (t) REVERT: T 122 LYS cc_start: 0.8446 (mmmm) cc_final: 0.7947 (mmtt) outliers start: 95 outliers final: 81 residues processed: 746 average time/residue: 0.4272 time to fit residues: 492.7366 Evaluate side-chains 750 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 665 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 169 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 169 TYR Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 169 TYR Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 129 SER Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 4.9990 chunk 360 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 171 optimal weight: 0.0970 chunk 250 optimal weight: 3.9990 chunk 378 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 39 GLN S 180 GLN T 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29060 Z= 0.318 Angle : 0.785 17.421 39560 Z= 0.392 Chirality : 0.047 0.209 4960 Planarity : 0.007 0.110 5020 Dihedral : 4.419 25.513 4080 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.83 % Favored : 92.65 % Rotamer: Outliers : 2.88 % Allowed : 21.01 % Favored : 76.11 % 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: 0.50 (0.14), residues: 3880 helix: 3.10 (0.15), residues: 1040 sheet: 0.58 (0.16), residues: 1180 loop : -1.79 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 136 PHE 0.026 0.002 PHE D 36 TYR 0.013 0.001 TYR F 138 ARG 0.016 0.001 ARG K 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 674 time to evaluate : 3.240 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: C 79 LYS cc_start: 0.8729 (pttp) cc_final: 0.8481 (pttp) REVERT: C 180 GLN cc_start: 0.8725 (pm20) cc_final: 0.8443 (pm20) REVERT: D 50 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8198 (mm-30) REVERT: D 138 TYR cc_start: 0.8500 (p90) cc_final: 0.8043 (p90) REVERT: E 46 GLN cc_start: 0.8992 (tt0) cc_final: 0.8641 (tm-30) REVERT: E 122 LYS cc_start: 0.8720 (tptp) cc_final: 0.8326 (tppt) REVERT: E 170 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: E 173 LYS cc_start: 0.8866 (tttt) cc_final: 0.8542 (tttm) REVERT: F 122 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7950 (mmmt) REVERT: G 19 PHE cc_start: 0.8513 (m-80) cc_final: 0.8144 (m-80) REVERT: G 46 GLN cc_start: 0.9052 (tt0) cc_final: 0.8668 (tm-30) REVERT: G 47 ARG cc_start: 0.8242 (tpp80) cc_final: 0.7890 (tpp80) REVERT: G 103 LYS cc_start: 0.7540 (mppt) cc_final: 0.7097 (mtmt) REVERT: G 138 TYR cc_start: 0.8837 (p90) cc_final: 0.8494 (p90) REVERT: H 50 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: H 59 ASP cc_start: 0.8355 (t0) cc_final: 0.8078 (t0) REVERT: H 93 LYS cc_start: 0.7174 (mttt) cc_final: 0.6201 (mmtp) REVERT: H 106 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7958 (tm-30) REVERT: I 16 LEU cc_start: 0.9295 (tp) cc_final: 0.9063 (tp) REVERT: I 19 PHE cc_start: 0.8883 (m-80) cc_final: 0.8586 (m-80) REVERT: I 99 MET cc_start: 0.8426 (tmm) cc_final: 0.8100 (tmm) REVERT: I 138 TYR cc_start: 0.8261 (p90) cc_final: 0.7304 (p90) REVERT: J 19 PHE cc_start: 0.8869 (m-80) cc_final: 0.8501 (m-80) REVERT: J 47 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7635 (mtp85) REVERT: J 148 ASN cc_start: 0.7918 (m-40) cc_final: 0.7648 (t0) REVERT: K 173 LYS cc_start: 0.8873 (tttt) cc_final: 0.8529 (tttm) REVERT: L 40 LYS cc_start: 0.9485 (tptt) cc_final: 0.9276 (tppt) REVERT: L 103 LYS cc_start: 0.8327 (mppt) cc_final: 0.7773 (mttt) REVERT: M 50 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7667 (mm-30) REVERT: N 19 PHE cc_start: 0.8519 (m-80) cc_final: 0.8097 (m-80) REVERT: N 46 GLN cc_start: 0.9049 (tt0) cc_final: 0.8673 (tm-30) REVERT: N 84 ARG cc_start: 0.7304 (mmt90) cc_final: 0.6754 (mmt90) REVERT: N 173 LYS cc_start: 0.9018 (tttt) cc_final: 0.8580 (tttm) REVERT: O 89 MET cc_start: 0.7700 (mmm) cc_final: 0.7425 (mmm) REVERT: O 92 ASP cc_start: 0.8927 (p0) cc_final: 0.8559 (p0) REVERT: O 120 ASP cc_start: 0.7107 (t0) cc_final: 0.6435 (p0) REVERT: P 19 PHE cc_start: 0.8675 (m-80) cc_final: 0.8410 (m-80) REVERT: P 173 LYS cc_start: 0.8990 (tttt) cc_final: 0.8649 (tttm) REVERT: Q 46 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8749 (tm-30) REVERT: Q 95 THR cc_start: 0.9260 (m) cc_final: 0.8772 (p) REVERT: Q 121 SER cc_start: 0.8316 (m) cc_final: 0.7346 (t) REVERT: R 84 ARG cc_start: 0.8032 (mpt180) cc_final: 0.7581 (mpt180) REVERT: R 122 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7717 (mptt) REVERT: R 155 LYS cc_start: 0.9029 (mmtm) cc_final: 0.7184 (tptt) REVERT: S 19 PHE cc_start: 0.8684 (m-80) cc_final: 0.8055 (m-80) REVERT: S 42 LYS cc_start: 0.9279 (tttt) cc_final: 0.8500 (tptt) REVERT: S 59 ASP cc_start: 0.8250 (t0) cc_final: 0.7857 (p0) REVERT: S 84 ARG cc_start: 0.8131 (mpt180) cc_final: 0.7929 (mtt90) REVERT: S 122 LYS cc_start: 0.9058 (mmmm) cc_final: 0.7632 (mmpt) REVERT: S 152 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8574 (tt) REVERT: S 155 LYS cc_start: 0.8947 (mmtm) cc_final: 0.7014 (tttt) REVERT: T 45 MET cc_start: 0.8580 (ptm) cc_final: 0.8206 (ptm) REVERT: T 121 SER cc_start: 0.8854 (m) cc_final: 0.8094 (t) REVERT: T 122 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8004 (mmtt) REVERT: T 173 LYS cc_start: 0.8529 (tttt) cc_final: 0.8307 (tttt) outliers start: 91 outliers final: 80 residues processed: 732 average time/residue: 0.4167 time to fit residues: 467.7201 Evaluate side-chains 738 residues out of total 3160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 655 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 169 TYR Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 50 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 92 ASP Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 169 TYR Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 189 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 187 GLU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 85 GLU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 129 SER Chi-restraints excluded: chain S residue 152 LEU Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 180 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 9.9990 chunk 321 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 277 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 301 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 143 ASN S 180 GLN T 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.093474 restraints weight = 58309.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.096915 restraints weight = 28171.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.099157 restraints weight = 16885.903| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29060 Z= 0.253 Angle : 0.766 17.483 39560 Z= 0.380 Chirality : 0.047 0.319 4960 Planarity : 0.007 0.106 5020 Dihedral : 4.354 24.641 4080 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.70 % Favored : 92.78 % Rotamer: Outliers : 2.72 % Allowed : 21.46 % Favored : 75.82 % 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: 0.50 (0.14), residues: 3880 helix: 3.13 (0.15), residues: 1040 sheet: 0.56 (0.16), residues: 1180 loop : -1.78 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 136 PHE 0.028 0.002 PHE N 28 TYR 0.014 0.001 TYR F 138 ARG 0.013 0.001 ARG R 47 =============================================================================== Job complete usr+sys time: 8024.28 seconds wall clock time: 143 minutes 38.54 seconds (8618.54 seconds total)