Starting phenix.real_space_refine on Tue Mar 12 18:51:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5i_12034/03_2024/7b5i_12034.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5i_12034/03_2024/7b5i_12034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5i_12034/03_2024/7b5i_12034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5i_12034/03_2024/7b5i_12034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5i_12034/03_2024/7b5i_12034.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5i_12034/03_2024/7b5i_12034.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 168 5.16 5 C 41124 2.51 5 N 10974 2.21 5 O 12192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AA GLU 33": "OE1" <-> "OE2" Residue "AA ASP 74": "OD1" <-> "OD2" Residue "AA ASP 140": "OD1" <-> "OD2" Residue "AB ARG 36": "NH1" <-> "NH2" Residue "AB ASP 98": "OD1" <-> "OD2" Residue "AB ARG 113": "NH1" <-> "NH2" Residue "AB ASP 177": "OD1" <-> "OD2" Residue "AB TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB ARG 359": "NH1" <-> "NH2" Residue "AB ASP 361": "OD1" <-> "OD2" Residue "AB ASP 366": "OD1" <-> "OD2" Residue "AC GLU 26": "OE1" <-> "OE2" Residue "AC ASP 155": "OD1" <-> "OD2" Residue "AC ASP 224": "OD1" <-> "OD2" Residue "AC TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC GLU 260": "OE1" <-> "OE2" Residue "AC ASP 263": "OD1" <-> "OD2" Residue "AC ASP 309": "OD1" <-> "OD2" Residue "AC GLU 397": "OE1" <-> "OE2" Residue "AC PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC GLU 446": "OE1" <-> "OE2" Residue "AD GLU 3": "OE1" <-> "OE2" Residue "AD PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD GLU 24": "OE1" <-> "OE2" Residue "AD ASP 29": "OD1" <-> "OD2" Residue "AD PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD GLU 125": "OE1" <-> "OE2" Residue "AE ARG 19": "NH1" <-> "NH2" Residue "AE GLU 24": "OE1" <-> "OE2" Residue "AE ASP 29": "OD1" <-> "OD2" Residue "AE PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE GLU 125": "OE1" <-> "OE2" Residue "BA GLU 33": "OE1" <-> "OE2" Residue "BA ASP 74": "OD1" <-> "OD2" Residue "BA ASP 140": "OD1" <-> "OD2" Residue "BB ARG 36": "NH1" <-> "NH2" Residue "BB ASP 98": "OD1" <-> "OD2" Residue "BB ARG 113": "NH1" <-> "NH2" Residue "BB ASP 177": "OD1" <-> "OD2" Residue "BB TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ARG 359": "NH1" <-> "NH2" Residue "BB ASP 361": "OD1" <-> "OD2" Residue "BB ASP 366": "OD1" <-> "OD2" Residue "BC GLU 26": "OE1" <-> "OE2" Residue "BC ASP 155": "OD1" <-> "OD2" Residue "BC ASP 224": "OD1" <-> "OD2" Residue "BC TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC GLU 260": "OE1" <-> "OE2" Residue "BC ASP 263": "OD1" <-> "OD2" Residue "BC ASP 309": "OD1" <-> "OD2" Residue "BC GLU 397": "OE1" <-> "OE2" Residue "BC PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC GLU 446": "OE1" <-> "OE2" Residue "BD GLU 3": "OE1" <-> "OE2" Residue "BD PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD GLU 24": "OE1" <-> "OE2" Residue "BD ASP 29": "OD1" <-> "OD2" Residue "BD PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD GLU 125": "OE1" <-> "OE2" Residue "BE ARG 19": "NH1" <-> "NH2" Residue "BE GLU 24": "OE1" <-> "OE2" Residue "BE ASP 29": "OD1" <-> "OD2" Residue "BE PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE GLU 125": "OE1" <-> "OE2" Residue "CA GLU 33": "OE1" <-> "OE2" Residue "CA ASP 74": "OD1" <-> "OD2" Residue "CA ASP 140": "OD1" <-> "OD2" Residue "CB ARG 36": "NH1" <-> "NH2" Residue "CB ASP 98": "OD1" <-> "OD2" Residue "CB ARG 113": "NH1" <-> "NH2" Residue "CB ASP 177": "OD1" <-> "OD2" Residue "CB TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB ARG 359": "NH1" <-> "NH2" Residue "CB ASP 361": "OD1" <-> "OD2" Residue "CB ASP 366": "OD1" <-> "OD2" Residue "CC GLU 26": "OE1" <-> "OE2" Residue "CC ASP 155": "OD1" <-> "OD2" Residue "CC ASP 224": "OD1" <-> "OD2" Residue "CC TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC GLU 260": "OE1" <-> "OE2" Residue "CC ASP 263": "OD1" <-> "OD2" Residue "CC ASP 309": "OD1" <-> "OD2" Residue "CC GLU 397": "OE1" <-> "OE2" Residue "CC PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC GLU 446": "OE1" <-> "OE2" Residue "CD GLU 3": "OE1" <-> "OE2" Residue "CD PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD GLU 24": "OE1" <-> "OE2" Residue "CD ASP 29": "OD1" <-> "OD2" Residue "CD PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD GLU 125": "OE1" <-> "OE2" Residue "CE ARG 19": "NH1" <-> "NH2" Residue "CE GLU 24": "OE1" <-> "OE2" Residue "CE ASP 29": "OD1" <-> "OD2" Residue "CE PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE GLU 125": "OE1" <-> "OE2" Residue "DA GLU 33": "OE1" <-> "OE2" Residue "DA ASP 74": "OD1" <-> "OD2" Residue "DA ASP 140": "OD1" <-> "OD2" Residue "DB ARG 36": "NH1" <-> "NH2" Residue "DB ASP 98": "OD1" <-> "OD2" Residue "DB ARG 113": "NH1" <-> "NH2" Residue "DB ASP 177": "OD1" <-> "OD2" Residue "DB TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DB ARG 359": "NH1" <-> "NH2" Residue "DB ASP 361": "OD1" <-> "OD2" Residue "DB ASP 366": "OD1" <-> "OD2" Residue "DC GLU 26": "OE1" <-> "OE2" Residue "DC ASP 155": "OD1" <-> "OD2" Residue "DC ASP 224": "OD1" <-> "OD2" Residue "DC TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC GLU 260": "OE1" <-> "OE2" Residue "DC ASP 263": "OD1" <-> "OD2" Residue "DC ASP 309": "OD1" <-> "OD2" Residue "DC GLU 397": "OE1" <-> "OE2" Residue "DC PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DC GLU 446": "OE1" <-> "OE2" Residue "DD GLU 3": "OE1" <-> "OE2" Residue "DD PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DD GLU 24": "OE1" <-> "OE2" Residue "DD ASP 29": "OD1" <-> "OD2" Residue "DD PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DD GLU 125": "OE1" <-> "OE2" Residue "DE ARG 19": "NH1" <-> "NH2" Residue "DE GLU 24": "OE1" <-> "OE2" Residue "DE ASP 29": "OD1" <-> "OD2" Residue "DE PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DE GLU 125": "OE1" <-> "OE2" Residue "EA GLU 33": "OE1" <-> "OE2" Residue "EA ASP 74": "OD1" <-> "OD2" Residue "EA ASP 140": "OD1" <-> "OD2" Residue "EB ARG 36": "NH1" <-> "NH2" Residue "EB ASP 98": "OD1" <-> "OD2" Residue "EB ARG 113": "NH1" <-> "NH2" Residue "EB ASP 177": "OD1" <-> "OD2" Residue "EB TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EB ARG 359": "NH1" <-> "NH2" Residue "EB ASP 361": "OD1" <-> "OD2" Residue "EB ASP 366": "OD1" <-> "OD2" Residue "EC GLU 26": "OE1" <-> "OE2" Residue "EC ASP 155": "OD1" <-> "OD2" Residue "EC ASP 224": "OD1" <-> "OD2" Residue "EC TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EC GLU 260": "OE1" <-> "OE2" Residue "EC ASP 263": "OD1" <-> "OD2" Residue "EC ASP 309": "OD1" <-> "OD2" Residue "EC GLU 397": "OE1" <-> "OE2" Residue "EC PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EC GLU 446": "OE1" <-> "OE2" Residue "ED GLU 3": "OE1" <-> "OE2" Residue "ED PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ED GLU 24": "OE1" <-> "OE2" Residue "ED ASP 29": "OD1" <-> "OD2" Residue "ED PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ED GLU 125": "OE1" <-> "OE2" Residue "EE ARG 19": "NH1" <-> "NH2" Residue "EE GLU 24": "OE1" <-> "OE2" Residue "EE ASP 29": "OD1" <-> "OD2" Residue "EE PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EE GLU 125": "OE1" <-> "OE2" Residue "FA GLU 33": "OE1" <-> "OE2" Residue "FA ASP 74": "OD1" <-> "OD2" Residue "FA ASP 140": "OD1" <-> "OD2" Residue "FB ARG 36": "NH1" <-> "NH2" Residue "FB ASP 98": "OD1" <-> "OD2" Residue "FB ARG 113": "NH1" <-> "NH2" Residue "FB ASP 177": "OD1" <-> "OD2" Residue "FB TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FB ARG 359": "NH1" <-> "NH2" Residue "FB ASP 361": "OD1" <-> "OD2" Residue "FB ASP 366": "OD1" <-> "OD2" Residue "FC GLU 26": "OE1" <-> "OE2" Residue "FC ASP 155": "OD1" <-> "OD2" Residue "FC ASP 224": "OD1" <-> "OD2" Residue "FC TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FC GLU 260": "OE1" <-> "OE2" Residue "FC ASP 263": "OD1" <-> "OD2" Residue "FC ASP 309": "OD1" <-> "OD2" Residue "FC GLU 397": "OE1" <-> "OE2" Residue "FC PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FC GLU 446": "OE1" <-> "OE2" Residue "FD GLU 3": "OE1" <-> "OE2" Residue "FD PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FD GLU 24": "OE1" <-> "OE2" Residue "FD ASP 29": "OD1" <-> "OD2" Residue "FD PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FD GLU 125": "OE1" <-> "OE2" Residue "FE ARG 19": "NH1" <-> "NH2" Residue "FE GLU 24": "OE1" <-> "OE2" Residue "FE ASP 29": "OD1" <-> "OD2" Residue "FE PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FE GLU 125": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 64458 Number of models: 1 Model: "" Number of chains: 30 Chain: "AA" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Chain: "AB" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3210 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 29, 'TRANS': 369} Chain: "AC" Number of atoms: 3716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3716 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 452} Chain: "AD" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "AE" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "BA" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Chain: "BB" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3210 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 29, 'TRANS': 369} Chain: "BC" Number of atoms: 3716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3716 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 452} Chain: "BD" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "BE" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "CA" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Chain: "CB" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3210 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 29, 'TRANS': 369} Chain: "CC" Number of atoms: 3716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3716 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 452} Chain: "CD" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "CE" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "DA" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Chain: "DB" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3210 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 29, 'TRANS': 369} Chain: "DC" Number of atoms: 3716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3716 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 452} Chain: "DD" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "DE" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "EA" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Chain: "EB" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3210 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 29, 'TRANS': 369} Chain: "EC" Number of atoms: 3716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3716 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 452} Chain: "ED" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "EE" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "FA" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Chain: "FB" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3210 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 29, 'TRANS': 369} Chain: "FC" Number of atoms: 3716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3716 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 452} Chain: "FD" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "FE" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1152 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Time building chain proxies: 24.80, per 1000 atoms: 0.38 Number of scatterers: 64458 At special positions: 0 Unit cell: (194.7, 196.9, 163.9, 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 168 16.00 O 12192 8.00 N 10974 7.00 C 41124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYSAB 331 " - pdb=" SG CYSAB 367 " distance=2.21 Simple disulfide: pdb=" SG CYSBB 331 " - pdb=" SG CYSBB 367 " distance=2.21 Simple disulfide: pdb=" SG CYSCB 331 " - pdb=" SG CYSCB 367 " distance=2.21 Simple disulfide: pdb=" SG CYSDB 331 " - pdb=" SG CYSDB 367 " distance=2.21 Simple disulfide: pdb=" SG CYSEB 331 " - pdb=" SG CYSEB 367 " distance=2.21 Simple disulfide: pdb=" SG CYSFB 331 " - pdb=" SG CYSFB 367 " distance=2.21 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: 18.19 Conformation dependent library (CDL) restraints added in 9.2 seconds 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15216 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 114 sheets defined 20.1% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.53 Creating SS restraints... Processing helix chain 'AA' and resid 2 through 21 removed outlier: 3.684A pdb=" N METAA 6 " --> pdb=" O ILEAA 2 " (cutoff:3.500A) Processing helix chain 'AA' and resid 22 through 25 removed outlier: 3.692A pdb=" N GLYAA 25 " --> pdb=" O PROAA 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 22 through 25' Processing helix chain 'AA' and resid 34 through 42 removed outlier: 3.594A pdb=" N METAA 37 " --> pdb=" O ASNAA 34 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLUAA 39 " --> pdb=" O ALAAA 36 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLUAA 40 " --> pdb=" O METAA 37 " (cutoff:3.500A) Processing helix chain 'AA' and resid 63 through 66 removed outlier: 3.579A pdb=" N LYSAA 66 " --> pdb=" O THRAA 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 63 through 66' Processing helix chain 'AA' and resid 99 through 117 removed outlier: 3.729A pdb=" N SERAA 103 " --> pdb=" O GLNAA 99 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEUAA 104 " --> pdb=" O TYRAA 100 " (cutoff:3.500A) Processing helix chain 'AA' and resid 145 through 156 Processing helix chain 'AB' and resid 16 through 20 Processing helix chain 'AB' and resid 43 through 54 Processing helix chain 'AB' and resid 100 through 104 Processing helix chain 'AB' and resid 186 through 188 No H-bonds generated for 'chain 'AB' and resid 186 through 188' Processing helix chain 'AC' and resid 62 through 70 Processing helix chain 'AC' and resid 109 through 120 Processing helix chain 'AC' and resid 140 through 151 removed outlier: 3.576A pdb=" N LEUAC 144 " --> pdb=" O GLNAC 140 " (cutoff:3.500A) Processing helix chain 'AC' and resid 152 through 154 No H-bonds generated for 'chain 'AC' and resid 152 through 154' Processing helix chain 'AC' and resid 169 through 188 Processing helix chain 'AC' and resid 208 through 218 Processing helix chain 'AC' and resid 225 through 227 No H-bonds generated for 'chain 'AC' and resid 225 through 227' Processing helix chain 'AC' and resid 268 through 275 Proline residue: AC 272 - end of helix Processing helix chain 'AC' and resid 277 through 289 removed outlier: 3.893A pdb=" N LEUAC 283 " --> pdb=" O ILEAC 279 " (cutoff:3.500A) Processing helix chain 'AC' and resid 297 through 309 removed outlier: 3.507A pdb=" N GLYAC 303 " --> pdb=" O PROAC 299 " (cutoff:3.500A) Processing helix chain 'AC' and resid 334 through 343 removed outlier: 3.882A pdb=" N ASNAC 340 " --> pdb=" O GLUAC 336 " (cutoff:3.500A) Processing helix chain 'AC' and resid 378 through 396 removed outlier: 3.599A pdb=" N ARGAC 382 " --> pdb=" O TYRAC 378 " (cutoff:3.500A) Processing helix chain 'AC' and resid 405 through 426 removed outlier: 3.785A pdb=" N ALAAC 426 " --> pdb=" O LEUAC 422 " (cutoff:3.500A) Processing helix chain 'AC' and resid 449 through 456 Processing helix chain 'AD' and resid 70 through 77 Processing helix chain 'AE' and resid 70 through 77 Processing helix chain 'BA' and resid 2 through 21 removed outlier: 3.684A pdb=" N METBA 6 " --> pdb=" O ILEBA 2 " (cutoff:3.500A) Processing helix chain 'BA' and resid 22 through 25 removed outlier: 3.692A pdb=" N GLYBA 25 " --> pdb=" O PROBA 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 22 through 25' Processing helix chain 'BA' and resid 34 through 42 removed outlier: 3.594A pdb=" N METBA 37 " --> pdb=" O ASNBA 34 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLUBA 39 " --> pdb=" O ALABA 36 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLUBA 40 " --> pdb=" O METBA 37 " (cutoff:3.500A) Processing helix chain 'BA' and resid 63 through 66 removed outlier: 3.580A pdb=" N LYSBA 66 " --> pdb=" O THRBA 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 63 through 66' Processing helix chain 'BA' and resid 99 through 117 removed outlier: 3.728A pdb=" N SERBA 103 " --> pdb=" O GLNBA 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEUBA 104 " --> pdb=" O TYRBA 100 " (cutoff:3.500A) Processing helix chain 'BA' and resid 145 through 156 Processing helix chain 'BB' and resid 16 through 20 Processing helix chain 'BB' and resid 43 through 54 Processing helix chain 'BB' and resid 100 through 104 Processing helix chain 'BB' and resid 186 through 188 No H-bonds generated for 'chain 'BB' and resid 186 through 188' Processing helix chain 'BC' and resid 62 through 70 Processing helix chain 'BC' and resid 109 through 120 Processing helix chain 'BC' and resid 140 through 151 removed outlier: 3.576A pdb=" N LEUBC 144 " --> pdb=" O GLNBC 140 " (cutoff:3.500A) Processing helix chain 'BC' and resid 152 through 154 No H-bonds generated for 'chain 'BC' and resid 152 through 154' Processing helix chain 'BC' and resid 169 through 188 Processing helix chain 'BC' and resid 208 through 218 Processing helix chain 'BC' and resid 225 through 227 No H-bonds generated for 'chain 'BC' and resid 225 through 227' Processing helix chain 'BC' and resid 268 through 275 Proline residue: BC 272 - end of helix Processing helix chain 'BC' and resid 277 through 289 removed outlier: 3.893A pdb=" N LEUBC 283 " --> pdb=" O ILEBC 279 " (cutoff:3.500A) Processing helix chain 'BC' and resid 297 through 309 removed outlier: 3.507A pdb=" N GLYBC 303 " --> pdb=" O PROBC 299 " (cutoff:3.500A) Processing helix chain 'BC' and resid 334 through 343 removed outlier: 3.882A pdb=" N ASNBC 340 " --> pdb=" O GLUBC 336 " (cutoff:3.500A) Processing helix chain 'BC' and resid 378 through 396 removed outlier: 3.599A pdb=" N ARGBC 382 " --> pdb=" O TYRBC 378 " (cutoff:3.500A) Processing helix chain 'BC' and resid 405 through 426 removed outlier: 3.785A pdb=" N ALABC 426 " --> pdb=" O LEUBC 422 " (cutoff:3.500A) Processing helix chain 'BC' and resid 449 through 456 Processing helix chain 'BD' and resid 70 through 77 Processing helix chain 'BE' and resid 70 through 77 Processing helix chain 'CA' and resid 2 through 21 removed outlier: 3.684A pdb=" N METCA 6 " --> pdb=" O ILECA 2 " (cutoff:3.500A) Processing helix chain 'CA' and resid 22 through 25 removed outlier: 3.691A pdb=" N GLYCA 25 " --> pdb=" O PROCA 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 22 through 25' Processing helix chain 'CA' and resid 34 through 42 removed outlier: 3.593A pdb=" N METCA 37 " --> pdb=" O ASNCA 34 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLUCA 39 " --> pdb=" O ALACA 36 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLUCA 40 " --> pdb=" O METCA 37 " (cutoff:3.500A) Processing helix chain 'CA' and resid 63 through 66 removed outlier: 3.580A pdb=" N LYSCA 66 " --> pdb=" O THRCA 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'CA' and resid 63 through 66' Processing helix chain 'CA' and resid 99 through 117 removed outlier: 3.728A pdb=" N SERCA 103 " --> pdb=" O GLNCA 99 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEUCA 104 " --> pdb=" O TYRCA 100 " (cutoff:3.500A) Processing helix chain 'CA' and resid 145 through 156 Processing helix chain 'CB' and resid 16 through 20 Processing helix chain 'CB' and resid 43 through 54 Processing helix chain 'CB' and resid 100 through 104 Processing helix chain 'CB' and resid 186 through 188 No H-bonds generated for 'chain 'CB' and resid 186 through 188' Processing helix chain 'CC' and resid 62 through 70 Processing helix chain 'CC' and resid 109 through 120 Processing helix chain 'CC' and resid 140 through 151 removed outlier: 3.576A pdb=" N LEUCC 144 " --> pdb=" O GLNCC 140 " (cutoff:3.500A) Processing helix chain 'CC' and resid 152 through 154 No H-bonds generated for 'chain 'CC' and resid 152 through 154' Processing helix chain 'CC' and resid 169 through 188 Processing helix chain 'CC' and resid 208 through 218 Processing helix chain 'CC' and resid 225 through 227 No H-bonds generated for 'chain 'CC' and resid 225 through 227' Processing helix chain 'CC' and resid 268 through 275 Proline residue: CC 272 - end of helix Processing helix chain 'CC' and resid 277 through 289 removed outlier: 3.893A pdb=" N LEUCC 283 " --> pdb=" O ILECC 279 " (cutoff:3.500A) Processing helix chain 'CC' and resid 297 through 309 removed outlier: 3.507A pdb=" N GLYCC 303 " --> pdb=" O PROCC 299 " (cutoff:3.500A) Processing helix chain 'CC' and resid 334 through 343 removed outlier: 3.882A pdb=" N ASNCC 340 " --> pdb=" O GLUCC 336 " (cutoff:3.500A) Processing helix chain 'CC' and resid 378 through 396 removed outlier: 3.599A pdb=" N ARGCC 382 " --> pdb=" O TYRCC 378 " (cutoff:3.500A) Processing helix chain 'CC' and resid 405 through 426 removed outlier: 3.785A pdb=" N ALACC 426 " --> pdb=" O LEUCC 422 " (cutoff:3.500A) Processing helix chain 'CC' and resid 449 through 456 Processing helix chain 'CD' and resid 70 through 77 Processing helix chain 'CE' and resid 70 through 77 Processing helix chain 'DA' and resid 2 through 21 removed outlier: 3.684A pdb=" N METDA 6 " --> pdb=" O ILEDA 2 " (cutoff:3.500A) Processing helix chain 'DA' and resid 22 through 25 removed outlier: 3.692A pdb=" N GLYDA 25 " --> pdb=" O PRODA 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'DA' and resid 22 through 25' Processing helix chain 'DA' and resid 34 through 42 removed outlier: 3.594A pdb=" N METDA 37 " --> pdb=" O ASNDA 34 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLUDA 39 " --> pdb=" O ALADA 36 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLUDA 40 " --> pdb=" O METDA 37 " (cutoff:3.500A) Processing helix chain 'DA' and resid 63 through 66 removed outlier: 3.579A pdb=" N LYSDA 66 " --> pdb=" O THRDA 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'DA' and resid 63 through 66' Processing helix chain 'DA' and resid 99 through 117 removed outlier: 3.729A pdb=" N SERDA 103 " --> pdb=" O GLNDA 99 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEUDA 104 " --> pdb=" O TYRDA 100 " (cutoff:3.500A) Processing helix chain 'DA' and resid 145 through 156 Processing helix chain 'DB' and resid 16 through 20 Processing helix chain 'DB' and resid 43 through 54 Processing helix chain 'DB' and resid 100 through 104 Processing helix chain 'DB' and resid 186 through 188 No H-bonds generated for 'chain 'DB' and resid 186 through 188' Processing helix chain 'DC' and resid 62 through 70 Processing helix chain 'DC' and resid 109 through 120 Processing helix chain 'DC' and resid 140 through 151 removed outlier: 3.576A pdb=" N LEUDC 144 " --> pdb=" O GLNDC 140 " (cutoff:3.500A) Processing helix chain 'DC' and resid 152 through 154 No H-bonds generated for 'chain 'DC' and resid 152 through 154' Processing helix chain 'DC' and resid 169 through 188 Processing helix chain 'DC' and resid 208 through 218 Processing helix chain 'DC' and resid 225 through 227 No H-bonds generated for 'chain 'DC' and resid 225 through 227' Processing helix chain 'DC' and resid 268 through 275 Proline residue: DC 272 - end of helix Processing helix chain 'DC' and resid 277 through 289 removed outlier: 3.893A pdb=" N LEUDC 283 " --> pdb=" O ILEDC 279 " (cutoff:3.500A) Processing helix chain 'DC' and resid 297 through 309 removed outlier: 3.507A pdb=" N GLYDC 303 " --> pdb=" O PRODC 299 " (cutoff:3.500A) Processing helix chain 'DC' and resid 334 through 343 removed outlier: 3.882A pdb=" N ASNDC 340 " --> pdb=" O GLUDC 336 " (cutoff:3.500A) Processing helix chain 'DC' and resid 378 through 396 removed outlier: 3.599A pdb=" N ARGDC 382 " --> pdb=" O TYRDC 378 " (cutoff:3.500A) Processing helix chain 'DC' and resid 405 through 426 removed outlier: 3.785A pdb=" N ALADC 426 " --> pdb=" O LEUDC 422 " (cutoff:3.500A) Processing helix chain 'DC' and resid 449 through 456 Processing helix chain 'DD' and resid 70 through 77 Processing helix chain 'DE' and resid 70 through 77 Processing helix chain 'EA' and resid 2 through 21 removed outlier: 3.684A pdb=" N METEA 6 " --> pdb=" O ILEEA 2 " (cutoff:3.500A) Processing helix chain 'EA' and resid 22 through 25 removed outlier: 3.692A pdb=" N GLYEA 25 " --> pdb=" O PROEA 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'EA' and resid 22 through 25' Processing helix chain 'EA' and resid 34 through 42 removed outlier: 3.594A pdb=" N METEA 37 " --> pdb=" O ASNEA 34 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLUEA 39 " --> pdb=" O ALAEA 36 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLUEA 40 " --> pdb=" O METEA 37 " (cutoff:3.500A) Processing helix chain 'EA' and resid 63 through 66 removed outlier: 3.579A pdb=" N LYSEA 66 " --> pdb=" O THREA 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'EA' and resid 63 through 66' Processing helix chain 'EA' and resid 99 through 117 removed outlier: 3.728A pdb=" N SEREA 103 " --> pdb=" O GLNEA 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEUEA 104 " --> pdb=" O TYREA 100 " (cutoff:3.500A) Processing helix chain 'EA' and resid 145 through 156 Processing helix chain 'EB' and resid 16 through 20 Processing helix chain 'EB' and resid 43 through 54 Processing helix chain 'EB' and resid 100 through 104 Processing helix chain 'EB' and resid 186 through 188 No H-bonds generated for 'chain 'EB' and resid 186 through 188' Processing helix chain 'EC' and resid 62 through 70 Processing helix chain 'EC' and resid 109 through 120 Processing helix chain 'EC' and resid 140 through 151 removed outlier: 3.575A pdb=" N LEUEC 144 " --> pdb=" O GLNEC 140 " (cutoff:3.500A) Processing helix chain 'EC' and resid 152 through 154 No H-bonds generated for 'chain 'EC' and resid 152 through 154' Processing helix chain 'EC' and resid 169 through 188 Processing helix chain 'EC' and resid 208 through 218 Processing helix chain 'EC' and resid 225 through 227 No H-bonds generated for 'chain 'EC' and resid 225 through 227' Processing helix chain 'EC' and resid 268 through 275 Proline residue: EC 272 - end of helix Processing helix chain 'EC' and resid 277 through 289 removed outlier: 3.893A pdb=" N LEUEC 283 " --> pdb=" O ILEEC 279 " (cutoff:3.500A) Processing helix chain 'EC' and resid 297 through 309 removed outlier: 3.507A pdb=" N GLYEC 303 " --> pdb=" O PROEC 299 " (cutoff:3.500A) Processing helix chain 'EC' and resid 334 through 343 removed outlier: 3.882A pdb=" N ASNEC 340 " --> pdb=" O GLUEC 336 " (cutoff:3.500A) Processing helix chain 'EC' and resid 378 through 396 removed outlier: 3.599A pdb=" N ARGEC 382 " --> pdb=" O TYREC 378 " (cutoff:3.500A) Processing helix chain 'EC' and resid 405 through 426 removed outlier: 3.785A pdb=" N ALAEC 426 " --> pdb=" O LEUEC 422 " (cutoff:3.500A) Processing helix chain 'EC' and resid 449 through 456 Processing helix chain 'ED' and resid 70 through 77 Processing helix chain 'EE' and resid 70 through 77 Processing helix chain 'FA' and resid 2 through 21 removed outlier: 3.684A pdb=" N METFA 6 " --> pdb=" O ILEFA 2 " (cutoff:3.500A) Processing helix chain 'FA' and resid 22 through 25 removed outlier: 3.691A pdb=" N GLYFA 25 " --> pdb=" O PROFA 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'FA' and resid 22 through 25' Processing helix chain 'FA' and resid 34 through 42 removed outlier: 3.593A pdb=" N METFA 37 " --> pdb=" O ASNFA 34 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLUFA 39 " --> pdb=" O ALAFA 36 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLUFA 40 " --> pdb=" O METFA 37 " (cutoff:3.500A) Processing helix chain 'FA' and resid 63 through 66 removed outlier: 3.580A pdb=" N LYSFA 66 " --> pdb=" O THRFA 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'FA' and resid 63 through 66' Processing helix chain 'FA' and resid 99 through 117 removed outlier: 3.728A pdb=" N SERFA 103 " --> pdb=" O GLNFA 99 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEUFA 104 " --> pdb=" O TYRFA 100 " (cutoff:3.500A) Processing helix chain 'FA' and resid 145 through 156 Processing helix chain 'FB' and resid 16 through 20 Processing helix chain 'FB' and resid 43 through 54 Processing helix chain 'FB' and resid 100 through 104 Processing helix chain 'FB' and resid 186 through 188 No H-bonds generated for 'chain 'FB' and resid 186 through 188' Processing helix chain 'FC' and resid 62 through 70 Processing helix chain 'FC' and resid 109 through 120 Processing helix chain 'FC' and resid 140 through 151 removed outlier: 3.575A pdb=" N LEUFC 144 " --> pdb=" O GLNFC 140 " (cutoff:3.500A) Processing helix chain 'FC' and resid 152 through 154 No H-bonds generated for 'chain 'FC' and resid 152 through 154' Processing helix chain 'FC' and resid 169 through 188 Processing helix chain 'FC' and resid 208 through 218 Processing helix chain 'FC' and resid 225 through 227 No H-bonds generated for 'chain 'FC' and resid 225 through 227' Processing helix chain 'FC' and resid 268 through 275 Proline residue: FC 272 - end of helix Processing helix chain 'FC' and resid 277 through 289 removed outlier: 3.893A pdb=" N LEUFC 283 " --> pdb=" O ILEFC 279 " (cutoff:3.500A) Processing helix chain 'FC' and resid 297 through 309 removed outlier: 3.507A pdb=" N GLYFC 303 " --> pdb=" O PROFC 299 " (cutoff:3.500A) Processing helix chain 'FC' and resid 334 through 343 removed outlier: 3.882A pdb=" N ASNFC 340 " --> pdb=" O GLUFC 336 " (cutoff:3.500A) Processing helix chain 'FC' and resid 378 through 396 removed outlier: 3.599A pdb=" N ARGFC 382 " --> pdb=" O TYRFC 378 " (cutoff:3.500A) Processing helix chain 'FC' and resid 405 through 426 removed outlier: 3.785A pdb=" N ALAFC 426 " --> pdb=" O LEUFC 422 " (cutoff:3.500A) Processing helix chain 'FC' and resid 449 through 456 Processing helix chain 'FD' and resid 70 through 77 Processing helix chain 'FE' and resid 70 through 77 Processing sheet with id=AA1, first strand: chain 'AA' and resid 30 through 32 removed outlier: 5.521A pdb=" N VALAA 52 " --> pdb=" O LEUAA 96 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEUAA 96 " --> pdb=" O VALAA 52 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N METAA 54 " --> pdb=" O SERAA 94 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SERAA 94 " --> pdb=" O METAA 54 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEUAA 56 " --> pdb=" O LEUAA 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEUAA 92 " --> pdb=" O LEUAA 56 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASNAA 58 " --> pdb=" O PHEAA 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHEAA 90 " --> pdb=" O ASNAA 58 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VALAA 85 " --> pdb=" O SERAA 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SERAA 172 " --> pdb=" O VALAA 85 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEUAA 87 " --> pdb=" O ILEAA 170 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILEAA 170 " --> pdb=" O LEUAA 87 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEUAA 165 " --> pdb=" O TYRAA 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 71 through 74 Processing sheet with id=AA3, first strand: chain 'AB' and resid 55 through 59 removed outlier: 7.217A pdb=" N ALAAB 64 " --> pdb=" O ASNAB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNAB 10 " --> pdb=" O ALAAB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUAB 66 " --> pdb=" O ILEAB 8 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEUAB 4 " --> pdb=" O VALAB 70 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYRAB 310 " --> pdb=" O ILEAB 8 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASNAB 10 " --> pdb=" O TYRAB 310 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILEAB 312 " --> pdb=" O ASNAB 10 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLUAB 12 " --> pdb=" O ILEAB 312 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N PHEAB 314 " --> pdb=" O GLUAB 12 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRPAB 14 " --> pdb=" O PHEAB 314 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEUAB 130 " --> pdb=" O VALAB 311 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARGAB 313 " --> pdb=" O LEUAB 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AB' and resid 55 through 59 removed outlier: 7.217A pdb=" N ALAAB 64 " --> pdb=" O ASNAB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNAB 10 " --> pdb=" O ALAAB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUAB 66 " --> pdb=" O ILEAB 8 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEUAB 4 " --> pdb=" O VALAB 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AB' and resid 38 through 42 removed outlier: 9.112A pdb=" N LEUAB 279 " --> pdb=" O GLNAB 115 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYRAB 117 " --> pdb=" O LEUAB 279 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLUAB 281 " --> pdb=" O TYRAB 117 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHEAB 119 " --> pdb=" O GLUAB 281 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILEAB 283 " --> pdb=" O PHEAB 119 " (cutoff:3.500A) removed outlier: 16.273A pdb=" N HISAB 190 " --> pdb=" O VALAB 263 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLUAB 265 " --> pdb=" O HISAB 190 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLNAB 262 " --> pdb=" O GLUAB 258 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLUAB 258 " --> pdb=" O GLNAB 262 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYRAB 211 " --> pdb=" O ASPAB 227 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASPAB 227 " --> pdb=" O TYRAB 211 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHEAB 213 " --> pdb=" O ALAAB 225 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALAAB 225 " --> pdb=" O PHEAB 213 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEUAB 215 " --> pdb=" O SERAB 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AB' and resid 150 through 153 removed outlier: 3.806A pdb=" N GLUAB 159 " --> pdb=" O ASPAB 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AB' and resid 197 through 202 Processing sheet with id=AA8, first strand: chain 'AB' and resid 296 through 299 Processing sheet with id=AA9, first strand: chain 'AB' and resid 340 through 344 removed outlier: 6.596A pdb=" N THRAB 347 " --> pdb=" O ILEAB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPAB 321 " --> pdb=" O THRAB 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'AB' and resid 340 through 344 removed outlier: 6.596A pdb=" N THRAB 347 " --> pdb=" O ILEAB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPAB 321 " --> pdb=" O THRAB 350 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ALAAB 318 " --> pdb=" O ALAAB 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILEAB 393 " --> pdb=" O ALAAB 318 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLUAB 383 " --> pdb=" O ALAAB 391 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILEAB 393 " --> pdb=" O GLNAB 381 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLNAB 381 " --> pdb=" O ILEAB 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'AC' and resid 9 through 14 removed outlier: 6.242A pdb=" N GLYAC 9 " --> pdb=" O ILEBC 473 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEUBC 475 " --> pdb=" O GLYAC 9 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYRAC 11 " --> pdb=" O LEUBC 475 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHEBC 477 " --> pdb=" O TYRAC 11 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLUAC 13 " --> pdb=" O PHEBC 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'AC' and resid 57 through 60 removed outlier: 5.012A pdb=" N THRAC 36 " --> pdb=" O VALAC 130 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALAAC 31 " --> pdb=" O VALAC 161 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALAC 193 " --> pdb=" O LEUAC 160 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THRAC 192 " --> pdb=" O ALAAC 230 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYRAC 232 " --> pdb=" O THRAC 192 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N METAC 194 " --> pdb=" O TYRAC 232 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASNAC 351 " --> pdb=" O GLYAC 229 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYSAC 231 " --> pdb=" O ASNAC 351 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILEAC 353 " --> pdb=" O CYSAC 231 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALAAC 233 " --> pdb=" O ILEAC 353 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ALAAC 355 " --> pdb=" O ALAAC 233 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLYAC 360 " --> pdb=" O PHEAC 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'AC' and resid 40 through 41 Processing sheet with id=AB5, first strand: chain 'AC' and resid 93 through 102 removed outlier: 5.483A pdb=" N ILEAC 251 " --> pdb=" O ASPAC 263 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AC' and resid 293 through 295 removed outlier: 4.045A pdb=" N LYSAC 328 " --> pdb=" O GLUAC 237 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'AC' and resid 472 through 477 Processing sheet with id=AB8, first strand: chain 'AD' and resid 11 through 14 removed outlier: 5.922A pdb=" N ARGAD 87 " --> pdb=" O ARGAD 108 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARGAD 108 " --> pdb=" O ARGAD 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALAD 102 " --> pdb=" O LEUAD 93 " (cutoff:3.500A) removed outlier: 16.642A pdb=" N ARGAD 108 " --> pdb=" O GLUBD 36 " (cutoff:3.500A) removed outlier: 12.582A pdb=" N GLUBD 36 " --> pdb=" O ARGAD 108 " (cutoff:3.500A) removed outlier: 12.910A pdb=" N TRPAD 110 " --> pdb=" O VALBD 34 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VALBD 34 " --> pdb=" O TRPAD 110 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THRAD 112 " --> pdb=" O THRBD 32 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASPBD 29 " --> pdb=" O PHEBD 56 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N PHEBD 56 " --> pdb=" O ASPBD 29 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLUBD 31 " --> pdb=" O GLNBD 54 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNBD 54 " --> pdb=" O GLUBD 31 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLUBD 33 " --> pdb=" O GLYBD 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'AD' and resid 138 through 142 removed outlier: 6.329A pdb=" N ALAAD 134 " --> pdb=" O PROAD 111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'AD' and resid 48 through 56 removed outlier: 5.192A pdb=" N GLUAD 33 " --> pdb=" O GLYAD 52 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNAD 54 " --> pdb=" O GLUAD 31 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLUAD 31 " --> pdb=" O GLNAD 54 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N PHEAD 56 " --> pdb=" O ASPAD 29 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASPAD 29 " --> pdb=" O PHEAD 56 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THRFD 112 " --> pdb=" O THRAD 32 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VALAD 34 " --> pdb=" O TRPFD 110 " (cutoff:3.500A) removed outlier: 12.910A pdb=" N TRPFD 110 " --> pdb=" O VALAD 34 " (cutoff:3.500A) removed outlier: 12.582A pdb=" N GLUAD 36 " --> pdb=" O ARGFD 108 " (cutoff:3.500A) removed outlier: 16.642A pdb=" N ARGFD 108 " --> pdb=" O GLUAD 36 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALFD 102 " --> pdb=" O LEUFD 93 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARGFD 108 " --> pdb=" O ARGFD 87 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARGFD 87 " --> pdb=" O ARGFD 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'ED' and resid 119 through 120 removed outlier: 6.329A pdb=" N ALAFD 134 " --> pdb=" O PROFD 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'AD' and resid 119 through 120 removed outlier: 6.329A pdb=" N ALABD 134 " --> pdb=" O PROBD 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'BD' and resid 11 through 14 removed outlier: 5.922A pdb=" N ARGBD 87 " --> pdb=" O ARGBD 108 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARGBD 108 " --> pdb=" O ARGBD 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALBD 102 " --> pdb=" O LEUBD 93 " (cutoff:3.500A) removed outlier: 16.643A pdb=" N ARGBD 108 " --> pdb=" O GLUCD 36 " (cutoff:3.500A) removed outlier: 12.582A pdb=" N GLUCD 36 " --> pdb=" O ARGBD 108 " (cutoff:3.500A) removed outlier: 12.909A pdb=" N TRPBD 110 " --> pdb=" O VALCD 34 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VALCD 34 " --> pdb=" O TRPBD 110 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THRBD 112 " --> pdb=" O THRCD 32 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASPCD 29 " --> pdb=" O PHECD 56 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N PHECD 56 " --> pdb=" O ASPCD 29 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLUCD 31 " --> pdb=" O GLNCD 54 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNCD 54 " --> pdb=" O GLUCD 31 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLUCD 33 " --> pdb=" O GLYCD 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'AE' and resid 11 through 14 removed outlier: 6.131A pdb=" N ARGAE 87 " --> pdb=" O ARGAE 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGAE 108 " --> pdb=" O ARGAE 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALAE 102 " --> pdb=" O LEUAE 93 " (cutoff:3.500A) removed outlier: 16.446A pdb=" N ARGAE 108 " --> pdb=" O GLUBE 36 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N GLUBE 36 " --> pdb=" O ARGAE 108 " (cutoff:3.500A) removed outlier: 12.848A pdb=" N TRPAE 110 " --> pdb=" O VALBE 34 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N VALBE 34 " --> pdb=" O TRPAE 110 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THRAE 112 " --> pdb=" O THRBE 32 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VALAE 114 " --> pdb=" O VALBE 30 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASPBE 29 " --> pdb=" O PHEBE 56 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHEBE 56 " --> pdb=" O ASPBE 29 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLUBE 31 " --> pdb=" O GLNBE 54 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNBE 54 " --> pdb=" O GLUBE 31 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLUBE 33 " --> pdb=" O GLYBE 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'AE' and resid 138 through 142 removed outlier: 6.329A pdb=" N ALAAE 134 " --> pdb=" O PROAE 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'AE' and resid 48 through 56 removed outlier: 5.264A pdb=" N GLUAE 33 " --> pdb=" O GLYAE 52 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNAE 54 " --> pdb=" O GLUAE 31 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLUAE 31 " --> pdb=" O GLNAE 54 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHEAE 56 " --> pdb=" O ASPAE 29 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASPAE 29 " --> pdb=" O PHEAE 56 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VALFE 114 " --> pdb=" O VALAE 30 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THRFE 112 " --> pdb=" O THRAE 32 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N VALAE 34 " --> pdb=" O TRPFE 110 " (cutoff:3.500A) removed outlier: 12.848A pdb=" N TRPFE 110 " --> pdb=" O VALAE 34 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N GLUAE 36 " --> pdb=" O ARGFE 108 " (cutoff:3.500A) removed outlier: 16.446A pdb=" N ARGFE 108 " --> pdb=" O GLUAE 36 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VALFE 102 " --> pdb=" O LEUFE 93 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGFE 108 " --> pdb=" O ARGFE 87 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARGFE 87 " --> pdb=" O ARGFE 108 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'EE' and resid 119 through 120 removed outlier: 6.329A pdb=" N ALAFE 134 " --> pdb=" O PROFE 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'AE' and resid 119 through 120 removed outlier: 6.328A pdb=" N ALABE 134 " --> pdb=" O PROBE 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'BE' and resid 11 through 14 removed outlier: 6.131A pdb=" N ARGBE 87 " --> pdb=" O ARGBE 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGBE 108 " --> pdb=" O ARGBE 87 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VALBE 102 " --> pdb=" O LEUBE 93 " (cutoff:3.500A) removed outlier: 16.445A pdb=" N ARGBE 108 " --> pdb=" O GLUCE 36 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N GLUCE 36 " --> pdb=" O ARGBE 108 " (cutoff:3.500A) removed outlier: 12.847A pdb=" N TRPBE 110 " --> pdb=" O VALCE 34 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N VALCE 34 " --> pdb=" O TRPBE 110 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THRBE 112 " --> pdb=" O THRCE 32 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VALBE 114 " --> pdb=" O VALCE 30 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASPCE 29 " --> pdb=" O PHECE 56 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHECE 56 " --> pdb=" O ASPCE 29 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLUCE 31 " --> pdb=" O GLNCE 54 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLNCE 54 " --> pdb=" O GLUCE 31 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLUCE 33 " --> pdb=" O GLYCE 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'BA' and resid 30 through 32 removed outlier: 5.521A pdb=" N VALBA 52 " --> pdb=" O LEUBA 96 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEUBA 96 " --> pdb=" O VALBA 52 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N METBA 54 " --> pdb=" O SERBA 94 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SERBA 94 " --> pdb=" O METBA 54 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEUBA 56 " --> pdb=" O LEUBA 92 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEUBA 92 " --> pdb=" O LEUBA 56 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASNBA 58 " --> pdb=" O PHEBA 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHEBA 90 " --> pdb=" O ASNBA 58 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VALBA 85 " --> pdb=" O SERBA 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SERBA 172 " --> pdb=" O VALBA 85 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEUBA 87 " --> pdb=" O ILEBA 170 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILEBA 170 " --> pdb=" O LEUBA 87 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEUBA 165 " --> pdb=" O TYRBA 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'BA' and resid 71 through 74 Processing sheet with id=AD4, first strand: chain 'BB' and resid 55 through 59 removed outlier: 7.216A pdb=" N ALABB 64 " --> pdb=" O ASNBB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNBB 10 " --> pdb=" O ALABB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUBB 66 " --> pdb=" O ILEBB 8 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEUBB 4 " --> pdb=" O VALBB 70 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYRBB 310 " --> pdb=" O ILEBB 8 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASNBB 10 " --> pdb=" O TYRBB 310 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILEBB 312 " --> pdb=" O ASNBB 10 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLUBB 12 " --> pdb=" O ILEBB 312 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHEBB 314 " --> pdb=" O GLUBB 12 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRPBB 14 " --> pdb=" O PHEBB 314 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEUBB 130 " --> pdb=" O VALBB 311 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARGBB 313 " --> pdb=" O LEUBB 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'BB' and resid 55 through 59 removed outlier: 7.216A pdb=" N ALABB 64 " --> pdb=" O ASNBB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNBB 10 " --> pdb=" O ALABB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUBB 66 " --> pdb=" O ILEBB 8 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEUBB 4 " --> pdb=" O VALBB 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'BB' and resid 38 through 42 removed outlier: 9.112A pdb=" N LEUBB 279 " --> pdb=" O GLNBB 115 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYRBB 117 " --> pdb=" O LEUBB 279 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLUBB 281 " --> pdb=" O TYRBB 117 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHEBB 119 " --> pdb=" O GLUBB 281 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILEBB 283 " --> pdb=" O PHEBB 119 " (cutoff:3.500A) removed outlier: 16.273A pdb=" N HISBB 190 " --> pdb=" O VALBB 263 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLUBB 265 " --> pdb=" O HISBB 190 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLNBB 262 " --> pdb=" O GLUBB 258 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLUBB 258 " --> pdb=" O GLNBB 262 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYRBB 211 " --> pdb=" O ASPBB 227 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPBB 227 " --> pdb=" O TYRBB 211 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHEBB 213 " --> pdb=" O ALABB 225 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALABB 225 " --> pdb=" O PHEBB 213 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEUBB 215 " --> pdb=" O SERBB 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'BB' and resid 150 through 153 removed outlier: 3.806A pdb=" N GLUBB 159 " --> pdb=" O ASPBB 177 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'BB' and resid 197 through 202 Processing sheet with id=AD9, first strand: chain 'BB' and resid 296 through 299 Processing sheet with id=AE1, first strand: chain 'BB' and resid 340 through 344 removed outlier: 6.596A pdb=" N THRBB 347 " --> pdb=" O ILEBB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPBB 321 " --> pdb=" O THRBB 350 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'BB' and resid 340 through 344 removed outlier: 6.596A pdb=" N THRBB 347 " --> pdb=" O ILEBB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPBB 321 " --> pdb=" O THRBB 350 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N ALABB 318 " --> pdb=" O ALABB 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILEBB 393 " --> pdb=" O ALABB 318 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLUBB 383 " --> pdb=" O ALABB 391 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILEBB 393 " --> pdb=" O GLNBB 381 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLNBB 381 " --> pdb=" O ILEBB 393 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'BC' and resid 9 through 14 removed outlier: 6.242A pdb=" N GLYBC 9 " --> pdb=" O ILECC 473 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEUCC 475 " --> pdb=" O GLYBC 9 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYRBC 11 " --> pdb=" O LEUCC 475 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHECC 477 " --> pdb=" O TYRBC 11 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLUBC 13 " --> pdb=" O PHECC 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'BC' and resid 57 through 60 removed outlier: 5.012A pdb=" N THRBC 36 " --> pdb=" O VALBC 130 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALABC 31 " --> pdb=" O VALBC 161 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALBC 193 " --> pdb=" O LEUBC 160 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THRBC 192 " --> pdb=" O ALABC 230 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYRBC 232 " --> pdb=" O THRBC 192 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N METBC 194 " --> pdb=" O TYRBC 232 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASNBC 351 " --> pdb=" O GLYBC 229 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYSBC 231 " --> pdb=" O ASNBC 351 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILEBC 353 " --> pdb=" O CYSBC 231 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALABC 233 " --> pdb=" O ILEBC 353 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ALABC 355 " --> pdb=" O ALABC 233 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLYBC 360 " --> pdb=" O PHEBC 356 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'BC' and resid 40 through 41 Processing sheet with id=AE6, first strand: chain 'BC' and resid 93 through 102 removed outlier: 5.484A pdb=" N ILEBC 251 " --> pdb=" O ASPBC 263 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'BC' and resid 293 through 295 removed outlier: 4.045A pdb=" N LYSBC 328 " --> pdb=" O GLUBC 237 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'BD' and resid 119 through 120 removed outlier: 6.329A pdb=" N ALACD 134 " --> pdb=" O PROCD 111 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'CD' and resid 11 through 14 removed outlier: 5.922A pdb=" N ARGCD 87 " --> pdb=" O ARGCD 108 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARGCD 108 " --> pdb=" O ARGCD 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALCD 102 " --> pdb=" O LEUCD 93 " (cutoff:3.500A) removed outlier: 16.642A pdb=" N ARGCD 108 " --> pdb=" O GLUDD 36 " (cutoff:3.500A) removed outlier: 12.582A pdb=" N GLUDD 36 " --> pdb=" O ARGCD 108 " (cutoff:3.500A) removed outlier: 12.910A pdb=" N TRPCD 110 " --> pdb=" O VALDD 34 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VALDD 34 " --> pdb=" O TRPCD 110 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THRCD 112 " --> pdb=" O THRDD 32 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASPDD 29 " --> pdb=" O PHEDD 56 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N PHEDD 56 " --> pdb=" O ASPDD 29 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLUDD 31 " --> pdb=" O GLNDD 54 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNDD 54 " --> pdb=" O GLUDD 31 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLUDD 33 " --> pdb=" O GLYDD 52 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'BE' and resid 119 through 120 removed outlier: 6.329A pdb=" N ALACE 134 " --> pdb=" O PROCE 111 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'CE' and resid 11 through 14 removed outlier: 6.130A pdb=" N ARGCE 87 " --> pdb=" O ARGCE 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGCE 108 " --> pdb=" O ARGCE 87 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VALCE 102 " --> pdb=" O LEUCE 93 " (cutoff:3.500A) removed outlier: 16.446A pdb=" N ARGCE 108 " --> pdb=" O GLUDE 36 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N GLUDE 36 " --> pdb=" O ARGCE 108 " (cutoff:3.500A) removed outlier: 12.847A pdb=" N TRPCE 110 " --> pdb=" O VALDE 34 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N VALDE 34 " --> pdb=" O TRPCE 110 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THRCE 112 " --> pdb=" O THRDE 32 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VALCE 114 " --> pdb=" O VALDE 30 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASPDE 29 " --> pdb=" O PHEDE 56 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHEDE 56 " --> pdb=" O ASPDE 29 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLUDE 31 " --> pdb=" O GLNDE 54 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNDE 54 " --> pdb=" O GLUDE 31 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLUDE 33 " --> pdb=" O GLYDE 52 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'CA' and resid 30 through 32 removed outlier: 5.520A pdb=" N VALCA 52 " --> pdb=" O LEUCA 96 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEUCA 96 " --> pdb=" O VALCA 52 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N METCA 54 " --> pdb=" O SERCA 94 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SERCA 94 " --> pdb=" O METCA 54 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEUCA 56 " --> pdb=" O LEUCA 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEUCA 92 " --> pdb=" O LEUCA 56 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASNCA 58 " --> pdb=" O PHECA 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHECA 90 " --> pdb=" O ASNCA 58 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VALCA 85 " --> pdb=" O SERCA 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SERCA 172 " --> pdb=" O VALCA 85 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEUCA 87 " --> pdb=" O ILECA 170 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILECA 170 " --> pdb=" O LEUCA 87 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEUCA 165 " --> pdb=" O TYRCA 142 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'CA' and resid 71 through 74 Processing sheet with id=AF5, first strand: chain 'CB' and resid 55 through 59 removed outlier: 7.217A pdb=" N ALACB 64 " --> pdb=" O ASNCB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNCB 10 " --> pdb=" O ALACB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUCB 66 " --> pdb=" O ILECB 8 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEUCB 4 " --> pdb=" O VALCB 70 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYRCB 310 " --> pdb=" O ILECB 8 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASNCB 10 " --> pdb=" O TYRCB 310 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILECB 312 " --> pdb=" O ASNCB 10 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLUCB 12 " --> pdb=" O ILECB 312 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N PHECB 314 " --> pdb=" O GLUCB 12 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRPCB 14 " --> pdb=" O PHECB 314 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEUCB 130 " --> pdb=" O VALCB 311 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARGCB 313 " --> pdb=" O LEUCB 130 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'CB' and resid 55 through 59 removed outlier: 7.217A pdb=" N ALACB 64 " --> pdb=" O ASNCB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNCB 10 " --> pdb=" O ALACB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUCB 66 " --> pdb=" O ILECB 8 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEUCB 4 " --> pdb=" O VALCB 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'CB' and resid 38 through 42 removed outlier: 9.112A pdb=" N LEUCB 279 " --> pdb=" O GLNCB 115 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYRCB 117 " --> pdb=" O LEUCB 279 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLUCB 281 " --> pdb=" O TYRCB 117 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHECB 119 " --> pdb=" O GLUCB 281 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILECB 283 " --> pdb=" O PHECB 119 " (cutoff:3.500A) removed outlier: 16.273A pdb=" N HISCB 190 " --> pdb=" O VALCB 263 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLUCB 265 " --> pdb=" O HISCB 190 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLNCB 262 " --> pdb=" O GLUCB 258 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLUCB 258 " --> pdb=" O GLNCB 262 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYRCB 211 " --> pdb=" O ASPCB 227 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPCB 227 " --> pdb=" O TYRCB 211 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHECB 213 " --> pdb=" O ALACB 225 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALACB 225 " --> pdb=" O PHECB 213 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEUCB 215 " --> pdb=" O SERCB 223 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'CB' and resid 150 through 153 removed outlier: 3.806A pdb=" N GLUCB 159 " --> pdb=" O ASPCB 177 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'CB' and resid 197 through 202 Processing sheet with id=AG1, first strand: chain 'CB' and resid 296 through 299 Processing sheet with id=AG2, first strand: chain 'CB' and resid 340 through 344 removed outlier: 6.596A pdb=" N THRCB 347 " --> pdb=" O ILECB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPCB 321 " --> pdb=" O THRCB 350 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'CB' and resid 340 through 344 removed outlier: 6.596A pdb=" N THRCB 347 " --> pdb=" O ILECB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPCB 321 " --> pdb=" O THRCB 350 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ALACB 318 " --> pdb=" O ALACB 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILECB 393 " --> pdb=" O ALACB 318 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLUCB 383 " --> pdb=" O ALACB 391 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILECB 393 " --> pdb=" O GLNCB 381 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLNCB 381 " --> pdb=" O ILECB 393 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'CC' and resid 9 through 14 removed outlier: 6.242A pdb=" N GLYCC 9 " --> pdb=" O ILEDC 473 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEUDC 475 " --> pdb=" O GLYCC 9 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYRCC 11 " --> pdb=" O LEUDC 475 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHEDC 477 " --> pdb=" O TYRCC 11 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLUCC 13 " --> pdb=" O PHEDC 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'CC' and resid 57 through 60 removed outlier: 5.012A pdb=" N THRCC 36 " --> pdb=" O VALCC 130 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALACC 31 " --> pdb=" O VALCC 161 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALCC 193 " --> pdb=" O LEUCC 160 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THRCC 192 " --> pdb=" O ALACC 230 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYRCC 232 " --> pdb=" O THRCC 192 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N METCC 194 " --> pdb=" O TYRCC 232 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASNCC 351 " --> pdb=" O GLYCC 229 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYSCC 231 " --> pdb=" O ASNCC 351 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILECC 353 " --> pdb=" O CYSCC 231 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALACC 233 " --> pdb=" O ILECC 353 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ALACC 355 " --> pdb=" O ALACC 233 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLYCC 360 " --> pdb=" O PHECC 356 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'CC' and resid 40 through 41 Processing sheet with id=AG7, first strand: chain 'CC' and resid 93 through 102 removed outlier: 5.484A pdb=" N ILECC 251 " --> pdb=" O ASPCC 263 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'CC' and resid 293 through 295 removed outlier: 4.044A pdb=" N LYSCC 328 " --> pdb=" O GLUCC 237 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'CD' and resid 119 through 120 removed outlier: 6.329A pdb=" N ALADD 134 " --> pdb=" O PRODD 111 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'DD' and resid 11 through 14 removed outlier: 5.922A pdb=" N ARGDD 87 " --> pdb=" O ARGDD 108 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARGDD 108 " --> pdb=" O ARGDD 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALDD 102 " --> pdb=" O LEUDD 93 " (cutoff:3.500A) removed outlier: 16.642A pdb=" N ARGDD 108 " --> pdb=" O GLUED 36 " (cutoff:3.500A) removed outlier: 12.582A pdb=" N GLUED 36 " --> pdb=" O ARGDD 108 " (cutoff:3.500A) removed outlier: 12.910A pdb=" N TRPDD 110 " --> pdb=" O VALED 34 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VALED 34 " --> pdb=" O TRPDD 110 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THRDD 112 " --> pdb=" O THRED 32 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASPED 29 " --> pdb=" O PHEED 56 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N PHEED 56 " --> pdb=" O ASPED 29 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLUED 31 " --> pdb=" O GLNED 54 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLNED 54 " --> pdb=" O GLUED 31 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLUED 33 " --> pdb=" O GLYED 52 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'CE' and resid 119 through 120 removed outlier: 6.329A pdb=" N ALADE 134 " --> pdb=" O PRODE 111 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'DE' and resid 11 through 14 removed outlier: 6.131A pdb=" N ARGDE 87 " --> pdb=" O ARGDE 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGDE 108 " --> pdb=" O ARGDE 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALDE 102 " --> pdb=" O LEUDE 93 " (cutoff:3.500A) removed outlier: 16.446A pdb=" N ARGDE 108 " --> pdb=" O GLUEE 36 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N GLUEE 36 " --> pdb=" O ARGDE 108 " (cutoff:3.500A) removed outlier: 12.848A pdb=" N TRPDE 110 " --> pdb=" O VALEE 34 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N VALEE 34 " --> pdb=" O TRPDE 110 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THRDE 112 " --> pdb=" O THREE 32 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VALDE 114 " --> pdb=" O VALEE 30 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASPEE 29 " --> pdb=" O PHEEE 56 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHEEE 56 " --> pdb=" O ASPEE 29 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLUEE 31 " --> pdb=" O GLNEE 54 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNEE 54 " --> pdb=" O GLUEE 31 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLUEE 33 " --> pdb=" O GLYEE 52 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'DA' and resid 30 through 32 removed outlier: 5.521A pdb=" N VALDA 52 " --> pdb=" O LEUDA 96 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEUDA 96 " --> pdb=" O VALDA 52 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N METDA 54 " --> pdb=" O SERDA 94 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SERDA 94 " --> pdb=" O METDA 54 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEUDA 56 " --> pdb=" O LEUDA 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEUDA 92 " --> pdb=" O LEUDA 56 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASNDA 58 " --> pdb=" O PHEDA 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHEDA 90 " --> pdb=" O ASNDA 58 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VALDA 85 " --> pdb=" O SERDA 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SERDA 172 " --> pdb=" O VALDA 85 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEUDA 87 " --> pdb=" O ILEDA 170 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILEDA 170 " --> pdb=" O LEUDA 87 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEUDA 165 " --> pdb=" O TYRDA 142 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'DA' and resid 71 through 74 Processing sheet with id=AH6, first strand: chain 'DB' and resid 55 through 59 removed outlier: 7.217A pdb=" N ALADB 64 " --> pdb=" O ASNDB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNDB 10 " --> pdb=" O ALADB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUDB 66 " --> pdb=" O ILEDB 8 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEUDB 4 " --> pdb=" O VALDB 70 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYRDB 310 " --> pdb=" O ILEDB 8 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASNDB 10 " --> pdb=" O TYRDB 310 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILEDB 312 " --> pdb=" O ASNDB 10 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLUDB 12 " --> pdb=" O ILEDB 312 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N PHEDB 314 " --> pdb=" O GLUDB 12 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRPDB 14 " --> pdb=" O PHEDB 314 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEUDB 130 " --> pdb=" O VALDB 311 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARGDB 313 " --> pdb=" O LEUDB 130 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'DB' and resid 55 through 59 removed outlier: 7.217A pdb=" N ALADB 64 " --> pdb=" O ASNDB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNDB 10 " --> pdb=" O ALADB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUDB 66 " --> pdb=" O ILEDB 8 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEUDB 4 " --> pdb=" O VALDB 70 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'DB' and resid 38 through 42 removed outlier: 9.112A pdb=" N LEUDB 279 " --> pdb=" O GLNDB 115 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYRDB 117 " --> pdb=" O LEUDB 279 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLUDB 281 " --> pdb=" O TYRDB 117 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHEDB 119 " --> pdb=" O GLUDB 281 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILEDB 283 " --> pdb=" O PHEDB 119 " (cutoff:3.500A) removed outlier: 16.273A pdb=" N HISDB 190 " --> pdb=" O VALDB 263 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N GLUDB 265 " --> pdb=" O HISDB 190 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLNDB 262 " --> pdb=" O GLUDB 258 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLUDB 258 " --> pdb=" O GLNDB 262 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYRDB 211 " --> pdb=" O ASPDB 227 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASPDB 227 " --> pdb=" O TYRDB 211 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHEDB 213 " --> pdb=" O ALADB 225 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALADB 225 " --> pdb=" O PHEDB 213 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEUDB 215 " --> pdb=" O SERDB 223 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'DB' and resid 150 through 153 removed outlier: 3.806A pdb=" N GLUDB 159 " --> pdb=" O ASPDB 177 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'DB' and resid 197 through 202 Processing sheet with id=AI2, first strand: chain 'DB' and resid 296 through 299 Processing sheet with id=AI3, first strand: chain 'DB' and resid 340 through 344 removed outlier: 6.596A pdb=" N THRDB 347 " --> pdb=" O ILEDB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPDB 321 " --> pdb=" O THRDB 350 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'DB' and resid 340 through 344 removed outlier: 6.596A pdb=" N THRDB 347 " --> pdb=" O ILEDB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPDB 321 " --> pdb=" O THRDB 350 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ALADB 318 " --> pdb=" O ALADB 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILEDB 393 " --> pdb=" O ALADB 318 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLUDB 383 " --> pdb=" O ALADB 391 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILEDB 393 " --> pdb=" O GLNDB 381 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLNDB 381 " --> pdb=" O ILEDB 393 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'DC' and resid 9 through 14 removed outlier: 6.242A pdb=" N GLYDC 9 " --> pdb=" O ILEEC 473 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEUEC 475 " --> pdb=" O GLYDC 9 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYRDC 11 " --> pdb=" O LEUEC 475 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHEEC 477 " --> pdb=" O TYRDC 11 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLUDC 13 " --> pdb=" O PHEEC 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'DC' and resid 57 through 60 removed outlier: 5.012A pdb=" N THRDC 36 " --> pdb=" O VALDC 130 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALADC 31 " --> pdb=" O VALDC 161 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALDC 193 " --> pdb=" O LEUDC 160 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THRDC 192 " --> pdb=" O ALADC 230 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYRDC 232 " --> pdb=" O THRDC 192 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N METDC 194 " --> pdb=" O TYRDC 232 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASNDC 351 " --> pdb=" O GLYDC 229 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYSDC 231 " --> pdb=" O ASNDC 351 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILEDC 353 " --> pdb=" O CYSDC 231 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALADC 233 " --> pdb=" O ILEDC 353 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ALADC 355 " --> pdb=" O ALADC 233 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLYDC 360 " --> pdb=" O PHEDC 356 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'DC' and resid 40 through 41 Processing sheet with id=AI8, first strand: chain 'DC' and resid 93 through 102 removed outlier: 5.483A pdb=" N ILEDC 251 " --> pdb=" O ASPDC 263 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'DC' and resid 293 through 295 removed outlier: 4.045A pdb=" N LYSDC 328 " --> pdb=" O GLUDC 237 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'DD' and resid 119 through 120 removed outlier: 6.329A pdb=" N ALAED 134 " --> pdb=" O PROED 111 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'ED' and resid 11 through 14 removed outlier: 5.922A pdb=" N ARGED 87 " --> pdb=" O ARGED 108 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARGED 108 " --> pdb=" O ARGED 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALED 102 " --> pdb=" O LEUED 93 " (cutoff:3.500A) removed outlier: 16.643A pdb=" N ARGED 108 " --> pdb=" O GLUFD 36 " (cutoff:3.500A) removed outlier: 12.582A pdb=" N GLUFD 36 " --> pdb=" O ARGED 108 " (cutoff:3.500A) removed outlier: 12.909A pdb=" N TRPED 110 " --> pdb=" O VALFD 34 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N VALFD 34 " --> pdb=" O TRPED 110 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THRED 112 " --> pdb=" O THRFD 32 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASPFD 29 " --> pdb=" O PHEFD 56 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N PHEFD 56 " --> pdb=" O ASPFD 29 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLUFD 31 " --> pdb=" O GLNFD 54 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNFD 54 " --> pdb=" O GLUFD 31 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLUFD 33 " --> pdb=" O GLYFD 52 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'DE' and resid 119 through 120 removed outlier: 6.328A pdb=" N ALAEE 134 " --> pdb=" O PROEE 111 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'EE' and resid 11 through 14 removed outlier: 6.131A pdb=" N ARGEE 87 " --> pdb=" O ARGEE 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGEE 108 " --> pdb=" O ARGEE 87 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VALEE 102 " --> pdb=" O LEUEE 93 " (cutoff:3.500A) removed outlier: 16.445A pdb=" N ARGEE 108 " --> pdb=" O GLUFE 36 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N GLUFE 36 " --> pdb=" O ARGEE 108 " (cutoff:3.500A) removed outlier: 12.847A pdb=" N TRPEE 110 " --> pdb=" O VALFE 34 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N VALFE 34 " --> pdb=" O TRPEE 110 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THREE 112 " --> pdb=" O THRFE 32 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VALEE 114 " --> pdb=" O VALFE 30 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASPFE 29 " --> pdb=" O PHEFE 56 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N PHEFE 56 " --> pdb=" O ASPFE 29 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLUFE 31 " --> pdb=" O GLNFE 54 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLNFE 54 " --> pdb=" O GLUFE 31 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLUFE 33 " --> pdb=" O GLYFE 52 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'EA' and resid 30 through 32 removed outlier: 5.521A pdb=" N VALEA 52 " --> pdb=" O LEUEA 96 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEUEA 96 " --> pdb=" O VALEA 52 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N METEA 54 " --> pdb=" O SEREA 94 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SEREA 94 " --> pdb=" O METEA 54 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEUEA 56 " --> pdb=" O LEUEA 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEUEA 92 " --> pdb=" O LEUEA 56 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASNEA 58 " --> pdb=" O PHEEA 90 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHEEA 90 " --> pdb=" O ASNEA 58 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VALEA 85 " --> pdb=" O SEREA 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SEREA 172 " --> pdb=" O VALEA 85 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEUEA 87 " --> pdb=" O ILEEA 170 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILEEA 170 " --> pdb=" O LEUEA 87 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEUEA 165 " --> pdb=" O TYREA 142 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'EA' and resid 71 through 74 Processing sheet with id=AJ7, first strand: chain 'EB' and resid 55 through 59 removed outlier: 7.216A pdb=" N ALAEB 64 " --> pdb=" O ASNEB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNEB 10 " --> pdb=" O ALAEB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUEB 66 " --> pdb=" O ILEEB 8 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEUEB 4 " --> pdb=" O VALEB 70 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYREB 310 " --> pdb=" O ILEEB 8 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASNEB 10 " --> pdb=" O TYREB 310 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILEEB 312 " --> pdb=" O ASNEB 10 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLUEB 12 " --> pdb=" O ILEEB 312 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHEEB 314 " --> pdb=" O GLUEB 12 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRPEB 14 " --> pdb=" O PHEEB 314 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEUEB 130 " --> pdb=" O VALEB 311 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARGEB 313 " --> pdb=" O LEUEB 130 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'EB' and resid 55 through 59 removed outlier: 7.216A pdb=" N ALAEB 64 " --> pdb=" O ASNEB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNEB 10 " --> pdb=" O ALAEB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUEB 66 " --> pdb=" O ILEEB 8 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEUEB 4 " --> pdb=" O VALEB 70 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'EB' and resid 38 through 42 removed outlier: 9.112A pdb=" N LEUEB 279 " --> pdb=" O GLNEB 115 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYREB 117 " --> pdb=" O LEUEB 279 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLUEB 281 " --> pdb=" O TYREB 117 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHEEB 119 " --> pdb=" O GLUEB 281 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ILEEB 283 " --> pdb=" O PHEEB 119 " (cutoff:3.500A) removed outlier: 16.273A pdb=" N HISEB 190 " --> pdb=" O VALEB 263 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N GLUEB 265 " --> pdb=" O HISEB 190 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLNEB 262 " --> pdb=" O GLUEB 258 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLUEB 258 " --> pdb=" O GLNEB 262 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYREB 211 " --> pdb=" O ASPEB 227 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPEB 227 " --> pdb=" O TYREB 211 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHEEB 213 " --> pdb=" O ALAEB 225 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALAEB 225 " --> pdb=" O PHEEB 213 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEUEB 215 " --> pdb=" O SEREB 223 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'EB' and resid 150 through 153 removed outlier: 3.806A pdb=" N GLUEB 159 " --> pdb=" O ASPEB 177 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'EB' and resid 197 through 202 Processing sheet with id=AK3, first strand: chain 'EB' and resid 296 through 299 Processing sheet with id=AK4, first strand: chain 'EB' and resid 340 through 344 removed outlier: 6.595A pdb=" N THREB 347 " --> pdb=" O ILEEB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPEB 321 " --> pdb=" O THREB 350 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'EB' and resid 340 through 344 removed outlier: 6.595A pdb=" N THREB 347 " --> pdb=" O ILEEB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPEB 321 " --> pdb=" O THREB 350 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ALAEB 318 " --> pdb=" O ALAEB 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILEEB 393 " --> pdb=" O ALAEB 318 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLUEB 383 " --> pdb=" O ALAEB 391 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILEEB 393 " --> pdb=" O GLNEB 381 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLNEB 381 " --> pdb=" O ILEEB 393 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'EC' and resid 9 through 14 removed outlier: 6.242A pdb=" N GLYEC 9 " --> pdb=" O ILEFC 473 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEUFC 475 " --> pdb=" O GLYEC 9 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TYREC 11 " --> pdb=" O LEUFC 475 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHEFC 477 " --> pdb=" O TYREC 11 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLUEC 13 " --> pdb=" O PHEFC 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK6 Processing sheet with id=AK7, first strand: chain 'EC' and resid 57 through 60 removed outlier: 5.012A pdb=" N THREC 36 " --> pdb=" O VALEC 130 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALAEC 31 " --> pdb=" O VALEC 161 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALEC 193 " --> pdb=" O LEUEC 160 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THREC 192 " --> pdb=" O ALAEC 230 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYREC 232 " --> pdb=" O THREC 192 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N METEC 194 " --> pdb=" O TYREC 232 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASNEC 351 " --> pdb=" O GLYEC 229 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYSEC 231 " --> pdb=" O ASNEC 351 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILEEC 353 " --> pdb=" O CYSEC 231 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALAEC 233 " --> pdb=" O ILEEC 353 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ALAEC 355 " --> pdb=" O ALAEC 233 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLYEC 360 " --> pdb=" O PHEEC 356 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'EC' and resid 40 through 41 Processing sheet with id=AK9, first strand: chain 'EC' and resid 93 through 102 removed outlier: 5.484A pdb=" N ILEEC 251 " --> pdb=" O ASPEC 263 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'EC' and resid 293 through 295 removed outlier: 4.046A pdb=" N LYSEC 328 " --> pdb=" O GLUEC 237 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'FA' and resid 30 through 32 removed outlier: 5.520A pdb=" N VALFA 52 " --> pdb=" O LEUFA 96 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEUFA 96 " --> pdb=" O VALFA 52 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N METFA 54 " --> pdb=" O SERFA 94 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SERFA 94 " --> pdb=" O METFA 54 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEUFA 56 " --> pdb=" O LEUFA 92 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEUFA 92 " --> pdb=" O LEUFA 56 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASNFA 58 " --> pdb=" O PHEFA 90 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHEFA 90 " --> pdb=" O ASNFA 58 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VALFA 85 " --> pdb=" O SERFA 172 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SERFA 172 " --> pdb=" O VALFA 85 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEUFA 87 " --> pdb=" O ILEFA 170 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILEFA 170 " --> pdb=" O LEUFA 87 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEUFA 165 " --> pdb=" O TYRFA 142 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'FA' and resid 71 through 74 Processing sheet with id=AL4, first strand: chain 'FB' and resid 55 through 59 removed outlier: 7.217A pdb=" N ALAFB 64 " --> pdb=" O ASNFB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNFB 10 " --> pdb=" O ALAFB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUFB 66 " --> pdb=" O ILEFB 8 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEUFB 4 " --> pdb=" O VALFB 70 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N TYRFB 310 " --> pdb=" O ILEFB 8 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASNFB 10 " --> pdb=" O TYRFB 310 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILEFB 312 " --> pdb=" O ASNFB 10 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLUFB 12 " --> pdb=" O ILEFB 312 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N PHEFB 314 " --> pdb=" O GLUFB 12 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRPFB 14 " --> pdb=" O PHEFB 314 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEUFB 130 " --> pdb=" O VALFB 311 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARGFB 313 " --> pdb=" O LEUFB 130 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'FB' and resid 55 through 59 removed outlier: 7.217A pdb=" N ALAFB 64 " --> pdb=" O ASNFB 10 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASNFB 10 " --> pdb=" O ALAFB 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEUFB 66 " --> pdb=" O ILEFB 8 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEUFB 4 " --> pdb=" O VALFB 70 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'FB' and resid 38 through 42 removed outlier: 9.112A pdb=" N LEUFB 279 " --> pdb=" O GLNFB 115 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYRFB 117 " --> pdb=" O LEUFB 279 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLUFB 281 " --> pdb=" O TYRFB 117 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHEFB 119 " --> pdb=" O GLUFB 281 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ILEFB 283 " --> pdb=" O PHEFB 119 " (cutoff:3.500A) removed outlier: 16.273A pdb=" N HISFB 190 " --> pdb=" O VALFB 263 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N GLUFB 265 " --> pdb=" O HISFB 190 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLNFB 262 " --> pdb=" O GLUFB 258 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLUFB 258 " --> pdb=" O GLNFB 262 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYRFB 211 " --> pdb=" O ASPFB 227 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPFB 227 " --> pdb=" O TYRFB 211 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHEFB 213 " --> pdb=" O ALAFB 225 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALAFB 225 " --> pdb=" O PHEFB 213 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEUFB 215 " --> pdb=" O SERFB 223 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'FB' and resid 150 through 153 removed outlier: 3.806A pdb=" N GLUFB 159 " --> pdb=" O ASPFB 177 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'FB' and resid 197 through 202 Processing sheet with id=AL9, first strand: chain 'FB' and resid 296 through 299 Processing sheet with id=AM1, first strand: chain 'FB' and resid 340 through 344 removed outlier: 6.595A pdb=" N THRFB 347 " --> pdb=" O ILEFB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPFB 321 " --> pdb=" O THRFB 350 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'FB' and resid 340 through 344 removed outlier: 6.595A pdb=" N THRFB 347 " --> pdb=" O ILEFB 343 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TRPFB 321 " --> pdb=" O THRFB 350 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N ALAFB 318 " --> pdb=" O ALAFB 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILEFB 393 " --> pdb=" O ALAFB 318 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLUFB 383 " --> pdb=" O ALAFB 391 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILEFB 393 " --> pdb=" O GLNFB 381 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLNFB 381 " --> pdb=" O ILEFB 393 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'FC' and resid 57 through 60 removed outlier: 5.012A pdb=" N THRFC 36 " --> pdb=" O VALFC 130 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALAFC 31 " --> pdb=" O VALFC 161 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VALFC 193 " --> pdb=" O LEUFC 160 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THRFC 192 " --> pdb=" O ALAFC 230 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYRFC 232 " --> pdb=" O THRFC 192 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N METFC 194 " --> pdb=" O TYRFC 232 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASNFC 351 " --> pdb=" O GLYFC 229 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYSFC 231 " --> pdb=" O ASNFC 351 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILEFC 353 " --> pdb=" O CYSFC 231 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALAFC 233 " --> pdb=" O ILEFC 353 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ALAFC 355 " --> pdb=" O ALAFC 233 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLYFC 360 " --> pdb=" O PHEFC 356 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'FC' and resid 40 through 41 Processing sheet with id=AM5, first strand: chain 'FC' and resid 93 through 102 removed outlier: 5.484A pdb=" N ILEFC 251 " --> pdb=" O ASPFC 263 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'FC' and resid 293 through 295 removed outlier: 4.045A pdb=" N LYSFC 328 " --> pdb=" O GLUFC 237 " (cutoff:3.500A) 2291 hydrogen bonds defined for protein. 6333 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: 28.46 Time building geometry restraints manager: 20.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 10850 1.30 - 1.43: 17458 1.43 - 1.56: 37380 1.56 - 1.68: 0 1.68 - 1.81: 300 Bond restraints: 65988 Sorted by residual: bond pdb=" C ASNCE 95 " pdb=" O ASNCE 95 " ideal model delta sigma weight residual 1.234 1.178 0.056 1.41e-02 5.03e+03 1.58e+01 bond pdb=" C ASNEE 95 " pdb=" O ASNEE 95 " ideal model delta sigma weight residual 1.234 1.179 0.056 1.41e-02 5.03e+03 1.57e+01 bond pdb=" C ASNFE 95 " pdb=" O ASNFE 95 " ideal model delta sigma weight residual 1.234 1.179 0.056 1.41e-02 5.03e+03 1.55e+01 bond pdb=" C ASNAE 95 " pdb=" O ASNAE 95 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.41e-02 5.03e+03 1.55e+01 bond pdb=" C ASNDE 95 " pdb=" O ASNDE 95 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.41e-02 5.03e+03 1.55e+01 ... (remaining 65983 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.55: 2146 106.55 - 113.42: 35486 113.42 - 120.30: 24005 120.30 - 127.18: 27474 127.18 - 134.05: 751 Bond angle restraints: 89862 Sorted by residual: angle pdb=" N ARGBB 359 " pdb=" CA ARGBB 359 " pdb=" C ARGBB 359 " ideal model delta sigma weight residual 108.75 102.16 6.59 1.70e+00 3.46e-01 1.50e+01 angle pdb=" N ARGEB 359 " pdb=" CA ARGEB 359 " pdb=" C ARGEB 359 " ideal model delta sigma weight residual 108.75 102.16 6.59 1.70e+00 3.46e-01 1.50e+01 angle pdb=" N ARGCB 359 " pdb=" CA ARGCB 359 " pdb=" C ARGCB 359 " ideal model delta sigma weight residual 108.75 102.17 6.58 1.70e+00 3.46e-01 1.50e+01 angle pdb=" N ARGFB 359 " pdb=" CA ARGFB 359 " pdb=" C ARGFB 359 " ideal model delta sigma weight residual 108.75 102.17 6.58 1.70e+00 3.46e-01 1.50e+01 angle pdb=" N ARGDB 359 " pdb=" CA ARGDB 359 " pdb=" C ARGDB 359 " ideal model delta sigma weight residual 108.75 102.18 6.57 1.70e+00 3.46e-01 1.49e+01 ... (remaining 89857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 36543 17.81 - 35.62: 2205 35.62 - 53.43: 420 53.43 - 71.24: 174 71.24 - 89.05: 60 Dihedral angle restraints: 39402 sinusoidal: 15798 harmonic: 23604 Sorted by residual: dihedral pdb=" CA ALABA 168 " pdb=" C ALABA 168 " pdb=" N ARGBA 169 " pdb=" CA ARGBA 169 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ALAEA 168 " pdb=" C ALAEA 168 " pdb=" N ARGEA 169 " pdb=" CA ARGEA 169 " ideal model delta harmonic sigma weight residual 180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ALAFA 168 " pdb=" C ALAFA 168 " pdb=" N ARGFA 169 " pdb=" CA ARGFA 169 " ideal model delta harmonic sigma weight residual 180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 39399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 8174 0.067 - 0.135: 1680 0.135 - 0.202: 136 0.202 - 0.269: 11 0.269 - 0.337: 13 Chirality restraints: 10014 Sorted by residual: chirality pdb=" CA CYSAB 331 " pdb=" N CYSAB 331 " pdb=" C CYSAB 331 " pdb=" CB CYSAB 331 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA CYSDB 331 " pdb=" N CYSDB 331 " pdb=" C CYSDB 331 " pdb=" CB CYSDB 331 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA CYSEB 331 " pdb=" N CYSEB 331 " pdb=" C CYSEB 331 " pdb=" CB CYSEB 331 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 10011 not shown) Planarity restraints: 11730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEUFE 94 " 0.023 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C LEUFE 94 " -0.082 2.00e-02 2.50e+03 pdb=" O LEUFE 94 " 0.032 2.00e-02 2.50e+03 pdb=" N ASNFE 95 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEUCE 94 " -0.023 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C LEUCE 94 " 0.082 2.00e-02 2.50e+03 pdb=" O LEUCE 94 " -0.032 2.00e-02 2.50e+03 pdb=" N ASNCE 95 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEUAE 94 " 0.023 2.00e-02 2.50e+03 4.76e-02 2.27e+01 pdb=" C LEUAE 94 " -0.082 2.00e-02 2.50e+03 pdb=" O LEUAE 94 " 0.032 2.00e-02 2.50e+03 pdb=" N ASNAE 95 " 0.027 2.00e-02 2.50e+03 ... (remaining 11727 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 19939 2.83 - 3.35: 50445 3.35 - 3.86: 99638 3.86 - 4.38: 115672 4.38 - 4.90: 204704 Nonbonded interactions: 490398 Sorted by model distance: nonbonded pdb=" O PHEFB 101 " pdb=" OG1 THRFB 105 " model vdw 2.309 2.440 nonbonded pdb=" O PHECB 101 " pdb=" OG1 THRCB 105 " model vdw 2.309 2.440 nonbonded pdb=" O PHEBB 101 " pdb=" OG1 THRBB 105 " model vdw 2.309 2.440 nonbonded pdb=" O PHEEB 101 " pdb=" OG1 THREB 105 " model vdw 2.309 2.440 nonbonded pdb=" O PHEAB 101 " pdb=" OG1 THRAB 105 " model vdw 2.310 2.440 ... (remaining 490393 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 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'EA' selection = chain 'FA' } ncs_group { reference = chain 'AB' selection = chain 'BB' selection = chain 'CB' selection = chain 'DB' selection = chain 'EB' selection = chain 'FB' } ncs_group { reference = chain 'AC' selection = chain 'BC' selection = chain 'CC' selection = chain 'DC' selection = chain 'EC' selection = chain 'FC' } ncs_group { reference = chain 'AD' selection = chain 'AE' selection = chain 'BD' selection = chain 'BE' selection = chain 'CD' selection = chain 'CE' selection = chain 'DD' selection = chain 'DE' selection = chain 'ED' selection = chain 'EE' selection = chain 'FD' selection = chain 'FE' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 28.650 Check model and map are aligned: 0.720 Set scattering table: 0.570 Process input model: 133.870 Find NCS groups from input model: 3.630 Set up NCS constraints: 0.560 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.006 0.058 65988 Z= 0.399 Angle : 0.809 7.692 89862 Z= 0.490 Chirality : 0.054 0.337 10014 Planarity : 0.006 0.075 11730 Dihedral : 13.151 89.048 24168 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.26 % Allowed : 8.28 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -1.72 (0.08), residues: 8028 helix: -0.51 (0.12), residues: 1374 sheet: -0.12 (0.10), residues: 2280 loop : -1.98 (0.08), residues: 4374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPFE 15 HIS 0.005 0.001 HISDA 151 PHE 0.030 0.002 PHEFE 72 TYR 0.023 0.002 TYRDE 4 ARG 0.006 0.001 ARGBC 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 756 time to evaluate : 5.985 Fit side-chains REVERT: BC 194 MET cc_start: 0.7512 (mtt) cc_final: 0.7290 (mtt) REVERT: BD 53 MET cc_start: 0.8464 (mtp) cc_final: 0.8085 (mtp) REVERT: BE 50 MET cc_start: 0.9002 (ptt) cc_final: 0.8786 (ptt) REVERT: CD 53 MET cc_start: 0.8342 (mtp) cc_final: 0.7976 (mtp) REVERT: CE 50 MET cc_start: 0.9014 (ptt) cc_final: 0.8730 (ptt) REVERT: EC 194 MET cc_start: 0.7516 (mtt) cc_final: 0.7295 (mtt) REVERT: ED 53 MET cc_start: 0.8461 (mtp) cc_final: 0.8089 (mtp) REVERT: EE 50 MET cc_start: 0.9002 (ptt) cc_final: 0.8787 (ptt) REVERT: FD 53 MET cc_start: 0.8342 (mtp) cc_final: 0.7966 (mtp) REVERT: FE 50 MET cc_start: 0.9018 (ptt) cc_final: 0.8727 (ptt) outliers start: 18 outliers final: 0 residues processed: 768 average time/residue: 1.8596 time to fit residues: 1745.4331 Evaluate side-chains 298 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 673 optimal weight: 10.0000 chunk 604 optimal weight: 0.9980 chunk 335 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 407 optimal weight: 5.9990 chunk 323 optimal weight: 1.9990 chunk 625 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 380 optimal weight: 6.9990 chunk 465 optimal weight: 7.9990 chunk 724 optimal weight: 0.0470 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 160 GLN AB 15 HIS AB 21 GLN ** AB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 164 GLN AB 271 ASN AB 368 GLN AC 24 GLN AC 75 ASN AC 241 ASN AC 245 GLN AD 115 GLN AE 115 GLN BB 15 HIS BB 21 GLN ** BB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 164 GLN BB 271 ASN BB 365 ASN BB 368 GLN BC 75 ASN BC 241 ASN BC 245 GLN BE 115 GLN CA 160 GLN CB 15 HIS CB 21 GLN ** CB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 164 GLN CB 271 ASN CB 365 ASN CB 368 GLN CC 75 ASN CC 241 ASN CC 245 GLN CE 67 GLN CE 124 ASN DA 160 GLN DB 15 HIS DB 21 GLN ** DB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 164 GLN DB 206 ASN DB 271 ASN DB 368 GLN DC 24 GLN DC 75 ASN DC 241 ASN DC 245 GLN DD 115 GLN DE 115 GLN EA 160 GLN EB 15 HIS EB 21 GLN ** EB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 164 GLN EB 271 ASN EB 365 ASN EB 368 GLN EC 75 ASN EC 241 ASN EC 245 GLN EE 115 GLN FA 160 GLN FB 15 HIS FB 21 GLN ** FB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 164 GLN FB 271 ASN FB 365 ASN FB 368 GLN FC 75 ASN FC 241 ASN FC 245 GLN FE 67 GLN FE 124 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 65988 Z= 0.147 Angle : 0.510 6.816 89862 Z= 0.271 Chirality : 0.044 0.147 10014 Planarity : 0.004 0.046 11730 Dihedral : 4.344 19.568 8772 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.91 % Allowed : 12.57 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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 (0.09), residues: 8028 helix: 0.64 (0.13), residues: 1416 sheet: 0.33 (0.11), residues: 2154 loop : -1.50 (0.08), residues: 4458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCA 153 HIS 0.003 0.001 HISDE 10 PHE 0.018 0.001 PHECE 72 TYR 0.011 0.001 TYRFE 73 ARG 0.006 0.000 ARGEB 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 338 time to evaluate : 5.884 Fit side-chains REVERT: AA 61 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: AB 206 ASN cc_start: 0.6902 (OUTLIER) cc_final: 0.6580 (t0) REVERT: AB 359 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6937 (mtp180) REVERT: BC 194 MET cc_start: 0.7605 (mtt) cc_final: 0.7393 (mtt) REVERT: BC 448 MET cc_start: 0.8802 (mtp) cc_final: 0.8450 (mtp) REVERT: BE 8 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8574 (ptmt) REVERT: BE 50 MET cc_start: 0.8936 (ptt) cc_final: 0.8667 (ptt) REVERT: BE 125 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: CB 2 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7949 (mptt) REVERT: CB 206 ASN cc_start: 0.6785 (OUTLIER) cc_final: 0.6359 (t0) REVERT: CC 97 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8018 (mtpm) REVERT: CE 50 MET cc_start: 0.8877 (ptt) cc_final: 0.8602 (ptt) REVERT: CE 108 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7850 (mmp-170) REVERT: DA 61 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: DB 359 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6937 (mtp180) REVERT: EC 194 MET cc_start: 0.7606 (mtt) cc_final: 0.7394 (mtt) REVERT: EC 448 MET cc_start: 0.8795 (mtp) cc_final: 0.8454 (mtp) REVERT: EE 8 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8576 (ptmt) REVERT: EE 50 MET cc_start: 0.8937 (ptt) cc_final: 0.8670 (ptt) REVERT: EE 125 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: FB 2 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7945 (mptt) REVERT: FB 206 ASN cc_start: 0.6781 (OUTLIER) cc_final: 0.6347 (t0) REVERT: FC 97 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8018 (mtpm) REVERT: FE 50 MET cc_start: 0.8873 (ptt) cc_final: 0.8593 (ptt) REVERT: FE 108 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7862 (mmp-170) outliers start: 134 outliers final: 40 residues processed: 458 average time/residue: 1.5585 time to fit residues: 914.9027 Evaluate side-chains 331 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 276 time to evaluate : 6.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 61 GLU Chi-restraints excluded: chain AA residue 74 ASP Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 206 ASN Chi-restraints excluded: chain AB residue 359 ARG Chi-restraints excluded: chain AB residue 367 CYS Chi-restraints excluded: chain AC residue 224 ASP Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AE residue 125 GLU Chi-restraints excluded: chain BA residue 53 VAL Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BC residue 210 VAL Chi-restraints excluded: chain BC residue 224 ASP Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 116 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 143 SER Chi-restraints excluded: chain CB residue 206 ASN Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CD residue 57 SER Chi-restraints excluded: chain CE residue 108 ARG Chi-restraints excluded: chain CE residue 122 ASP Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain DA residue 61 GLU Chi-restraints excluded: chain DA residue 74 ASP Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 359 ARG Chi-restraints excluded: chain DB residue 367 CYS Chi-restraints excluded: chain DC residue 224 ASP Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DE residue 125 GLU Chi-restraints excluded: chain EA residue 53 VAL Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EC residue 210 VAL Chi-restraints excluded: chain EC residue 224 ASP Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 116 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 143 SER Chi-restraints excluded: chain FB residue 206 ASN Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FD residue 57 SER Chi-restraints excluded: chain FE residue 108 ARG Chi-restraints excluded: chain FE residue 122 ASP Chi-restraints excluded: chain FE residue 125 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 402 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 603 optimal weight: 0.0000 chunk 493 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 chunk 725 optimal weight: 9.9990 chunk 784 optimal weight: 0.6980 chunk 646 optimal weight: 4.9990 chunk 719 optimal weight: 9.9990 chunk 247 optimal weight: 6.9990 chunk 582 optimal weight: 10.0000 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 111 ASN ** AB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 271 ASN AD 54 GLN BA 75 ASN BA 160 GLN ** BB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 271 ASN BC 52 ASN BD 54 GLN CB 111 ASN ** CB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 164 GLN CB 271 ASN CB 365 ASN CC 52 ASN CD 54 GLN CE 54 GLN CE 115 GLN ** DB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 271 ASN DD 54 GLN EA 75 ASN EA 160 GLN ** EB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 271 ASN EC 52 ASN ED 54 GLN FB 111 ASN ** FB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 164 GLN FB 271 ASN FB 365 ASN FC 52 ASN FC 75 ASN FD 54 GLN FE 54 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 65988 Z= 0.159 Angle : 0.500 6.142 89862 Z= 0.265 Chirality : 0.043 0.145 10014 Planarity : 0.004 0.035 11730 Dihedral : 4.205 19.712 8772 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.73 % Allowed : 13.96 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.57 (0.09), residues: 8028 helix: 1.10 (0.14), residues: 1416 sheet: 0.42 (0.11), residues: 2190 loop : -1.35 (0.08), residues: 4422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPCA 153 HIS 0.003 0.001 HISBA 151 PHE 0.019 0.001 PHECE 72 TYR 0.012 0.001 TYRAC 112 ARG 0.006 0.000 ARGFD 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 280 time to evaluate : 5.884 Fit side-chains REVERT: AA 61 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: AB 220 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: BC 133 MET cc_start: 0.7775 (ptm) cc_final: 0.7473 (ptp) REVERT: BE 115 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: CB 206 ASN cc_start: 0.6848 (OUTLIER) cc_final: 0.6416 (t0) REVERT: CC 97 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8043 (mtpm) REVERT: CE 50 MET cc_start: 0.8988 (ptt) cc_final: 0.8694 (ptt) REVERT: DA 61 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: DB 220 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: EC 133 MET cc_start: 0.7780 (ptm) cc_final: 0.7474 (ptp) REVERT: EE 115 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: FB 206 ASN cc_start: 0.6845 (OUTLIER) cc_final: 0.6412 (t0) REVERT: FC 97 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8042 (mtpm) REVERT: FE 50 MET cc_start: 0.8987 (ptt) cc_final: 0.8689 (ptt) outliers start: 122 outliers final: 48 residues processed: 380 average time/residue: 1.5871 time to fit residues: 768.3713 Evaluate side-chains 326 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 268 time to evaluate : 5.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 61 GLU Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 220 GLU Chi-restraints excluded: chain AB residue 367 CYS Chi-restraints excluded: chain AC residue 52 ASN Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AD residue 130 SER Chi-restraints excluded: chain AE residue 125 GLU Chi-restraints excluded: chain BA residue 1 MET Chi-restraints excluded: chain BA residue 124 THR Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BB residue 178 SER Chi-restraints excluded: chain BC residue 224 ASP Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 116 SER Chi-restraints excluded: chain BD residue 130 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 53 VAL Chi-restraints excluded: chain CB residue 178 SER Chi-restraints excluded: chain CB residue 206 ASN Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 194 MET Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain DA residue 61 GLU Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 220 GLU Chi-restraints excluded: chain DB residue 367 CYS Chi-restraints excluded: chain DC residue 52 ASN Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DD residue 130 SER Chi-restraints excluded: chain DE residue 125 GLU Chi-restraints excluded: chain EA residue 1 MET Chi-restraints excluded: chain EA residue 124 THR Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EB residue 178 SER Chi-restraints excluded: chain EC residue 224 ASP Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 116 SER Chi-restraints excluded: chain ED residue 130 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 115 GLN Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 53 VAL Chi-restraints excluded: chain FB residue 178 SER Chi-restraints excluded: chain FB residue 206 ASN Chi-restraints excluded: chain FC residue 75 ASN Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FE residue 125 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 717 optimal weight: 10.0000 chunk 545 optimal weight: 20.0000 chunk 376 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 346 optimal weight: 0.2980 chunk 487 optimal weight: 10.0000 chunk 728 optimal weight: 10.0000 chunk 771 optimal weight: 9.9990 chunk 380 optimal weight: 2.9990 chunk 690 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 143 ASN AB 271 ASN AC 75 ASN ** AC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 143 ASN BB 190 HIS BB 271 ASN BC 75 ASN ** BC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 75 ASN CA 160 GLN CB 143 ASN CB 164 GLN CB 271 ASN ** CB 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 111 ASN DB 143 ASN DB 271 ASN DC 75 ASN ** DC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 190 HIS EB 271 ASN EC 75 ASN ** EC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 75 ASN FA 160 GLN ** FB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 164 GLN FB 271 ASN ** FB 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 65988 Z= 0.205 Angle : 0.534 6.647 89862 Z= 0.284 Chirality : 0.044 0.145 10014 Planarity : 0.004 0.036 11730 Dihedral : 4.393 21.409 8772 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.03 % Allowed : 13.96 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.54 (0.09), residues: 8028 helix: 1.19 (0.14), residues: 1428 sheet: 0.49 (0.11), residues: 2196 loop : -1.39 (0.08), residues: 4404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPFA 153 HIS 0.004 0.001 HISCA 151 PHE 0.023 0.002 PHEFD 56 TYR 0.012 0.001 TYRFC 112 ARG 0.005 0.000 ARGAD 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 284 time to evaluate : 6.016 Fit side-chains REVERT: AB 220 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: AE 33 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6568 (tt0) REVERT: BA 61 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: BC 133 MET cc_start: 0.7849 (ptm) cc_final: 0.7454 (ptp) REVERT: BE 115 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7961 (mt0) REVERT: CA 61 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: CC 97 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8051 (mtpm) REVERT: CE 33 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: CE 50 MET cc_start: 0.9008 (ptt) cc_final: 0.8705 (ptt) REVERT: DB 220 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: DE 33 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: EA 61 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: EC 133 MET cc_start: 0.7849 (ptm) cc_final: 0.7453 (ptp) REVERT: EE 115 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: FA 61 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7573 (tt0) REVERT: FC 97 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8051 (mtpm) REVERT: FE 33 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: FE 50 MET cc_start: 0.9005 (ptt) cc_final: 0.8699 (ptt) outliers start: 143 outliers final: 69 residues processed: 408 average time/residue: 1.5867 time to fit residues: 823.6361 Evaluate side-chains 357 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 274 time to evaluate : 6.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 53 VAL Chi-restraints excluded: chain AA residue 124 THR Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 178 SER Chi-restraints excluded: chain AB residue 220 GLU Chi-restraints excluded: chain AB residue 367 CYS Chi-restraints excluded: chain AC residue 52 ASN Chi-restraints excluded: chain AC residue 75 ASN Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AD residue 130 SER Chi-restraints excluded: chain AE residue 31 GLU Chi-restraints excluded: chain AE residue 33 GLU Chi-restraints excluded: chain AE residue 55 LYS Chi-restraints excluded: chain AE residue 125 GLU Chi-restraints excluded: chain BA residue 26 LEU Chi-restraints excluded: chain BA residue 53 VAL Chi-restraints excluded: chain BA residue 61 GLU Chi-restraints excluded: chain BA residue 124 THR Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BC residue 75 ASN Chi-restraints excluded: chain BC residue 224 ASP Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BC residue 478 SER Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 116 SER Chi-restraints excluded: chain BD residue 130 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 53 VAL Chi-restraints excluded: chain CA residue 61 GLU Chi-restraints excluded: chain CB residue 178 SER Chi-restraints excluded: chain CB residue 186 SER Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 194 MET Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CC residue 478 SER Chi-restraints excluded: chain CE residue 33 GLU Chi-restraints excluded: chain CE residue 122 ASP Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain DA residue 53 VAL Chi-restraints excluded: chain DA residue 124 THR Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 178 SER Chi-restraints excluded: chain DB residue 220 GLU Chi-restraints excluded: chain DB residue 367 CYS Chi-restraints excluded: chain DC residue 52 ASN Chi-restraints excluded: chain DC residue 75 ASN Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DD residue 130 SER Chi-restraints excluded: chain DE residue 31 GLU Chi-restraints excluded: chain DE residue 33 GLU Chi-restraints excluded: chain DE residue 55 LYS Chi-restraints excluded: chain DE residue 125 GLU Chi-restraints excluded: chain EA residue 26 LEU Chi-restraints excluded: chain EA residue 53 VAL Chi-restraints excluded: chain EA residue 61 GLU Chi-restraints excluded: chain EA residue 124 THR Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EC residue 75 ASN Chi-restraints excluded: chain EC residue 224 ASP Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain EC residue 478 SER Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 116 SER Chi-restraints excluded: chain ED residue 130 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 115 GLN Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 53 VAL Chi-restraints excluded: chain FA residue 61 GLU Chi-restraints excluded: chain FB residue 178 SER Chi-restraints excluded: chain FB residue 186 SER Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FC residue 478 SER Chi-restraints excluded: chain FE residue 33 GLU Chi-restraints excluded: chain FE residue 122 ASP Chi-restraints excluded: chain FE residue 125 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 642 optimal weight: 5.9990 chunk 437 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 574 optimal weight: 0.9990 chunk 318 optimal weight: 4.9990 chunk 658 optimal weight: 4.9990 chunk 533 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 393 optimal weight: 0.6980 chunk 692 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 271 ASN AC 75 ASN ** AC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 75 ASN BB 190 HIS BB 271 ASN ** BB 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 75 ASN ** BC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 164 GLN CB 271 ASN CB 329 HIS CC 75 ASN ** CC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 75 ASN DB 271 ASN DC 75 ASN ** DC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 143 ASN EB 190 HIS EB 271 ASN ** EB 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 75 ASN FB 143 ASN FB 164 GLN FB 271 ASN FB 329 HIS ** FC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 65988 Z= 0.196 Angle : 0.520 6.494 89862 Z= 0.276 Chirality : 0.044 0.141 10014 Planarity : 0.004 0.036 11730 Dihedral : 4.343 21.378 8772 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.36 % Allowed : 14.23 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.49 (0.09), residues: 8028 helix: 1.30 (0.14), residues: 1428 sheet: 0.54 (0.11), residues: 2196 loop : -1.39 (0.08), residues: 4404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPCA 153 HIS 0.004 0.001 HISCA 151 PHE 0.018 0.001 PHEED 56 TYR 0.011 0.001 TYRCE 37 ARG 0.003 0.000 ARGCD 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 278 time to evaluate : 5.943 Fit side-chains REVERT: AB 220 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: AE 33 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6533 (tt0) REVERT: BB 164 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7792 (mp-120) REVERT: BC 133 MET cc_start: 0.7856 (ptm) cc_final: 0.7541 (ptp) REVERT: BC 223 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6092 (mt0) REVERT: BC 448 MET cc_start: 0.9133 (mtp) cc_final: 0.8620 (mtp) REVERT: BE 115 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: CB 206 ASN cc_start: 0.7004 (OUTLIER) cc_final: 0.6386 (t0) REVERT: CC 97 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8054 (mtpm) REVERT: CE 33 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: CE 50 MET cc_start: 0.9003 (ptt) cc_final: 0.8708 (ptt) REVERT: DB 220 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: DE 33 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: EB 164 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7791 (mp-120) REVERT: EC 133 MET cc_start: 0.7761 (ptm) cc_final: 0.7558 (ptp) REVERT: EC 223 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6092 (mt0) REVERT: EC 448 MET cc_start: 0.9133 (mtp) cc_final: 0.8624 (mtp) REVERT: EE 115 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7920 (mt0) REVERT: FB 206 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6384 (t0) REVERT: FC 97 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8051 (mtpm) REVERT: FE 33 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: FE 50 MET cc_start: 0.9001 (ptt) cc_final: 0.8706 (ptt) outliers start: 166 outliers final: 85 residues processed: 429 average time/residue: 1.4704 time to fit residues: 813.2905 Evaluate side-chains 375 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 274 time to evaluate : 6.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 53 VAL Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 178 SER Chi-restraints excluded: chain AB residue 186 SER Chi-restraints excluded: chain AB residue 208 ASP Chi-restraints excluded: chain AB residue 210 THR Chi-restraints excluded: chain AB residue 220 GLU Chi-restraints excluded: chain AB residue 367 CYS Chi-restraints excluded: chain AC residue 52 ASN Chi-restraints excluded: chain AC residue 210 VAL Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AC residue 407 ASN Chi-restraints excluded: chain AD residue 130 SER Chi-restraints excluded: chain AE residue 31 GLU Chi-restraints excluded: chain AE residue 33 GLU Chi-restraints excluded: chain AE residue 125 GLU Chi-restraints excluded: chain BA residue 53 VAL Chi-restraints excluded: chain BA residue 124 THR Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BA residue 186 THR Chi-restraints excluded: chain BB residue 164 GLN Chi-restraints excluded: chain BB residue 178 SER Chi-restraints excluded: chain BB residue 354 ILE Chi-restraints excluded: chain BC residue 210 VAL Chi-restraints excluded: chain BC residue 223 GLN Chi-restraints excluded: chain BC residue 224 ASP Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BC residue 415 MET Chi-restraints excluded: chain BC residue 478 SER Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 116 SER Chi-restraints excluded: chain BD residue 120 LYS Chi-restraints excluded: chain BD residue 130 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 31 GLU Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 53 VAL Chi-restraints excluded: chain CA residue 186 THR Chi-restraints excluded: chain CB residue 186 SER Chi-restraints excluded: chain CB residue 206 ASN Chi-restraints excluded: chain CC residue 75 ASN Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 194 MET Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CC residue 324 SER Chi-restraints excluded: chain CC residue 478 SER Chi-restraints excluded: chain CE residue 33 GLU Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain DA residue 53 VAL Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 178 SER Chi-restraints excluded: chain DB residue 186 SER Chi-restraints excluded: chain DB residue 208 ASP Chi-restraints excluded: chain DB residue 210 THR Chi-restraints excluded: chain DB residue 220 GLU Chi-restraints excluded: chain DB residue 367 CYS Chi-restraints excluded: chain DC residue 52 ASN Chi-restraints excluded: chain DC residue 210 VAL Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DC residue 407 ASN Chi-restraints excluded: chain DD residue 130 SER Chi-restraints excluded: chain DE residue 31 GLU Chi-restraints excluded: chain DE residue 33 GLU Chi-restraints excluded: chain DE residue 125 GLU Chi-restraints excluded: chain EA residue 53 VAL Chi-restraints excluded: chain EA residue 124 THR Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EA residue 186 THR Chi-restraints excluded: chain EB residue 164 GLN Chi-restraints excluded: chain EB residue 178 SER Chi-restraints excluded: chain EB residue 354 ILE Chi-restraints excluded: chain EC residue 210 VAL Chi-restraints excluded: chain EC residue 223 GLN Chi-restraints excluded: chain EC residue 224 ASP Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain EC residue 415 MET Chi-restraints excluded: chain EC residue 478 SER Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 116 SER Chi-restraints excluded: chain ED residue 120 LYS Chi-restraints excluded: chain ED residue 130 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 31 GLU Chi-restraints excluded: chain EE residue 115 GLN Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 53 VAL Chi-restraints excluded: chain FA residue 186 THR Chi-restraints excluded: chain FB residue 186 SER Chi-restraints excluded: chain FB residue 206 ASN Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 194 MET Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FC residue 324 SER Chi-restraints excluded: chain FC residue 478 SER Chi-restraints excluded: chain FE residue 33 GLU Chi-restraints excluded: chain FE residue 125 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 259 optimal weight: 8.9990 chunk 694 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 452 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 772 optimal weight: 8.9990 chunk 640 optimal weight: 8.9990 chunk 357 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 405 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 75 ASN AB 271 ASN ** AC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 190 HIS BB 271 ASN ** BC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 190 HIS CB 271 ASN CC 75 ASN ** CC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 190 HIS DB 271 ASN ** DC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 190 HIS EB 271 ASN EC 75 ASN ** EC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 75 ASN FB 190 HIS FB 271 ASN ** FC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 65988 Z= 0.285 Angle : 0.593 7.587 89862 Z= 0.315 Chirality : 0.046 0.148 10014 Planarity : 0.005 0.040 11730 Dihedral : 4.660 22.829 8772 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.32 % Allowed : 14.52 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.66 (0.09), residues: 8028 helix: 1.10 (0.13), residues: 1434 sheet: 0.24 (0.10), residues: 2502 loop : -1.48 (0.09), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPFB 224 HIS 0.006 0.001 HISCB 190 PHE 0.023 0.002 PHEED 56 TYR 0.014 0.002 TYRCE 37 ARG 0.004 0.001 ARGBB 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 284 time to evaluate : 5.979 Fit side-chains REVERT: AB 220 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: AE 33 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6417 (tt0) REVERT: BA 61 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: BB 82 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8487 (p90) REVERT: BB 164 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7917 (mp-120) REVERT: BC 223 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6400 (mt0) REVERT: BC 448 MET cc_start: 0.9177 (mtp) cc_final: 0.8697 (mtp) REVERT: BE 115 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: CC 97 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8079 (mtpm) REVERT: CE 33 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6851 (tt0) REVERT: CE 50 MET cc_start: 0.9082 (ptt) cc_final: 0.8791 (ptt) REVERT: CE 132 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: DB 220 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: DE 33 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6416 (tt0) REVERT: EA 61 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: EB 82 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8491 (p90) REVERT: EB 164 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7916 (mp-120) REVERT: EC 133 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7602 (ptp) REVERT: EC 223 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6403 (mt0) REVERT: EC 448 MET cc_start: 0.9177 (mtp) cc_final: 0.8700 (mtp) REVERT: EE 115 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: FC 97 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8082 (mtpm) REVERT: FE 33 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: FE 50 MET cc_start: 0.9082 (ptt) cc_final: 0.8795 (ptt) REVERT: FE 132 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7464 (tm-30) outliers start: 163 outliers final: 93 residues processed: 431 average time/residue: 1.4982 time to fit residues: 830.0027 Evaluate side-chains 388 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 274 time to evaluate : 5.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 53 VAL Chi-restraints excluded: chain AA residue 124 THR Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 178 SER Chi-restraints excluded: chain AB residue 186 SER Chi-restraints excluded: chain AB residue 208 ASP Chi-restraints excluded: chain AB residue 210 THR Chi-restraints excluded: chain AB residue 220 GLU Chi-restraints excluded: chain AB residue 235 LYS Chi-restraints excluded: chain AB residue 272 SER Chi-restraints excluded: chain AB residue 367 CYS Chi-restraints excluded: chain AC residue 52 ASN Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 210 VAL Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AC residue 407 ASN Chi-restraints excluded: chain AD residue 130 SER Chi-restraints excluded: chain AE residue 33 GLU Chi-restraints excluded: chain AE residue 125 GLU Chi-restraints excluded: chain BA residue 26 LEU Chi-restraints excluded: chain BA residue 53 VAL Chi-restraints excluded: chain BA residue 61 GLU Chi-restraints excluded: chain BA residue 124 THR Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BA residue 186 THR Chi-restraints excluded: chain BB residue 82 PHE Chi-restraints excluded: chain BB residue 164 GLN Chi-restraints excluded: chain BB residue 178 SER Chi-restraints excluded: chain BB residue 354 ILE Chi-restraints excluded: chain BC residue 52 ASN Chi-restraints excluded: chain BC residue 210 VAL Chi-restraints excluded: chain BC residue 223 GLN Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BC residue 478 SER Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 116 SER Chi-restraints excluded: chain BD residue 120 LYS Chi-restraints excluded: chain BD residue 130 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 31 GLU Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 53 VAL Chi-restraints excluded: chain CA residue 186 THR Chi-restraints excluded: chain CB residue 186 SER Chi-restraints excluded: chain CC residue 75 ASN Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 194 MET Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CC residue 324 SER Chi-restraints excluded: chain CC residue 478 SER Chi-restraints excluded: chain CE residue 33 GLU Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain CE residue 132 GLU Chi-restraints excluded: chain DA residue 53 VAL Chi-restraints excluded: chain DA residue 124 THR Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 178 SER Chi-restraints excluded: chain DB residue 186 SER Chi-restraints excluded: chain DB residue 208 ASP Chi-restraints excluded: chain DB residue 210 THR Chi-restraints excluded: chain DB residue 220 GLU Chi-restraints excluded: chain DB residue 235 LYS Chi-restraints excluded: chain DB residue 272 SER Chi-restraints excluded: chain DB residue 367 CYS Chi-restraints excluded: chain DC residue 52 ASN Chi-restraints excluded: chain DC residue 151 VAL Chi-restraints excluded: chain DC residue 210 VAL Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DC residue 407 ASN Chi-restraints excluded: chain DC residue 478 SER Chi-restraints excluded: chain DD residue 130 SER Chi-restraints excluded: chain DE residue 33 GLU Chi-restraints excluded: chain DE residue 125 GLU Chi-restraints excluded: chain EA residue 26 LEU Chi-restraints excluded: chain EA residue 53 VAL Chi-restraints excluded: chain EA residue 61 GLU Chi-restraints excluded: chain EA residue 124 THR Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EA residue 186 THR Chi-restraints excluded: chain EB residue 82 PHE Chi-restraints excluded: chain EB residue 164 GLN Chi-restraints excluded: chain EB residue 178 SER Chi-restraints excluded: chain EB residue 354 ILE Chi-restraints excluded: chain EC residue 52 ASN Chi-restraints excluded: chain EC residue 133 MET Chi-restraints excluded: chain EC residue 210 VAL Chi-restraints excluded: chain EC residue 223 GLN Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain EC residue 478 SER Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 116 SER Chi-restraints excluded: chain ED residue 120 LYS Chi-restraints excluded: chain ED residue 130 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 31 GLU Chi-restraints excluded: chain EE residue 115 GLN Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 53 VAL Chi-restraints excluded: chain FA residue 186 THR Chi-restraints excluded: chain FB residue 186 SER Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 194 MET Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FC residue 324 SER Chi-restraints excluded: chain FC residue 478 SER Chi-restraints excluded: chain FD residue 120 LYS Chi-restraints excluded: chain FE residue 33 GLU Chi-restraints excluded: chain FE residue 125 GLU Chi-restraints excluded: chain FE residue 132 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 744 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 439 optimal weight: 0.0060 chunk 563 optimal weight: 8.9990 chunk 436 optimal weight: 7.9990 chunk 649 optimal weight: 10.0000 chunk 431 optimal weight: 20.0000 chunk 769 optimal weight: 8.9990 chunk 481 optimal weight: 1.9990 chunk 468 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 overall best weight: 4.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 271 ASN ** AC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 190 HIS BB 271 ASN BC 75 ASN ** BC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 271 ASN ** CC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 190 HIS DB 271 ASN ** DC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 190 HIS EB 271 ASN EC 75 ASN ** EC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 75 ASN ** FC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 65988 Z= 0.247 Angle : 0.562 7.642 89862 Z= 0.299 Chirality : 0.045 0.144 10014 Planarity : 0.004 0.039 11730 Dihedral : 4.576 22.439 8772 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.42 % Allowed : 14.51 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.61 (0.09), residues: 8028 helix: 1.16 (0.13), residues: 1434 sheet: 0.50 (0.11), residues: 2232 loop : -1.49 (0.08), residues: 4362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPFA 153 HIS 0.004 0.001 HISCB 190 PHE 0.017 0.002 PHEBD 56 TYR 0.012 0.002 TYRCE 37 ARG 0.003 0.000 ARGFB 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 281 time to evaluate : 6.004 Fit side-chains REVERT: AB 82 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8436 (p90) REVERT: AB 220 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: AC 236 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8881 (mm) REVERT: AE 33 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6515 (tt0) REVERT: AE 125 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8006 (pm20) REVERT: BA 61 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: BB 82 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8471 (p90) REVERT: BB 164 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7873 (mp-120) REVERT: BB 235 LYS cc_start: 0.6963 (mppt) cc_final: 0.6733 (mmtm) REVERT: BC 223 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6434 (mt0) REVERT: BC 415 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8047 (ptm) REVERT: BC 448 MET cc_start: 0.9194 (mtp) cc_final: 0.8785 (mtp) REVERT: BE 115 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: CA 61 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: CC 97 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8068 (mtpm) REVERT: CE 33 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: CE 50 MET cc_start: 0.9063 (ptt) cc_final: 0.8741 (ptt) REVERT: CE 132 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: DB 82 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8435 (p90) REVERT: DB 220 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: DC 236 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8879 (mm) REVERT: DE 33 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6516 (tt0) REVERT: DE 125 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: EA 61 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: EB 82 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8475 (p90) REVERT: EB 164 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7873 (mp-120) REVERT: EB 235 LYS cc_start: 0.6968 (mppt) cc_final: 0.6737 (mmtm) REVERT: EC 133 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7620 (ptp) REVERT: EC 223 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6438 (mt0) REVERT: EC 415 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8053 (ptm) REVERT: EC 448 MET cc_start: 0.9193 (mtp) cc_final: 0.8790 (mtp) REVERT: EE 115 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: FA 61 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: FC 97 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8067 (mtpm) REVERT: FE 33 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6811 (tt0) REVERT: FE 50 MET cc_start: 0.9062 (ptt) cc_final: 0.8741 (ptt) REVERT: FE 132 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7528 (tm-30) outliers start: 170 outliers final: 102 residues processed: 432 average time/residue: 1.4610 time to fit residues: 815.2297 Evaluate side-chains 409 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 276 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 53 VAL Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 82 PHE Chi-restraints excluded: chain AB residue 178 SER Chi-restraints excluded: chain AB residue 186 SER Chi-restraints excluded: chain AB residue 208 ASP Chi-restraints excluded: chain AB residue 210 THR Chi-restraints excluded: chain AB residue 220 GLU Chi-restraints excluded: chain AB residue 235 LYS Chi-restraints excluded: chain AB residue 272 SER Chi-restraints excluded: chain AB residue 367 CYS Chi-restraints excluded: chain AC residue 52 ASN Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 194 MET Chi-restraints excluded: chain AC residue 210 VAL Chi-restraints excluded: chain AC residue 236 ILE Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AC residue 324 SER Chi-restraints excluded: chain AC residue 407 ASN Chi-restraints excluded: chain AD residue 130 SER Chi-restraints excluded: chain AE residue 33 GLU Chi-restraints excluded: chain AE residue 125 GLU Chi-restraints excluded: chain BA residue 26 LEU Chi-restraints excluded: chain BA residue 53 VAL Chi-restraints excluded: chain BA residue 61 GLU Chi-restraints excluded: chain BA residue 124 THR Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BA residue 164 VAL Chi-restraints excluded: chain BA residue 186 THR Chi-restraints excluded: chain BB residue 82 PHE Chi-restraints excluded: chain BB residue 164 GLN Chi-restraints excluded: chain BB residue 178 SER Chi-restraints excluded: chain BB residue 354 ILE Chi-restraints excluded: chain BC residue 52 ASN Chi-restraints excluded: chain BC residue 75 ASN Chi-restraints excluded: chain BC residue 210 VAL Chi-restraints excluded: chain BC residue 223 GLN Chi-restraints excluded: chain BC residue 224 ASP Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BC residue 415 MET Chi-restraints excluded: chain BC residue 478 SER Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 106 VAL Chi-restraints excluded: chain BD residue 116 SER Chi-restraints excluded: chain BD residue 120 LYS Chi-restraints excluded: chain BD residue 130 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 31 GLU Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 53 VAL Chi-restraints excluded: chain CA residue 61 GLU Chi-restraints excluded: chain CA residue 186 THR Chi-restraints excluded: chain CB residue 186 SER Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 194 MET Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CC residue 324 SER Chi-restraints excluded: chain CC residue 478 SER Chi-restraints excluded: chain CD residue 120 LYS Chi-restraints excluded: chain CD residue 130 SER Chi-restraints excluded: chain CE residue 33 GLU Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain CE residue 132 GLU Chi-restraints excluded: chain DA residue 53 VAL Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 82 PHE Chi-restraints excluded: chain DB residue 178 SER Chi-restraints excluded: chain DB residue 186 SER Chi-restraints excluded: chain DB residue 208 ASP Chi-restraints excluded: chain DB residue 210 THR Chi-restraints excluded: chain DB residue 220 GLU Chi-restraints excluded: chain DB residue 235 LYS Chi-restraints excluded: chain DB residue 272 SER Chi-restraints excluded: chain DB residue 367 CYS Chi-restraints excluded: chain DC residue 52 ASN Chi-restraints excluded: chain DC residue 151 VAL Chi-restraints excluded: chain DC residue 194 MET Chi-restraints excluded: chain DC residue 210 VAL Chi-restraints excluded: chain DC residue 236 ILE Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DC residue 324 SER Chi-restraints excluded: chain DC residue 407 ASN Chi-restraints excluded: chain DD residue 130 SER Chi-restraints excluded: chain DE residue 33 GLU Chi-restraints excluded: chain DE residue 125 GLU Chi-restraints excluded: chain EA residue 26 LEU Chi-restraints excluded: chain EA residue 53 VAL Chi-restraints excluded: chain EA residue 61 GLU Chi-restraints excluded: chain EA residue 124 THR Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EA residue 164 VAL Chi-restraints excluded: chain EA residue 186 THR Chi-restraints excluded: chain EB residue 82 PHE Chi-restraints excluded: chain EB residue 164 GLN Chi-restraints excluded: chain EB residue 178 SER Chi-restraints excluded: chain EB residue 354 ILE Chi-restraints excluded: chain EC residue 52 ASN Chi-restraints excluded: chain EC residue 133 MET Chi-restraints excluded: chain EC residue 210 VAL Chi-restraints excluded: chain EC residue 223 GLN Chi-restraints excluded: chain EC residue 224 ASP Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain EC residue 415 MET Chi-restraints excluded: chain EC residue 478 SER Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 106 VAL Chi-restraints excluded: chain ED residue 116 SER Chi-restraints excluded: chain ED residue 120 LYS Chi-restraints excluded: chain ED residue 130 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 31 GLU Chi-restraints excluded: chain EE residue 115 GLN Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 53 VAL Chi-restraints excluded: chain FA residue 61 GLU Chi-restraints excluded: chain FA residue 186 THR Chi-restraints excluded: chain FB residue 186 SER Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 194 MET Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FC residue 324 SER Chi-restraints excluded: chain FC residue 478 SER Chi-restraints excluded: chain FD residue 120 LYS Chi-restraints excluded: chain FD residue 130 SER Chi-restraints excluded: chain FE residue 33 GLU Chi-restraints excluded: chain FE residue 55 LYS Chi-restraints excluded: chain FE residue 125 GLU Chi-restraints excluded: chain FE residue 132 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 475 optimal weight: 6.9990 chunk 307 optimal weight: 7.9990 chunk 459 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 488 optimal weight: 2.9990 chunk 524 optimal weight: 8.9990 chunk 380 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 604 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 190 HIS AB 271 ASN ** AC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 190 HIS BB 271 ASN BC 75 ASN ** BC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 75 ASN ** CC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 190 HIS DB 271 ASN ** DC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 75 ASN EB 190 HIS EB 271 ASN EC 75 ASN ** EC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 65988 Z= 0.218 Angle : 0.542 7.212 89862 Z= 0.288 Chirality : 0.044 0.142 10014 Planarity : 0.004 0.038 11730 Dihedral : 4.471 22.105 8772 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.26 % Allowed : 14.56 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.58 (0.09), residues: 8028 helix: 1.23 (0.14), residues: 1434 sheet: 0.22 (0.10), residues: 2556 loop : -1.43 (0.09), residues: 4038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPFA 153 HIS 0.004 0.001 HISFB 190 PHE 0.015 0.001 PHEED 56 TYR 0.012 0.001 TYRCC 35 ARG 0.003 0.000 ARGFA 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 282 time to evaluate : 6.056 Fit side-chains REVERT: AB 82 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8390 (p90) REVERT: AC 236 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8883 (mm) REVERT: AE 33 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: BA 61 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7546 (tt0) REVERT: BB 82 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8464 (p90) REVERT: BB 164 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7826 (mp-120) REVERT: BC 177 MET cc_start: 0.8051 (mmt) cc_final: 0.7809 (mmt) REVERT: BC 415 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8021 (ptm) REVERT: BC 448 MET cc_start: 0.9192 (mtp) cc_final: 0.8750 (mtp) REVERT: BE 115 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: CA 61 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: CC 97 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8066 (mtpm) REVERT: CE 33 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: CE 50 MET cc_start: 0.9058 (ptt) cc_final: 0.8719 (ptt) REVERT: CE 132 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: DB 82 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8391 (p90) REVERT: DC 236 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8881 (mm) REVERT: DE 33 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6528 (tt0) REVERT: EA 61 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: EB 82 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8465 (p90) REVERT: EB 164 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7826 (mp-120) REVERT: EC 133 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7642 (ptp) REVERT: EC 177 MET cc_start: 0.8051 (mmt) cc_final: 0.7810 (mmt) REVERT: EC 415 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8021 (ptm) REVERT: EC 448 MET cc_start: 0.9194 (mtp) cc_final: 0.8755 (mtp) REVERT: EE 115 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: FA 61 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: FB 206 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6422 (t0) REVERT: FC 97 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8064 (mtpm) REVERT: FE 33 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: FE 50 MET cc_start: 0.9057 (ptt) cc_final: 0.8717 (ptt) REVERT: FE 132 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7539 (tm-30) outliers start: 159 outliers final: 97 residues processed: 423 average time/residue: 1.5129 time to fit residues: 827.0923 Evaluate side-chains 405 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 282 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 53 VAL Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AA residue 164 VAL Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 82 PHE Chi-restraints excluded: chain AB residue 178 SER Chi-restraints excluded: chain AB residue 186 SER Chi-restraints excluded: chain AB residue 208 ASP Chi-restraints excluded: chain AB residue 210 THR Chi-restraints excluded: chain AB residue 235 LYS Chi-restraints excluded: chain AB residue 367 CYS Chi-restraints excluded: chain AC residue 52 ASN Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 194 MET Chi-restraints excluded: chain AC residue 210 VAL Chi-restraints excluded: chain AC residue 236 ILE Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AC residue 407 ASN Chi-restraints excluded: chain AD residue 130 SER Chi-restraints excluded: chain AE residue 33 GLU Chi-restraints excluded: chain BA residue 53 VAL Chi-restraints excluded: chain BA residue 61 GLU Chi-restraints excluded: chain BA residue 124 THR Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BA residue 164 VAL Chi-restraints excluded: chain BA residue 186 THR Chi-restraints excluded: chain BB residue 82 PHE Chi-restraints excluded: chain BB residue 164 GLN Chi-restraints excluded: chain BB residue 178 SER Chi-restraints excluded: chain BB residue 354 ILE Chi-restraints excluded: chain BC residue 52 ASN Chi-restraints excluded: chain BC residue 210 VAL Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BC residue 415 MET Chi-restraints excluded: chain BC residue 478 SER Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 106 VAL Chi-restraints excluded: chain BD residue 116 SER Chi-restraints excluded: chain BD residue 120 LYS Chi-restraints excluded: chain BD residue 130 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 31 GLU Chi-restraints excluded: chain BE residue 33 GLU Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 53 VAL Chi-restraints excluded: chain CA residue 61 GLU Chi-restraints excluded: chain CA residue 160 GLN Chi-restraints excluded: chain CA residue 186 THR Chi-restraints excluded: chain CB residue 186 SER Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 194 MET Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CC residue 324 SER Chi-restraints excluded: chain CC residue 478 SER Chi-restraints excluded: chain CD residue 120 LYS Chi-restraints excluded: chain CD residue 130 SER Chi-restraints excluded: chain CE residue 33 GLU Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain CE residue 132 GLU Chi-restraints excluded: chain DA residue 53 VAL Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DA residue 164 VAL Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 82 PHE Chi-restraints excluded: chain DB residue 178 SER Chi-restraints excluded: chain DB residue 186 SER Chi-restraints excluded: chain DB residue 208 ASP Chi-restraints excluded: chain DB residue 210 THR Chi-restraints excluded: chain DB residue 235 LYS Chi-restraints excluded: chain DB residue 367 CYS Chi-restraints excluded: chain DC residue 52 ASN Chi-restraints excluded: chain DC residue 151 VAL Chi-restraints excluded: chain DC residue 194 MET Chi-restraints excluded: chain DC residue 210 VAL Chi-restraints excluded: chain DC residue 236 ILE Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DC residue 407 ASN Chi-restraints excluded: chain DD residue 130 SER Chi-restraints excluded: chain DE residue 33 GLU Chi-restraints excluded: chain EA residue 53 VAL Chi-restraints excluded: chain EA residue 61 GLU Chi-restraints excluded: chain EA residue 124 THR Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EA residue 164 VAL Chi-restraints excluded: chain EA residue 186 THR Chi-restraints excluded: chain EB residue 82 PHE Chi-restraints excluded: chain EB residue 164 GLN Chi-restraints excluded: chain EB residue 178 SER Chi-restraints excluded: chain EB residue 354 ILE Chi-restraints excluded: chain EC residue 52 ASN Chi-restraints excluded: chain EC residue 133 MET Chi-restraints excluded: chain EC residue 210 VAL Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain EC residue 415 MET Chi-restraints excluded: chain EC residue 478 SER Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 106 VAL Chi-restraints excluded: chain ED residue 116 SER Chi-restraints excluded: chain ED residue 120 LYS Chi-restraints excluded: chain ED residue 130 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 31 GLU Chi-restraints excluded: chain EE residue 33 GLU Chi-restraints excluded: chain EE residue 115 GLN Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 53 VAL Chi-restraints excluded: chain FA residue 61 GLU Chi-restraints excluded: chain FA residue 160 GLN Chi-restraints excluded: chain FA residue 186 THR Chi-restraints excluded: chain FB residue 186 SER Chi-restraints excluded: chain FB residue 206 ASN Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 194 MET Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FC residue 324 SER Chi-restraints excluded: chain FC residue 478 SER Chi-restraints excluded: chain FD residue 130 SER Chi-restraints excluded: chain FE residue 33 GLU Chi-restraints excluded: chain FE residue 125 GLU Chi-restraints excluded: chain FE residue 132 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 699 optimal weight: 4.9990 chunk 736 optimal weight: 9.9990 chunk 672 optimal weight: 8.9990 chunk 716 optimal weight: 20.0000 chunk 431 optimal weight: 20.0000 chunk 312 optimal weight: 7.9990 chunk 562 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 647 optimal weight: 10.0000 chunk 677 optimal weight: 7.9990 chunk 714 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 190 HIS AB 271 ASN ** AC 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 374 ASN BB 190 HIS BB 271 ASN BC 52 ASN ** BC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 67 GLN CB 190 HIS CB 271 ASN ** CC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 190 HIS DB 271 ASN ** DC 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 190 HIS EB 271 ASN ** EC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ED 67 GLN FB 190 HIS FC 75 ASN ** FC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 65988 Z= 0.397 Angle : 0.673 7.275 89862 Z= 0.358 Chirality : 0.048 0.162 10014 Planarity : 0.005 0.043 11730 Dihedral : 4.993 23.808 8772 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.29 % Allowed : 14.58 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.86 (0.09), residues: 8028 helix: 0.83 (0.13), residues: 1440 sheet: 0.21 (0.10), residues: 2436 loop : -1.61 (0.09), residues: 4152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPCD 15 HIS 0.008 0.002 HISFB 190 PHE 0.021 0.002 PHEED 56 TYR 0.017 0.002 TYRCE 37 ARG 0.006 0.001 ARGCB 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 272 time to evaluate : 6.042 Fit side-chains REVERT: AA 61 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: AB 82 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8512 (p90) REVERT: AC 236 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8886 (mm) REVERT: AE 88 ASP cc_start: 0.8301 (m-30) cc_final: 0.8070 (m-30) REVERT: AE 125 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: BA 61 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: BB 82 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8522 (p90) REVERT: BB 164 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7986 (mp-120) REVERT: BC 177 MET cc_start: 0.8127 (mmt) cc_final: 0.7811 (mmt) REVERT: BC 448 MET cc_start: 0.9189 (mtp) cc_final: 0.8782 (mtp) REVERT: BE 115 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: CA 61 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: CC 97 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8118 (mtpm) REVERT: CE 33 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6790 (tt0) REVERT: CE 50 MET cc_start: 0.9156 (ptt) cc_final: 0.8860 (ptt) REVERT: CE 132 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: DA 61 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: DB 82 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8509 (p90) REVERT: DC 236 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8883 (mm) REVERT: DE 88 ASP cc_start: 0.8306 (m-30) cc_final: 0.8075 (m-30) REVERT: DE 125 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: EA 61 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: EB 82 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8524 (p90) REVERT: EB 164 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7978 (mp-120) REVERT: EC 133 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7743 (ptp) REVERT: EC 177 MET cc_start: 0.8126 (mmt) cc_final: 0.7811 (mmt) REVERT: EC 448 MET cc_start: 0.9193 (mtp) cc_final: 0.8789 (mtp) REVERT: EE 115 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7986 (mt0) REVERT: FA 61 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7529 (tt0) REVERT: FC 97 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8118 (mtpm) REVERT: FE 33 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: FE 50 MET cc_start: 0.9159 (ptt) cc_final: 0.8859 (ptt) REVERT: FE 132 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7450 (tm-30) outliers start: 161 outliers final: 106 residues processed: 416 average time/residue: 1.5365 time to fit residues: 824.8483 Evaluate side-chains 399 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 268 time to evaluate : 5.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 53 VAL Chi-restraints excluded: chain AA residue 61 GLU Chi-restraints excluded: chain AA residue 124 THR Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AA residue 164 VAL Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 24 THR Chi-restraints excluded: chain AB residue 82 PHE Chi-restraints excluded: chain AB residue 178 SER Chi-restraints excluded: chain AB residue 186 SER Chi-restraints excluded: chain AB residue 208 ASP Chi-restraints excluded: chain AB residue 210 THR Chi-restraints excluded: chain AB residue 235 LYS Chi-restraints excluded: chain AB residue 367 CYS Chi-restraints excluded: chain AC residue 52 ASN Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 210 VAL Chi-restraints excluded: chain AC residue 236 ILE Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AC residue 324 SER Chi-restraints excluded: chain AC residue 407 ASN Chi-restraints excluded: chain AC residue 478 SER Chi-restraints excluded: chain AD residue 130 SER Chi-restraints excluded: chain AE residue 125 GLU Chi-restraints excluded: chain BA residue 53 VAL Chi-restraints excluded: chain BA residue 61 GLU Chi-restraints excluded: chain BA residue 124 THR Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BA residue 164 VAL Chi-restraints excluded: chain BA residue 186 THR Chi-restraints excluded: chain BB residue 82 PHE Chi-restraints excluded: chain BB residue 164 GLN Chi-restraints excluded: chain BB residue 178 SER Chi-restraints excluded: chain BB residue 271 ASN Chi-restraints excluded: chain BB residue 354 ILE Chi-restraints excluded: chain BC residue 210 VAL Chi-restraints excluded: chain BC residue 224 ASP Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BC residue 478 SER Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 106 VAL Chi-restraints excluded: chain BD residue 116 SER Chi-restraints excluded: chain BD residue 120 LYS Chi-restraints excluded: chain BD residue 130 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 31 GLU Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 53 VAL Chi-restraints excluded: chain CA residue 61 GLU Chi-restraints excluded: chain CA residue 74 ASP Chi-restraints excluded: chain CA residue 160 GLN Chi-restraints excluded: chain CA residue 186 THR Chi-restraints excluded: chain CB residue 186 SER Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 194 MET Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CC residue 324 SER Chi-restraints excluded: chain CC residue 478 SER Chi-restraints excluded: chain CD residue 120 LYS Chi-restraints excluded: chain CD residue 130 SER Chi-restraints excluded: chain CE residue 33 GLU Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain CE residue 132 GLU Chi-restraints excluded: chain DA residue 53 VAL Chi-restraints excluded: chain DA residue 61 GLU Chi-restraints excluded: chain DA residue 124 THR Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DA residue 164 VAL Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 24 THR Chi-restraints excluded: chain DB residue 82 PHE Chi-restraints excluded: chain DB residue 178 SER Chi-restraints excluded: chain DB residue 186 SER Chi-restraints excluded: chain DB residue 208 ASP Chi-restraints excluded: chain DB residue 210 THR Chi-restraints excluded: chain DB residue 235 LYS Chi-restraints excluded: chain DB residue 367 CYS Chi-restraints excluded: chain DC residue 52 ASN Chi-restraints excluded: chain DC residue 151 VAL Chi-restraints excluded: chain DC residue 210 VAL Chi-restraints excluded: chain DC residue 236 ILE Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DC residue 324 SER Chi-restraints excluded: chain DC residue 407 ASN Chi-restraints excluded: chain DC residue 478 SER Chi-restraints excluded: chain DD residue 130 SER Chi-restraints excluded: chain DE residue 125 GLU Chi-restraints excluded: chain EA residue 53 VAL Chi-restraints excluded: chain EA residue 61 GLU Chi-restraints excluded: chain EA residue 124 THR Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EA residue 164 VAL Chi-restraints excluded: chain EA residue 186 THR Chi-restraints excluded: chain EB residue 82 PHE Chi-restraints excluded: chain EB residue 164 GLN Chi-restraints excluded: chain EB residue 178 SER Chi-restraints excluded: chain EB residue 271 ASN Chi-restraints excluded: chain EB residue 354 ILE Chi-restraints excluded: chain EC residue 52 ASN Chi-restraints excluded: chain EC residue 133 MET Chi-restraints excluded: chain EC residue 210 VAL Chi-restraints excluded: chain EC residue 224 ASP Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain EC residue 478 SER Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 106 VAL Chi-restraints excluded: chain ED residue 116 SER Chi-restraints excluded: chain ED residue 120 LYS Chi-restraints excluded: chain ED residue 130 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 31 GLU Chi-restraints excluded: chain EE residue 115 GLN Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 53 VAL Chi-restraints excluded: chain FA residue 61 GLU Chi-restraints excluded: chain FA residue 160 GLN Chi-restraints excluded: chain FA residue 186 THR Chi-restraints excluded: chain FB residue 186 SER Chi-restraints excluded: chain FC residue 75 ASN Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FC residue 324 SER Chi-restraints excluded: chain FC residue 478 SER Chi-restraints excluded: chain FD residue 120 LYS Chi-restraints excluded: chain FD residue 130 SER Chi-restraints excluded: chain FE residue 33 GLU Chi-restraints excluded: chain FE residue 125 GLU Chi-restraints excluded: chain FE residue 132 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 470 optimal weight: 9.9990 chunk 757 optimal weight: 7.9990 chunk 462 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 526 optimal weight: 6.9990 chunk 795 optimal weight: 4.9990 chunk 731 optimal weight: 8.9990 chunk 633 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 489 optimal weight: 0.9990 chunk 388 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 190 HIS AB 271 ASN ** AC 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 374 ASN BB 190 HIS ** BC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 190 HIS DB 271 ASN ** DC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 190 HIS EB 271 ASN ** EC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 65988 Z= 0.201 Angle : 0.536 8.304 89862 Z= 0.285 Chirality : 0.044 0.173 10014 Planarity : 0.004 0.040 11730 Dihedral : 4.543 22.058 8772 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.83 % Allowed : 15.22 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.63 (0.09), residues: 8028 helix: 1.11 (0.14), residues: 1440 sheet: 0.52 (0.11), residues: 2166 loop : -1.48 (0.08), residues: 4422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPCA 153 HIS 0.005 0.001 HISCB 190 PHE 0.012 0.001 PHEBD 56 TYR 0.013 0.001 TYRFC 35 ARG 0.003 0.000 ARGCA 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16056 Ramachandran restraints generated. 8028 Oldfield, 0 Emsley, 8028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 277 time to evaluate : 6.019 Fit side-chains REVERT: AC 236 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8885 (mm) REVERT: AE 33 GLU cc_start: 0.7150 (pt0) cc_final: 0.6856 (tt0) REVERT: BA 61 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: BB 164 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7792 (mp-120) REVERT: BB 235 LYS cc_start: 0.7110 (mppt) cc_final: 0.6652 (mmtm) REVERT: BC 177 MET cc_start: 0.8051 (mmt) cc_final: 0.7816 (mmt) REVERT: BC 223 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6534 (mp10) REVERT: BC 448 MET cc_start: 0.9210 (mtp) cc_final: 0.8761 (mtp) REVERT: BE 115 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: CA 61 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: CC 97 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8068 (mtpm) REVERT: CE 50 MET cc_start: 0.9059 (ptt) cc_final: 0.8731 (ptt) REVERT: DC 236 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8883 (mm) REVERT: DE 33 GLU cc_start: 0.7144 (pt0) cc_final: 0.6857 (tt0) REVERT: EA 61 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: EB 164 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7790 (mp-120) REVERT: EB 235 LYS cc_start: 0.7109 (mppt) cc_final: 0.6649 (mmtm) REVERT: EC 133 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7728 (ptp) REVERT: EC 177 MET cc_start: 0.8050 (mmt) cc_final: 0.7817 (mmt) REVERT: EC 223 GLN cc_start: 0.7477 (OUTLIER) cc_final: 0.6514 (mp10) REVERT: EC 448 MET cc_start: 0.9213 (mtp) cc_final: 0.8768 (mtp) REVERT: EE 115 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: FA 61 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: FC 97 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8073 (mtpm) REVERT: FE 50 MET cc_start: 0.9057 (ptt) cc_final: 0.8728 (ptt) outliers start: 129 outliers final: 88 residues processed: 395 average time/residue: 1.4831 time to fit residues: 757.4664 Evaluate side-chains 373 residues out of total 7032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 270 time to evaluate : 6.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AA residue 53 VAL Chi-restraints excluded: chain AA residue 143 SER Chi-restraints excluded: chain AA residue 164 VAL Chi-restraints excluded: chain AB residue 11 LEU Chi-restraints excluded: chain AB residue 178 SER Chi-restraints excluded: chain AB residue 186 SER Chi-restraints excluded: chain AB residue 208 ASP Chi-restraints excluded: chain AB residue 210 THR Chi-restraints excluded: chain AB residue 235 LYS Chi-restraints excluded: chain AC residue 52 ASN Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 210 VAL Chi-restraints excluded: chain AC residue 236 ILE Chi-restraints excluded: chain AC residue 298 SER Chi-restraints excluded: chain AC residue 324 SER Chi-restraints excluded: chain AC residue 407 ASN Chi-restraints excluded: chain AD residue 130 SER Chi-restraints excluded: chain BA residue 53 VAL Chi-restraints excluded: chain BA residue 61 GLU Chi-restraints excluded: chain BA residue 124 THR Chi-restraints excluded: chain BA residue 143 SER Chi-restraints excluded: chain BA residue 164 VAL Chi-restraints excluded: chain BA residue 186 THR Chi-restraints excluded: chain BB residue 164 GLN Chi-restraints excluded: chain BB residue 178 SER Chi-restraints excluded: chain BB residue 354 ILE Chi-restraints excluded: chain BC residue 210 VAL Chi-restraints excluded: chain BC residue 223 GLN Chi-restraints excluded: chain BC residue 224 ASP Chi-restraints excluded: chain BC residue 298 SER Chi-restraints excluded: chain BC residue 359 LYS Chi-restraints excluded: chain BC residue 478 SER Chi-restraints excluded: chain BD residue 89 LEU Chi-restraints excluded: chain BD residue 106 VAL Chi-restraints excluded: chain BD residue 120 LYS Chi-restraints excluded: chain BD residue 130 SER Chi-restraints excluded: chain BE residue 8 LYS Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 125 GLU Chi-restraints excluded: chain CA residue 53 VAL Chi-restraints excluded: chain CA residue 61 GLU Chi-restraints excluded: chain CA residue 186 THR Chi-restraints excluded: chain CB residue 186 SER Chi-restraints excluded: chain CC residue 97 LYS Chi-restraints excluded: chain CC residue 194 MET Chi-restraints excluded: chain CC residue 298 SER Chi-restraints excluded: chain CC residue 324 SER Chi-restraints excluded: chain CC residue 478 SER Chi-restraints excluded: chain CD residue 120 LYS Chi-restraints excluded: chain CD residue 130 SER Chi-restraints excluded: chain CE residue 125 GLU Chi-restraints excluded: chain DA residue 53 VAL Chi-restraints excluded: chain DA residue 143 SER Chi-restraints excluded: chain DA residue 164 VAL Chi-restraints excluded: chain DB residue 11 LEU Chi-restraints excluded: chain DB residue 178 SER Chi-restraints excluded: chain DB residue 186 SER Chi-restraints excluded: chain DB residue 208 ASP Chi-restraints excluded: chain DB residue 210 THR Chi-restraints excluded: chain DB residue 235 LYS Chi-restraints excluded: chain DC residue 52 ASN Chi-restraints excluded: chain DC residue 151 VAL Chi-restraints excluded: chain DC residue 210 VAL Chi-restraints excluded: chain DC residue 236 ILE Chi-restraints excluded: chain DC residue 298 SER Chi-restraints excluded: chain DC residue 324 SER Chi-restraints excluded: chain DC residue 407 ASN Chi-restraints excluded: chain DD residue 130 SER Chi-restraints excluded: chain EA residue 53 VAL Chi-restraints excluded: chain EA residue 61 GLU Chi-restraints excluded: chain EA residue 124 THR Chi-restraints excluded: chain EA residue 143 SER Chi-restraints excluded: chain EA residue 164 VAL Chi-restraints excluded: chain EA residue 186 THR Chi-restraints excluded: chain EB residue 164 GLN Chi-restraints excluded: chain EB residue 178 SER Chi-restraints excluded: chain EB residue 354 ILE Chi-restraints excluded: chain EC residue 133 MET Chi-restraints excluded: chain EC residue 210 VAL Chi-restraints excluded: chain EC residue 223 GLN Chi-restraints excluded: chain EC residue 224 ASP Chi-restraints excluded: chain EC residue 298 SER Chi-restraints excluded: chain EC residue 359 LYS Chi-restraints excluded: chain EC residue 478 SER Chi-restraints excluded: chain ED residue 89 LEU Chi-restraints excluded: chain ED residue 106 VAL Chi-restraints excluded: chain ED residue 120 LYS Chi-restraints excluded: chain ED residue 130 SER Chi-restraints excluded: chain EE residue 8 LYS Chi-restraints excluded: chain EE residue 115 GLN Chi-restraints excluded: chain EE residue 125 GLU Chi-restraints excluded: chain FA residue 53 VAL Chi-restraints excluded: chain FA residue 61 GLU Chi-restraints excluded: chain FA residue 186 THR Chi-restraints excluded: chain FB residue 186 SER Chi-restraints excluded: chain FC residue 97 LYS Chi-restraints excluded: chain FC residue 194 MET Chi-restraints excluded: chain FC residue 298 SER Chi-restraints excluded: chain FC residue 324 SER Chi-restraints excluded: chain FC residue 478 SER Chi-restraints excluded: chain FD residue 120 LYS Chi-restraints excluded: chain FD residue 130 SER Chi-restraints excluded: chain FE residue 125 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 502 optimal weight: 10.0000 chunk 674 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 583 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 634 optimal weight: 9.9990 chunk 265 optimal weight: 6.9990 chunk 651 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 190 HIS AB 271 ASN ** AC 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 374 ASN BB 190 HIS BB 271 ASN ** BC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DB 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 190 HIS DB 271 ASN ** DC 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DC 374 ASN EB 190 HIS EB 271 ASN ** EC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FC 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.091336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077904 restraints weight = 145967.495| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.92 r_work: 0.3052 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 65988 Z= 0.295 Angle : 0.602 8.275 89862 Z= 0.319 Chirality : 0.046 0.151 10014 Planarity : 0.005 0.043 11730 Dihedral : 4.729 22.879 8772 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.86 % Allowed : 15.16 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.74 (0.09), residues: 8028 helix: 1.04 (0.14), residues: 1434 sheet: 0.26 (0.10), residues: 2448 loop : -1.56 (0.09), residues: 4146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPDB 224 HIS 0.008 0.001 HISCB 190 PHE 0.017 0.002 PHEED 56 TYR 0.014 0.002 TYRFE 37 ARG 0.004 0.001 ARGCA 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15870.47 seconds wall clock time: 278 minutes 25.42 seconds (16705.42 seconds total)