Starting phenix.real_space_refine on Sat Feb 24 08:03:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d84_30612/02_2024/7d84_30612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d84_30612/02_2024/7d84_30612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d84_30612/02_2024/7d84_30612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d84_30612/02_2024/7d84_30612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d84_30612/02_2024/7d84_30612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d84_30612/02_2024/7d84_30612.pdb" } resolution = 3.7 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= -0.004 sd= 0.093 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 102 5.16 5 C 26044 2.51 5 N 7990 2.21 5 O 8568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 244": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ASP 414": "OD1" <-> "OD2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E ASP 414": "OD1" <-> "OD2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ASP 414": "OD1" <-> "OD2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 384": "NH1" <-> "NH2" Residue "G ASP 414": "OD1" <-> "OD2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 384": "NH1" <-> "NH2" Residue "H ASP 414": "OD1" <-> "OD2" Residue "I ARG 244": "NH1" <-> "NH2" Residue "I TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 384": "NH1" <-> "NH2" Residue "I ASP 414": "OD1" <-> "OD2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 384": "NH1" <-> "NH2" Residue "J ASP 414": "OD1" <-> "OD2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 384": "NH1" <-> "NH2" Residue "K ASP 414": "OD1" <-> "OD2" Residue "L ARG 244": "NH1" <-> "NH2" Residue "L TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L ASP 414": "OD1" <-> "OD2" Residue "M ARG 244": "NH1" <-> "NH2" Residue "M TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 384": "NH1" <-> "NH2" Residue "M ASP 414": "OD1" <-> "OD2" Residue "N ARG 244": "NH1" <-> "NH2" Residue "N TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 384": "NH1" <-> "NH2" Residue "N ASP 414": "OD1" <-> "OD2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 384": "NH1" <-> "NH2" Residue "O ASP 414": "OD1" <-> "OD2" Residue "P ARG 244": "NH1" <-> "NH2" Residue "P TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 384": "NH1" <-> "NH2" Residue "P ASP 414": "OD1" <-> "OD2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 384": "NH1" <-> "NH2" Residue "Q ASP 414": "OD1" <-> "OD2" Residue "R ARG 244": "NH1" <-> "NH2" Residue "R TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 384": "NH1" <-> "NH2" Residue "R ASP 414": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 384": "NH1" <-> "NH2" Residue "S ASP 414": "OD1" <-> "OD2" Residue "T ARG 244": "NH1" <-> "NH2" Residue "T TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 384": "NH1" <-> "NH2" Residue "T ASP 414": "OD1" <-> "OD2" Residue "U ARG 244": "NH1" <-> "NH2" Residue "U TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 384": "NH1" <-> "NH2" Residue "U ASP 414": "OD1" <-> "OD2" Residue "V ARG 244": "NH1" <-> "NH2" Residue "V TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 384": "NH1" <-> "NH2" Residue "V ASP 414": "OD1" <-> "OD2" Residue "W ARG 244": "NH1" <-> "NH2" Residue "W TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 384": "NH1" <-> "NH2" Residue "W ASP 414": "OD1" <-> "OD2" Residue "X ARG 244": "NH1" <-> "NH2" Residue "X TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 384": "NH1" <-> "NH2" Residue "X ASP 414": "OD1" <-> "OD2" Residue "Y ARG 244": "NH1" <-> "NH2" Residue "Y TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 384": "NH1" <-> "NH2" Residue "Y ASP 414": "OD1" <-> "OD2" Residue "Z ARG 244": "NH1" <-> "NH2" Residue "Z TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 384": "NH1" <-> "NH2" Residue "Z ASP 414": "OD1" <-> "OD2" Residue "a ARG 244": "NH1" <-> "NH2" Residue "a TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "a ASP 414": "OD1" <-> "OD2" Residue "b ARG 244": "NH1" <-> "NH2" Residue "b TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "b ASP 414": "OD1" <-> "OD2" Residue "c ARG 244": "NH1" <-> "NH2" Residue "c TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "c ASP 414": "OD1" <-> "OD2" Residue "d ARG 244": "NH1" <-> "NH2" Residue "d TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "d ASP 414": "OD1" <-> "OD2" Residue "e ARG 244": "NH1" <-> "NH2" Residue "e TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "e ASP 414": "OD1" <-> "OD2" Residue "f ARG 244": "NH1" <-> "NH2" Residue "f TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "f ASP 414": "OD1" <-> "OD2" Residue "g ARG 244": "NH1" <-> "NH2" Residue "g TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 384": "NH1" <-> "NH2" Residue "g ASP 414": "OD1" <-> "OD2" Residue "h ARG 244": "NH1" <-> "NH2" Residue "h TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 384": "NH1" <-> "NH2" Residue "h ASP 414": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42704 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "B" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "C" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "E" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "F" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "G" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "I" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "J" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "K" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "L" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "M" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "N" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "O" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "P" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "Q" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "R" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "S" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "T" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "U" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "V" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "W" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "X" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "Y" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "Z" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "a" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "b" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "c" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "d" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "e" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "f" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "g" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Chain: "h" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1256 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 2 Time building chain proxies: 20.47, per 1000 atoms: 0.48 Number of scatterers: 42704 At special positions: 0 Unit cell: (262.15, 260.01, 96.3, 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 102 16.00 O 8568 8.00 N 7990 7.00 C 26044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.87 Conformation dependent library (CDL) restraints added in 8.2 seconds 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10404 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 36 sheets defined 32.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.10 Creating SS restraints... Processing helix chain 'A' and resid 228 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA A 291 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA B 291 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA C 291 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA D 291 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.533A pdb=" N ALA E 291 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA F 291 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA G 291 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA H 291 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA I 291 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA J 291 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA K 291 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA L 291 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA M 291 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA N 291 " --> pdb=" O ALA N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA O 291 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 229 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA P 291 " --> pdb=" O ALA P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 229 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Q 291 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA R 291 " --> pdb=" O ALA R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 229 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA S 291 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 229 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 287 through 291 removed outlier: 3.533A pdb=" N ALA T 291 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA U 291 " --> pdb=" O ALA U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 229 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA V 291 " --> pdb=" O ALA V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 229 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA W 291 " --> pdb=" O ALA W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 229 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA X 291 " --> pdb=" O ALA X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 229 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Y 291 " --> pdb=" O ALA Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 229 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA Z 291 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 229 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA a 291 " --> pdb=" O ALA a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 229 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA b 291 " --> pdb=" O ALA b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'c' and resid 229 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA c 291 " --> pdb=" O ALA c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY c 421 " --> pdb=" O ARG c 417 " (cutoff:3.500A) Processing helix chain 'd' and resid 229 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA d 291 " --> pdb=" O ALA d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY d 421 " --> pdb=" O ARG d 417 " (cutoff:3.500A) Processing helix chain 'e' and resid 229 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA e 291 " --> pdb=" O ALA e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 229 through 258 Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA f 291 " --> pdb=" O ALA f 288 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY f 421 " --> pdb=" O ARG f 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 229 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA g 291 " --> pdb=" O ALA g 288 " (cutoff:3.500A) Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.565A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing helix chain 'h' and resid 229 through 258 Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 287 through 291 removed outlier: 3.534A pdb=" N ALA h 291 " --> pdb=" O ALA h 288 " (cutoff:3.500A) Processing helix chain 'h' and resid 405 through 421 removed outlier: 3.566A pdb=" N GLY h 421 " --> pdb=" O ARG h 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 279 removed outlier: 3.518A pdb=" N GLU B 276 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN B 274 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 276 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 274 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU D 276 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN D 274 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 276 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN E 274 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 276 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN F 274 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU G 276 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN G 274 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU H 276 " --> pdb=" O HIS G 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN H 274 " --> pdb=" O LYS G 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU I 276 " --> pdb=" O HIS H 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN I 274 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU J 276 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN J 274 " --> pdb=" O LYS I 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU K 276 " --> pdb=" O HIS J 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN K 274 " --> pdb=" O LYS J 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU L 276 " --> pdb=" O HIS K 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN L 274 " --> pdb=" O LYS K 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU M 276 " --> pdb=" O HIS L 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN M 274 " --> pdb=" O LYS L 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 276 " --> pdb=" O HIS M 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN N 274 " --> pdb=" O LYS M 376 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 276 " --> pdb=" O HIS O 374 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN P 274 " --> pdb=" O LYS O 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Q 276 " --> pdb=" O HIS P 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN Q 274 " --> pdb=" O LYS P 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU R 276 " --> pdb=" O HIS Q 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN R 274 " --> pdb=" O LYS Q 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU S 276 " --> pdb=" O HIS R 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN S 274 " --> pdb=" O LYS R 376 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU T 276 " --> pdb=" O HIS S 374 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN T 274 " --> pdb=" O LYS S 376 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN U 274 " --> pdb=" O LYS T 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU V 276 " --> pdb=" O HIS U 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN V 274 " --> pdb=" O LYS U 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU W 276 " --> pdb=" O HIS V 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN W 274 " --> pdb=" O LYS V 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU X 276 " --> pdb=" O HIS W 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN X 274 " --> pdb=" O LYS W 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU Y 276 " --> pdb=" O HIS X 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN Y 274 " --> pdb=" O LYS X 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Z 276 " --> pdb=" O HIS Y 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN Z 274 " --> pdb=" O LYS Y 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU a 276 " --> pdb=" O HIS Z 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN a 274 " --> pdb=" O LYS Z 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU b 276 " --> pdb=" O HIS a 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN b 274 " --> pdb=" O LYS a 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU c 276 " --> pdb=" O HIS b 374 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN c 274 " --> pdb=" O LYS b 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU d 276 " --> pdb=" O HIS c 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN d 274 " --> pdb=" O LYS c 376 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU e 276 " --> pdb=" O HIS d 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN e 274 " --> pdb=" O LYS d 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU f 276 " --> pdb=" O HIS e 374 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN f 274 " --> pdb=" O LYS e 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU g 276 " --> pdb=" O HIS f 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN g 274 " --> pdb=" O LYS f 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU h 276 " --> pdb=" O HIS g 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN h 274 " --> pdb=" O LYS g 376 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 276 " --> pdb=" O HIS h 374 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN A 274 " --> pdb=" O LYS h 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 302 removed outlier: 3.787A pdb=" N SER A 295 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 365 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 301 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 359 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG h 296 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER h 295 " --> pdb=" O ASN h 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN h 365 " --> pdb=" O SER h 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER h 301 " --> pdb=" O GLN h 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN h 359 " --> pdb=" O SER h 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG g 296 " --> pdb=" O SER h 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER g 295 " --> pdb=" O ASN g 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN g 365 " --> pdb=" O SER g 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER g 301 " --> pdb=" O GLN g 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN g 359 " --> pdb=" O SER g 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG f 296 " --> pdb=" O SER g 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER f 295 " --> pdb=" O ASN f 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN f 365 " --> pdb=" O SER f 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER f 301 " --> pdb=" O GLN f 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN f 359 " --> pdb=" O SER f 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG e 296 " --> pdb=" O SER f 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN e 365 " --> pdb=" O SER e 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER e 301 " --> pdb=" O GLN e 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN e 359 " --> pdb=" O SER e 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG d 296 " --> pdb=" O SER e 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER d 295 " --> pdb=" O ASN d 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN d 365 " --> pdb=" O SER d 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER d 301 " --> pdb=" O GLN d 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN d 359 " --> pdb=" O SER d 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG c 296 " --> pdb=" O SER d 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER c 295 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN c 365 " --> pdb=" O SER c 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER c 301 " --> pdb=" O GLN c 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN c 359 " --> pdb=" O SER c 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG b 296 " --> pdb=" O SER c 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER b 295 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN b 365 " --> pdb=" O SER b 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER b 301 " --> pdb=" O GLN b 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN b 359 " --> pdb=" O SER b 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG a 296 " --> pdb=" O SER b 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN a 365 " --> pdb=" O SER a 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER a 301 " --> pdb=" O GLN a 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN a 359 " --> pdb=" O SER a 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG Z 296 " --> pdb=" O SER a 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER Z 295 " --> pdb=" O ASN Z 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN Z 365 " --> pdb=" O SER Z 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER Z 301 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN Z 359 " --> pdb=" O SER Z 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG Y 296 " --> pdb=" O SER Z 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER Y 295 " --> pdb=" O ASN Y 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN Y 365 " --> pdb=" O SER Y 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER Y 301 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN Y 359 " --> pdb=" O SER Y 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG X 296 " --> pdb=" O SER Y 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER X 295 " --> pdb=" O ASN X 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN X 365 " --> pdb=" O SER X 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER X 301 " --> pdb=" O GLN X 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN X 359 " --> pdb=" O SER X 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG W 296 " --> pdb=" O SER X 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN W 365 " --> pdb=" O SER W 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER W 301 " --> pdb=" O GLN W 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN W 359 " --> pdb=" O SER W 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG V 296 " --> pdb=" O SER W 364 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER V 295 " --> pdb=" O ASN V 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN V 365 " --> pdb=" O SER V 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER V 301 " --> pdb=" O GLN V 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN V 359 " --> pdb=" O SER V 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG U 296 " --> pdb=" O SER V 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN U 365 " --> pdb=" O SER U 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER U 301 " --> pdb=" O GLN U 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN U 359 " --> pdb=" O SER U 301 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG T 296 " --> pdb=" O SER U 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER T 295 " --> pdb=" O ASN T 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN T 365 " --> pdb=" O SER T 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER T 301 " --> pdb=" O GLN T 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN T 359 " --> pdb=" O SER T 301 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG S 296 " --> pdb=" O SER T 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER S 295 " --> pdb=" O ASN S 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN S 365 " --> pdb=" O SER S 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER S 301 " --> pdb=" O GLN S 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN S 359 " --> pdb=" O SER S 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG R 296 " --> pdb=" O SER S 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER R 295 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN R 365 " --> pdb=" O SER R 295 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER R 301 " --> pdb=" O GLN R 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN R 359 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG Q 296 " --> pdb=" O SER R 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER Q 295 " --> pdb=" O ASN Q 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN Q 365 " --> pdb=" O SER Q 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER Q 301 " --> pdb=" O GLN Q 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN Q 359 " --> pdb=" O SER Q 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG P 296 " --> pdb=" O SER Q 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER P 295 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN P 365 " --> pdb=" O SER P 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER P 301 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN P 359 " --> pdb=" O SER P 301 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU O 302 " --> pdb=" O THR P 358 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG O 296 " --> pdb=" O SER P 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER O 295 " --> pdb=" O ASN O 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN O 365 " --> pdb=" O SER O 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER O 301 " --> pdb=" O GLN O 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN O 359 " --> pdb=" O SER O 301 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG N 296 " --> pdb=" O SER O 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER N 295 " --> pdb=" O ASN N 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN N 365 " --> pdb=" O SER N 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER N 301 " --> pdb=" O GLN N 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN N 359 " --> pdb=" O SER N 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG M 296 " --> pdb=" O SER N 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER M 295 " --> pdb=" O ASN M 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN M 365 " --> pdb=" O SER M 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER M 301 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN M 359 " --> pdb=" O SER M 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG L 296 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER L 295 " --> pdb=" O ASN L 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN L 365 " --> pdb=" O SER L 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER L 301 " --> pdb=" O GLN L 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN L 359 " --> pdb=" O SER L 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG K 296 " --> pdb=" O SER L 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER K 295 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN K 365 " --> pdb=" O SER K 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER K 301 " --> pdb=" O GLN K 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN K 359 " --> pdb=" O SER K 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG J 296 " --> pdb=" O SER K 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN J 365 " --> pdb=" O SER J 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER J 301 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN J 359 " --> pdb=" O SER J 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG I 296 " --> pdb=" O SER J 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER I 295 " --> pdb=" O ASN I 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN I 365 " --> pdb=" O SER I 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER I 301 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN I 359 " --> pdb=" O SER I 301 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG H 296 " --> pdb=" O SER I 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER H 295 " --> pdb=" O ASN H 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN H 365 " --> pdb=" O SER H 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 301 " --> pdb=" O GLN H 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN H 359 " --> pdb=" O SER H 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG G 296 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER G 295 " --> pdb=" O ASN G 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN G 365 " --> pdb=" O SER G 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER G 301 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN G 359 " --> pdb=" O SER G 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG F 296 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER F 295 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN F 365 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER F 301 " --> pdb=" O GLN F 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN F 359 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG E 296 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER E 295 " --> pdb=" O ASN E 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN E 365 " --> pdb=" O SER E 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER E 301 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN E 359 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 296 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER D 295 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN D 365 " --> pdb=" O SER D 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER D 301 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 359 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 296 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 295 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN C 365 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 301 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 359 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 296 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 295 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 365 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 301 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 359 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 296 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Q' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'f' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 262 through 270 removed outlier: 6.976A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 262 through 270 removed outlier: 6.977A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) 2043 hydrogen bonds defined for protein. 5718 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: 15.98 Time building geometry restraints manager: 19.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15229 1.34 - 1.45: 5119 1.45 - 1.57: 22594 1.57 - 1.68: 0 1.68 - 1.80: 204 Bond restraints: 43146 Sorted by residual: bond pdb=" CG ARG F 294 " pdb=" CD ARG F 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG W 294 " pdb=" CD ARG W 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG B 294 " pdb=" CD ARG B 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG S 294 " pdb=" CD ARG S 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CG ARG L 294 " pdb=" CD ARG L 294 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.62e+00 ... (remaining 43141 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.67: 1056 106.67 - 113.59: 25019 113.59 - 120.51: 16831 120.51 - 127.42: 14996 127.42 - 134.34: 272 Bond angle restraints: 58174 Sorted by residual: angle pdb=" N GLY P 421 " pdb=" CA GLY P 421 " pdb=" C GLY P 421 " ideal model delta sigma weight residual 114.16 108.65 5.51 2.00e+00 2.50e-01 7.58e+00 angle pdb=" N GLY g 421 " pdb=" CA GLY g 421 " pdb=" C GLY g 421 " ideal model delta sigma weight residual 114.16 108.65 5.51 2.00e+00 2.50e-01 7.58e+00 angle pdb=" N GLY H 421 " pdb=" CA GLY H 421 " pdb=" C GLY H 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 angle pdb=" N GLY Y 421 " pdb=" CA GLY Y 421 " pdb=" C GLY Y 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 angle pdb=" N GLY U 421 " pdb=" CA GLY U 421 " pdb=" C GLY U 421 " ideal model delta sigma weight residual 114.16 108.66 5.50 2.00e+00 2.50e-01 7.56e+00 ... (remaining 58169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.27: 21963 11.27 - 22.54: 2925 22.54 - 33.81: 1428 33.81 - 45.08: 374 45.08 - 56.35: 374 Dihedral angle restraints: 27064 sinusoidal: 11254 harmonic: 15810 Sorted by residual: dihedral pdb=" CA MET E 420 " pdb=" C MET E 420 " pdb=" N GLY E 421 " pdb=" CA GLY E 421 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET K 420 " pdb=" C MET K 420 " pdb=" N GLY K 421 " pdb=" CA GLY K 421 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA MET b 420 " pdb=" C MET b 420 " pdb=" N GLY b 421 " pdb=" CA GLY b 421 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 27061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3464 0.030 - 0.059: 2165 0.059 - 0.089: 640 0.089 - 0.118: 221 0.118 - 0.148: 208 Chirality restraints: 6698 Sorted by residual: chirality pdb=" CA PRO A 255 " pdb=" N PRO A 255 " pdb=" C PRO A 255 " pdb=" CB PRO A 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA PRO R 255 " pdb=" N PRO R 255 " pdb=" C PRO R 255 " pdb=" CB PRO R 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA PRO O 255 " pdb=" N PRO O 255 " pdb=" C PRO O 255 " pdb=" CB PRO O 255 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 6695 not shown) Planarity restraints: 7786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER d 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO d 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO d 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO d 255 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO M 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO M 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO M 255 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER Y 254 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.95e+00 pdb=" N PRO Y 255 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO Y 255 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 255 " -0.040 5.00e-02 4.00e+02 ... (remaining 7783 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 11711 2.80 - 3.32: 36254 3.32 - 3.85: 68608 3.85 - 4.37: 76405 4.37 - 4.90: 137058 Nonbonded interactions: 330036 Sorted by model distance: nonbonded pdb=" N ASP D 369 " pdb=" OD1 ASP D 369 " model vdw 2.271 2.520 nonbonded pdb=" N ASP U 369 " pdb=" OD1 ASP U 369 " model vdw 2.271 2.520 nonbonded pdb=" N ASP f 369 " pdb=" OD1 ASP f 369 " model vdw 2.271 2.520 nonbonded pdb=" N ASP C 369 " pdb=" OD1 ASP C 369 " model vdw 2.271 2.520 nonbonded pdb=" N ASP F 369 " pdb=" OD1 ASP F 369 " model vdw 2.271 2.520 ... (remaining 330031 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 19.690 Check model and map are aligned: 0.690 Set scattering table: 0.400 Process input model: 107.100 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.009 0.074 43146 Z= 0.595 Angle : 0.897 9.977 58174 Z= 0.496 Chirality : 0.047 0.148 6698 Planarity : 0.007 0.070 7786 Dihedral : 15.250 56.353 16660 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 7.78 % Allowed : 7.24 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.11), residues: 5202 helix: -0.63 (0.11), residues: 1462 sheet: -1.79 (0.10), residues: 2550 loop : -2.59 (0.15), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 263 PHE 0.015 0.003 PHE S 422 TYR 0.005 0.002 TYR I 366 ARG 0.003 0.001 ARG T 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1705 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 1332 time to evaluate : 5.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8295 (mt-10) REVERT: A 429 THR cc_start: 0.7766 (p) cc_final: 0.6995 (p) REVERT: B 246 GLN cc_start: 0.9040 (tt0) cc_final: 0.8758 (pt0) REVERT: B 267 THR cc_start: 0.9090 (m) cc_final: 0.8809 (p) REVERT: B 418 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8329 (mt-10) REVERT: C 267 THR cc_start: 0.9084 (m) cc_final: 0.8728 (p) REVERT: C 280 GLU cc_start: 0.7726 (tt0) cc_final: 0.7521 (tt0) REVERT: C 418 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8348 (mt-10) REVERT: D 250 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8088 (mt-10) REVERT: D 267 THR cc_start: 0.9076 (m) cc_final: 0.8837 (p) REVERT: D 409 MET cc_start: 0.8486 (mmm) cc_final: 0.8251 (tpp) REVERT: D 418 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8297 (mt-10) REVERT: E 246 GLN cc_start: 0.9072 (tt0) cc_final: 0.8754 (pt0) REVERT: E 267 THR cc_start: 0.9225 (m) cc_final: 0.8964 (p) REVERT: E 382 ILE cc_start: 0.9234 (mt) cc_final: 0.9033 (mt) REVERT: E 418 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8416 (mt-10) REVERT: F 246 GLN cc_start: 0.9024 (tt0) cc_final: 0.8730 (pt0) REVERT: F 267 THR cc_start: 0.9079 (m) cc_final: 0.8871 (p) REVERT: F 269 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8647 (mm-40) REVERT: F 302 GLU cc_start: 0.7877 (tt0) cc_final: 0.7473 (tm-30) REVERT: F 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8297 (mt-10) REVERT: G 267 THR cc_start: 0.9084 (m) cc_final: 0.8778 (p) REVERT: G 418 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8398 (mt-10) REVERT: H 267 THR cc_start: 0.9103 (m) cc_final: 0.8887 (p) REVERT: H 418 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8336 (mt-10) REVERT: I 267 THR cc_start: 0.9090 (m) cc_final: 0.8887 (p) REVERT: I 299 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7834 (m-40) REVERT: I 418 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8216 (mt-10) REVERT: J 267 THR cc_start: 0.9059 (m) cc_final: 0.8853 (p) REVERT: K 246 GLN cc_start: 0.9122 (tt0) cc_final: 0.8851 (pt0) REVERT: K 252 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9062 (tp) REVERT: K 267 THR cc_start: 0.9167 (m) cc_final: 0.8870 (p) REVERT: K 408 GLN cc_start: 0.8091 (tt0) cc_final: 0.7878 (tt0) REVERT: K 418 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8284 (mt-10) REVERT: L 246 GLN cc_start: 0.9035 (tt0) cc_final: 0.8777 (pt0) REVERT: L 267 THR cc_start: 0.9097 (m) cc_final: 0.8836 (p) REVERT: L 302 GLU cc_start: 0.7788 (tt0) cc_final: 0.7545 (tm-30) REVERT: L 418 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8253 (mt-10) REVERT: M 267 THR cc_start: 0.9115 (m) cc_final: 0.8868 (p) REVERT: M 418 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8258 (mt-10) REVERT: N 267 THR cc_start: 0.9104 (m) cc_final: 0.8861 (p) REVERT: N 418 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8227 (mt-10) REVERT: O 267 THR cc_start: 0.9091 (m) cc_final: 0.8843 (p) REVERT: O 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8162 (mt-10) REVERT: P 246 GLN cc_start: 0.9013 (tt0) cc_final: 0.8672 (pt0) REVERT: P 252 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9186 (tp) REVERT: P 267 THR cc_start: 0.9110 (m) cc_final: 0.8837 (p) REVERT: P 382 ILE cc_start: 0.9181 (mt) cc_final: 0.8953 (mm) REVERT: P 418 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8421 (mt-10) REVERT: Q 246 GLN cc_start: 0.9087 (tt0) cc_final: 0.8809 (pt0) REVERT: Q 252 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9132 (tp) REVERT: Q 267 THR cc_start: 0.9119 (m) cc_final: 0.8874 (p) REVERT: Q 302 GLU cc_start: 0.7770 (tt0) cc_final: 0.7470 (tm-30) REVERT: Q 418 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8371 (mt-10) REVERT: R 267 THR cc_start: 0.9039 (m) cc_final: 0.8826 (p) REVERT: R 418 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8295 (mt-10) REVERT: S 246 GLN cc_start: 0.9038 (tt0) cc_final: 0.8752 (pt0) REVERT: S 267 THR cc_start: 0.9094 (m) cc_final: 0.8810 (p) REVERT: S 418 GLU cc_start: 0.8667 (mm-30) cc_final: 0.7148 (mm-30) REVERT: T 267 THR cc_start: 0.9068 (m) cc_final: 0.8718 (p) REVERT: T 418 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8401 (mt-10) REVERT: T 429 THR cc_start: 0.7972 (p) cc_final: 0.7719 (p) REVERT: U 250 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8088 (mt-10) REVERT: U 267 THR cc_start: 0.9075 (m) cc_final: 0.8833 (p) REVERT: U 409 MET cc_start: 0.8482 (mmm) cc_final: 0.8243 (tpp) REVERT: U 418 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8298 (mt-10) REVERT: V 246 GLN cc_start: 0.9075 (tt0) cc_final: 0.8745 (pt0) REVERT: V 252 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9049 (tp) REVERT: V 267 THR cc_start: 0.9222 (m) cc_final: 0.8969 (p) REVERT: V 382 ILE cc_start: 0.9229 (mt) cc_final: 0.9029 (mt) REVERT: V 418 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8399 (mt-10) REVERT: W 246 GLN cc_start: 0.9029 (tt0) cc_final: 0.8719 (pt0) REVERT: W 269 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8634 (mm-40) REVERT: W 302 GLU cc_start: 0.7879 (tt0) cc_final: 0.7485 (tm-30) REVERT: W 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8286 (mt-10) REVERT: X 267 THR cc_start: 0.9084 (m) cc_final: 0.8775 (p) REVERT: X 418 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8399 (mt-10) REVERT: Y 267 THR cc_start: 0.9107 (m) cc_final: 0.8889 (p) REVERT: Y 418 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8336 (mt-10) REVERT: Z 267 THR cc_start: 0.9088 (m) cc_final: 0.8886 (p) REVERT: Z 299 ASN cc_start: 0.8086 (OUTLIER) cc_final: 0.7838 (m-40) REVERT: Z 418 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8208 (mt-10) REVERT: a 267 THR cc_start: 0.9063 (m) cc_final: 0.8856 (p) REVERT: b 246 GLN cc_start: 0.9125 (tt0) cc_final: 0.8853 (pt0) REVERT: b 252 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9067 (tp) REVERT: b 267 THR cc_start: 0.9170 (m) cc_final: 0.8873 (p) REVERT: b 408 GLN cc_start: 0.8091 (tt0) cc_final: 0.7873 (tt0) REVERT: b 418 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8279 (mt-10) REVERT: c 246 GLN cc_start: 0.9033 (tt0) cc_final: 0.8773 (pt0) REVERT: c 267 THR cc_start: 0.9100 (m) cc_final: 0.8841 (p) REVERT: c 302 GLU cc_start: 0.7795 (tt0) cc_final: 0.7548 (tm-30) REVERT: c 418 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8253 (mt-10) REVERT: d 267 THR cc_start: 0.9114 (m) cc_final: 0.8871 (p) REVERT: d 418 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8248 (mt-10) REVERT: e 267 THR cc_start: 0.9108 (m) cc_final: 0.8858 (p) REVERT: e 418 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8213 (mt-10) REVERT: f 267 THR cc_start: 0.9136 (m) cc_final: 0.8875 (p) REVERT: f 418 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8221 (mt-10) REVERT: g 246 GLN cc_start: 0.9009 (tt0) cc_final: 0.8676 (pt0) REVERT: g 252 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9181 (tp) REVERT: g 267 THR cc_start: 0.9105 (m) cc_final: 0.8844 (p) REVERT: g 418 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8421 (mt-10) REVERT: h 246 GLN cc_start: 0.9088 (tt0) cc_final: 0.8805 (pt0) REVERT: h 252 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9129 (tp) REVERT: h 267 THR cc_start: 0.9113 (m) cc_final: 0.8870 (p) REVERT: h 302 GLU cc_start: 0.7769 (tt0) cc_final: 0.7458 (tm-30) REVERT: h 418 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7509 (mm-30) outliers start: 373 outliers final: 138 residues processed: 1570 average time/residue: 0.5370 time to fit residues: 1357.5010 Evaluate side-chains 1290 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1143 time to evaluate : 5.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 435 SER Chi-restraints excluded: chain H residue 274 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 274 ASN Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 435 SER Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 287 ASP Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 252 ILE Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 435 SER Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 252 ILE Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 435 SER Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 274 ASN Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 435 SER Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 299 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 252 ILE Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 287 ASP Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 435 SER Chi-restraints excluded: chain h residue 252 ILE Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 0.0970 chunk 386 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 399 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 243 optimal weight: 4.9990 chunk 297 optimal weight: 8.9990 chunk 463 optimal weight: 1.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN A 434 ASN B 365 ASN B 408 GLN B 434 ASN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN D 365 ASN D 434 ASN E 365 ASN F 365 ASN F 434 ASN G 365 ASN H 365 ASN H 408 GLN H 434 ASN I 365 ASN ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 434 ASN J 365 ASN J 408 GLN J 434 ASN K 365 ASN K 434 ASN L 365 ASN L 408 GLN L 434 ASN M 365 ASN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 434 ASN N 365 ASN O 365 ASN P 365 ASN Q 365 ASN Q 408 GLN Q 434 ASN R 365 ASN R 434 ASN S 365 ASN S 408 GLN S 434 ASN ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 365 ASN U 365 ASN U 434 ASN V 365 ASN W 365 ASN W 434 ASN X 365 ASN Y 365 ASN Y 408 GLN Y 434 ASN Z 365 ASN ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 434 ASN a 365 ASN a 408 GLN a 434 ASN b 365 ASN b 434 ASN c 365 ASN c 408 GLN c 434 ASN d 365 ASN ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 434 ASN e 365 ASN f 365 ASN ** f 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 434 ASN g 365 ASN g 434 ASN h 365 ASN h 408 GLN h 434 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 43146 Z= 0.316 Angle : 0.666 6.906 58174 Z= 0.338 Chirality : 0.040 0.121 6698 Planarity : 0.004 0.042 7786 Dihedral : 6.840 53.996 6108 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.21 % Allowed : 19.67 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 5202 helix: 2.52 (0.13), residues: 1462 sheet: -1.31 (0.11), residues: 2482 loop : -2.30 (0.15), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 374 PHE 0.015 0.001 PHE G 422 TYR 0.012 0.001 TYR V 366 ARG 0.001 0.000 ARG f 384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1193 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: A 377 MET cc_start: 0.7846 (mmm) cc_final: 0.7483 (tmm) REVERT: A 418 GLU cc_start: 0.8701 (mm-30) cc_final: 0.7898 (mm-30) REVERT: B 267 THR cc_start: 0.9056 (m) cc_final: 0.8740 (p) REVERT: B 394 LYS cc_start: 0.7307 (ptpt) cc_final: 0.7076 (ptpt) REVERT: B 418 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7729 (mm-30) REVERT: C 267 THR cc_start: 0.9015 (m) cc_final: 0.8667 (p) REVERT: C 410 LYS cc_start: 0.8927 (tptt) cc_final: 0.8723 (tptt) REVERT: D 267 THR cc_start: 0.8979 (m) cc_final: 0.8704 (p) REVERT: D 275 LYS cc_start: 0.9068 (mttm) cc_final: 0.8725 (mttp) REVERT: D 418 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7601 (mm-30) REVERT: D 431 ASN cc_start: 0.8362 (t0) cc_final: 0.8137 (p0) REVERT: E 267 THR cc_start: 0.9130 (m) cc_final: 0.8904 (p) REVERT: E 394 LYS cc_start: 0.7126 (ptpt) cc_final: 0.6675 (pttm) REVERT: E 410 LYS cc_start: 0.8897 (tptt) cc_final: 0.8599 (tptt) REVERT: E 418 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7768 (mm-30) REVERT: F 256 ILE cc_start: 0.8960 (mm) cc_final: 0.8714 (mm) REVERT: F 410 LYS cc_start: 0.8929 (tptt) cc_final: 0.8719 (tptt) REVERT: F 418 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7680 (mm-30) REVERT: G 242 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: G 267 THR cc_start: 0.9062 (m) cc_final: 0.8679 (p) REVERT: G 418 GLU cc_start: 0.8535 (mm-30) cc_final: 0.6965 (mm-30) REVERT: H 267 THR cc_start: 0.9040 (m) cc_final: 0.8828 (p) REVERT: H 302 GLU cc_start: 0.7673 (tt0) cc_final: 0.7396 (tm-30) REVERT: H 394 LYS cc_start: 0.7124 (ptpt) cc_final: 0.6655 (pttm) REVERT: I 267 THR cc_start: 0.9059 (m) cc_final: 0.8793 (p) REVERT: I 299 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7555 (m-40) REVERT: I 410 LYS cc_start: 0.8888 (tptt) cc_final: 0.8535 (tptt) REVERT: I 418 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7510 (mm-30) REVERT: J 267 THR cc_start: 0.9040 (m) cc_final: 0.8786 (p) REVERT: J 394 LYS cc_start: 0.7517 (ptpp) cc_final: 0.7172 (ptpp) REVERT: J 400 LYS cc_start: 0.8771 (mppt) cc_final: 0.8557 (mtmm) REVERT: K 267 THR cc_start: 0.9109 (m) cc_final: 0.8811 (p) REVERT: K 410 LYS cc_start: 0.8822 (tptt) cc_final: 0.8588 (tptt) REVERT: K 418 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7685 (mm-30) REVERT: L 267 THR cc_start: 0.9089 (m) cc_final: 0.8806 (p) REVERT: L 275 LYS cc_start: 0.8895 (mttm) cc_final: 0.8560 (mttp) REVERT: L 418 GLU cc_start: 0.8684 (mm-30) cc_final: 0.7665 (mm-30) REVERT: M 267 THR cc_start: 0.9112 (m) cc_final: 0.8838 (p) REVERT: M 394 LYS cc_start: 0.7004 (ptpt) cc_final: 0.6718 (pttm) REVERT: M 410 LYS cc_start: 0.8919 (tptt) cc_final: 0.8653 (tptt) REVERT: N 267 THR cc_start: 0.9111 (m) cc_final: 0.8804 (p) REVERT: N 377 MET cc_start: 0.7689 (mmm) cc_final: 0.7437 (tmm) REVERT: N 410 LYS cc_start: 0.8944 (tptt) cc_final: 0.8716 (tptt) REVERT: O 242 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: O 267 THR cc_start: 0.9087 (m) cc_final: 0.8809 (p) REVERT: O 302 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7029 (tm-30) REVERT: O 410 LYS cc_start: 0.8951 (tptt) cc_final: 0.8685 (tptt) REVERT: O 418 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8028 (mm-30) REVERT: P 267 THR cc_start: 0.9054 (m) cc_final: 0.8817 (p) REVERT: P 377 MET cc_start: 0.7923 (tmm) cc_final: 0.7620 (tmm) REVERT: P 394 LYS cc_start: 0.7702 (ptpp) cc_final: 0.7390 (ptpp) REVERT: P 418 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7678 (mm-30) REVERT: Q 267 THR cc_start: 0.9097 (m) cc_final: 0.8826 (p) REVERT: Q 302 GLU cc_start: 0.7374 (tt0) cc_final: 0.7079 (tm-30) REVERT: Q 418 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7724 (mm-30) REVERT: R 242 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: R 267 THR cc_start: 0.9023 (m) cc_final: 0.8781 (p) REVERT: R 377 MET cc_start: 0.7843 (mmm) cc_final: 0.7483 (tmm) REVERT: R 418 GLU cc_start: 0.8695 (mm-30) cc_final: 0.7885 (mm-30) REVERT: S 267 THR cc_start: 0.9061 (m) cc_final: 0.8737 (p) REVERT: S 394 LYS cc_start: 0.7275 (ptpt) cc_final: 0.7041 (ptpt) REVERT: S 418 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7928 (mt-10) REVERT: T 242 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: T 252 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8874 (tp) REVERT: T 267 THR cc_start: 0.9022 (m) cc_final: 0.8664 (p) REVERT: T 418 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7645 (mm-30) REVERT: U 267 THR cc_start: 0.8991 (m) cc_final: 0.8730 (p) REVERT: U 418 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7602 (mm-30) REVERT: V 267 THR cc_start: 0.9146 (m) cc_final: 0.8890 (p) REVERT: V 377 MET cc_start: 0.8020 (mmm) cc_final: 0.7686 (tpp) REVERT: V 410 LYS cc_start: 0.8956 (tptt) cc_final: 0.8656 (tptt) REVERT: V 418 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7712 (mm-30) REVERT: W 256 ILE cc_start: 0.8954 (mm) cc_final: 0.8705 (mm) REVERT: W 394 LYS cc_start: 0.7322 (pttt) cc_final: 0.7107 (ptpp) REVERT: W 410 LYS cc_start: 0.8940 (tptt) cc_final: 0.8724 (tptt) REVERT: W 418 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7682 (mm-30) REVERT: X 242 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: X 267 THR cc_start: 0.9062 (m) cc_final: 0.8674 (p) REVERT: X 418 GLU cc_start: 0.8536 (mm-30) cc_final: 0.6964 (mm-30) REVERT: Y 267 THR cc_start: 0.9047 (m) cc_final: 0.8829 (p) REVERT: Y 302 GLU cc_start: 0.7676 (tt0) cc_final: 0.7401 (tm-30) REVERT: Z 267 THR cc_start: 0.9059 (m) cc_final: 0.8788 (p) REVERT: Z 299 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7556 (m-40) REVERT: Z 410 LYS cc_start: 0.8892 (tptt) cc_final: 0.8536 (tptt) REVERT: a 267 THR cc_start: 0.9059 (m) cc_final: 0.8808 (p) REVERT: b 267 THR cc_start: 0.9111 (m) cc_final: 0.8815 (p) REVERT: b 410 LYS cc_start: 0.8817 (tptt) cc_final: 0.8584 (tptt) REVERT: b 418 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7674 (mm-30) REVERT: c 267 THR cc_start: 0.9082 (m) cc_final: 0.8812 (p) REVERT: c 275 LYS cc_start: 0.8892 (mttm) cc_final: 0.8558 (mttp) REVERT: c 418 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7647 (mm-30) REVERT: d 267 THR cc_start: 0.9122 (m) cc_final: 0.8849 (p) REVERT: d 394 LYS cc_start: 0.6995 (ptpt) cc_final: 0.6712 (pttm) REVERT: d 410 LYS cc_start: 0.8920 (tptt) cc_final: 0.8650 (tptt) REVERT: e 267 THR cc_start: 0.9114 (m) cc_final: 0.8805 (p) REVERT: e 410 LYS cc_start: 0.8890 (tptt) cc_final: 0.8657 (tptt) REVERT: f 242 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: f 267 THR cc_start: 0.9088 (m) cc_final: 0.8798 (p) REVERT: f 302 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7412 (tm-30) REVERT: f 410 LYS cc_start: 0.8996 (tptt) cc_final: 0.8678 (tptt) REVERT: f 418 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8041 (mm-30) REVERT: g 267 THR cc_start: 0.9050 (m) cc_final: 0.8781 (p) REVERT: g 377 MET cc_start: 0.7920 (tmm) cc_final: 0.7615 (tmm) REVERT: h 302 GLU cc_start: 0.7372 (tt0) cc_final: 0.7063 (tm-30) outliers start: 250 outliers final: 148 residues processed: 1385 average time/residue: 0.5907 time to fit residues: 1294.5776 Evaluate side-chains 1212 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1054 time to evaluate : 5.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 435 SER Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 435 SER Chi-restraints excluded: chain H residue 274 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 435 SER Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 435 SER Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 435 SER Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 435 SER Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 413 GLU Chi-restraints excluded: chain P residue 435 SER Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 435 SER Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 394 LYS Chi-restraints excluded: chain R residue 435 SER Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 252 ILE Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 435 SER Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 413 GLU Chi-restraints excluded: chain U residue 435 SER Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 243 SER Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 435 SER Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 435 SER Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 361 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 435 SER Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 299 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 435 SER Chi-restraints excluded: chain h residue 243 SER Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 396 LEU Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 385 optimal weight: 10.0000 chunk 315 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 463 optimal weight: 0.8980 chunk 501 optimal weight: 0.6980 chunk 413 optimal weight: 5.9990 chunk 460 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 372 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 ASN F 411 GLN G 408 GLN G 411 GLN G 434 ASN H 411 GLN ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 411 GLN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 GLN N 434 ASN P 434 ASN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 231 ASN T 434 ASN V 434 ASN W 411 GLN X 408 GLN X 411 GLN X 434 ASN Y 411 GLN ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 411 GLN ** c 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 411 GLN ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 411 GLN e 434 ASN f 411 GLN ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43146 Z= 0.170 Angle : 0.580 7.239 58174 Z= 0.296 Chirality : 0.039 0.130 6698 Planarity : 0.003 0.034 7786 Dihedral : 5.453 34.774 6070 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 4.11 % Allowed : 20.71 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 5202 helix: 3.29 (0.14), residues: 1462 sheet: -0.86 (0.11), residues: 2448 loop : -1.83 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 281 PHE 0.023 0.001 PHE e 422 TYR 0.004 0.001 TYR G 366 ARG 0.007 0.000 ARG h 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1167 time to evaluate : 5.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: B 242 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: B 410 LYS cc_start: 0.8758 (tptt) cc_final: 0.8543 (tptt) REVERT: B 418 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7754 (mm-30) REVERT: C 410 LYS cc_start: 0.8990 (tptt) cc_final: 0.8701 (tptt) REVERT: C 413 GLU cc_start: 0.8292 (tt0) cc_final: 0.8038 (tt0) REVERT: D 242 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: D 377 MET cc_start: 0.8035 (mmm) cc_final: 0.7693 (mmm) REVERT: E 376 LYS cc_start: 0.8438 (tmtt) cc_final: 0.8159 (ttmm) REVERT: E 377 MET cc_start: 0.7983 (mmm) cc_final: 0.7617 (tpp) REVERT: E 402 LEU cc_start: 0.8989 (tp) cc_final: 0.8771 (tp) REVERT: E 410 LYS cc_start: 0.9004 (tptt) cc_final: 0.8726 (tptt) REVERT: E 418 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8097 (mt-10) REVERT: F 242 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: F 256 ILE cc_start: 0.8950 (mm) cc_final: 0.8720 (mm) REVERT: F 274 ASN cc_start: 0.8034 (OUTLIER) cc_final: 0.7344 (t0) REVERT: F 383 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F 394 LYS cc_start: 0.6963 (pttm) cc_final: 0.6464 (pttm) REVERT: F 410 LYS cc_start: 0.8941 (tptt) cc_final: 0.8722 (tptt) REVERT: F 418 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8170 (mt-10) REVERT: G 242 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: G 246 GLN cc_start: 0.9046 (pt0) cc_final: 0.8810 (pt0) REVERT: G 394 LYS cc_start: 0.7145 (pttm) cc_final: 0.6816 (pttm) REVERT: G 418 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8156 (mt-10) REVERT: H 242 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: I 242 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: I 299 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7522 (m-40) REVERT: I 376 LYS cc_start: 0.8502 (tptp) cc_final: 0.8293 (tppp) REVERT: I 377 MET cc_start: 0.7848 (mmm) cc_final: 0.7520 (mmm) REVERT: I 410 LYS cc_start: 0.8762 (tptt) cc_final: 0.8508 (tptt) REVERT: J 242 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: J 383 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7772 (mt-10) REVERT: K 418 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8118 (mt-10) REVERT: L 242 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: L 274 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7573 (t0) REVERT: L 418 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8263 (mt-10) REVERT: M 242 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: M 376 LYS cc_start: 0.8427 (tmtt) cc_final: 0.8150 (tptp) REVERT: M 394 LYS cc_start: 0.6612 (ptpt) cc_final: 0.6269 (pttm) REVERT: M 410 LYS cc_start: 0.8922 (tptt) cc_final: 0.8549 (tptt) REVERT: M 418 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7470 (mm-30) REVERT: N 242 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: N 410 LYS cc_start: 0.8990 (tptt) cc_final: 0.8697 (tptt) REVERT: O 242 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: O 302 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7049 (tm-30) REVERT: O 410 LYS cc_start: 0.8952 (tptt) cc_final: 0.8620 (tptt) REVERT: O 418 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8133 (mt-10) REVERT: P 274 ASN cc_start: 0.8055 (OUTLIER) cc_final: 0.7461 (t0) REVERT: Q 274 ASN cc_start: 0.8005 (OUTLIER) cc_final: 0.7457 (t0) REVERT: Q 418 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8131 (mt-10) REVERT: R 242 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: S 242 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: S 418 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7973 (mt-10) REVERT: T 242 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: U 242 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: V 410 LYS cc_start: 0.8989 (tptt) cc_final: 0.8693 (tptt) REVERT: V 418 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8097 (mt-10) REVERT: W 242 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: W 256 ILE cc_start: 0.8939 (mm) cc_final: 0.8713 (mm) REVERT: W 274 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7369 (t0) REVERT: W 383 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7858 (mt-10) REVERT: W 410 LYS cc_start: 0.8945 (tptt) cc_final: 0.8727 (tptt) REVERT: W 418 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8139 (mt-10) REVERT: X 242 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: X 246 GLN cc_start: 0.9050 (pt0) cc_final: 0.8811 (pt0) REVERT: X 394 LYS cc_start: 0.7166 (pttm) cc_final: 0.6781 (pttm) REVERT: X 418 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8155 (mt-10) REVERT: Y 242 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: Y 410 LYS cc_start: 0.8765 (tptt) cc_final: 0.8541 (tptt) REVERT: Z 242 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: Z 299 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7523 (m-40) REVERT: Z 376 LYS cc_start: 0.8501 (tptp) cc_final: 0.8292 (tppp) REVERT: Z 377 MET cc_start: 0.7843 (mmm) cc_final: 0.7517 (mmm) REVERT: Z 410 LYS cc_start: 0.8782 (tptt) cc_final: 0.8539 (tptt) REVERT: a 242 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: a 383 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7777 (mt-10) REVERT: b 418 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8129 (mt-10) REVERT: c 242 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6876 (mp0) REVERT: c 274 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7564 (t0) REVERT: c 418 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8250 (mt-10) REVERT: d 242 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: d 376 LYS cc_start: 0.8438 (tmtt) cc_final: 0.8157 (tptp) REVERT: d 394 LYS cc_start: 0.6594 (ptpt) cc_final: 0.6262 (pttm) REVERT: d 410 LYS cc_start: 0.8922 (tptt) cc_final: 0.8550 (tptt) REVERT: d 418 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7467 (mm-30) REVERT: e 242 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: e 376 LYS cc_start: 0.8363 (tmtt) cc_final: 0.8160 (tptp) REVERT: e 410 LYS cc_start: 0.9000 (tptt) cc_final: 0.8745 (tptt) REVERT: f 242 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: f 302 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7190 (tm-30) REVERT: f 394 LYS cc_start: 0.6836 (ptpt) cc_final: 0.6617 (ptpt) REVERT: f 418 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8113 (mt-10) REVERT: g 274 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7473 (t0) REVERT: h 274 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7451 (t0) outliers start: 197 outliers final: 105 residues processed: 1304 average time/residue: 0.6021 time to fit residues: 1246.6131 Evaluate side-chains 1177 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1037 time to evaluate : 5.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 230 LEU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 402 LEU Chi-restraints excluded: chain Z residue 242 GLU Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 435 SER Chi-restraints excluded: chain d residue 242 GLU Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 230 LEU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 1.9990 chunk 348 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 51 optimal weight: 0.0050 chunk 221 optimal weight: 4.9990 chunk 311 optimal weight: 3.9990 chunk 465 optimal weight: 2.9990 chunk 492 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 441 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN C 434 ASN ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 408 GLN ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 411 GLN ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 408 GLN O 434 ASN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 GLN ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 246 GLN ** T 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 246 GLN W 408 GLN X 408 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 246 GLN ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 411 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 43146 Z= 0.257 Angle : 0.601 7.791 58174 Z= 0.304 Chirality : 0.040 0.139 6698 Planarity : 0.003 0.026 7786 Dihedral : 5.657 37.687 6027 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.01 % Allowed : 23.61 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 5202 helix: 3.03 (0.13), residues: 1428 sheet: -0.89 (0.11), residues: 2482 loop : -1.52 (0.18), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 281 PHE 0.024 0.002 PHE Z 422 TYR 0.009 0.001 TYR V 366 ARG 0.005 0.000 ARG h 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1093 time to evaluate : 5.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: B 242 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: C 274 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7650 (t0) REVERT: C 280 GLU cc_start: 0.7566 (tt0) cc_final: 0.7340 (tt0) REVERT: D 242 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: E 240 ASP cc_start: 0.9215 (t0) cc_final: 0.8981 (t0) REVERT: E 383 GLU cc_start: 0.8366 (tt0) cc_final: 0.7750 (mt-10) REVERT: E 418 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7967 (mt-10) REVERT: E 430 LEU cc_start: 0.8951 (tp) cc_final: 0.8674 (tt) REVERT: F 242 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: F 256 ILE cc_start: 0.8965 (mm) cc_final: 0.8743 (mm) REVERT: F 383 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7843 (mt-10) REVERT: F 418 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8088 (mt-10) REVERT: G 242 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: G 267 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8785 (p) REVERT: G 302 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7062 (tm-30) REVERT: G 377 MET cc_start: 0.8126 (mmm) cc_final: 0.7896 (tpt) REVERT: G 418 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8086 (mt-10) REVERT: H 242 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: H 302 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7023 (tm-30) REVERT: H 410 LYS cc_start: 0.8944 (tptt) cc_final: 0.8736 (tptt) REVERT: H 418 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7585 (mm-30) REVERT: I 299 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7564 (m-40) REVERT: I 376 LYS cc_start: 0.8665 (tptp) cc_final: 0.8399 (tppp) REVERT: I 377 MET cc_start: 0.7959 (mmm) cc_final: 0.7634 (mmm) REVERT: J 242 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: J 246 GLN cc_start: 0.9264 (pt0) cc_final: 0.9005 (pt0) REVERT: J 377 MET cc_start: 0.8146 (mmm) cc_final: 0.7744 (tpp) REVERT: K 418 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8066 (mt-10) REVERT: L 242 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: L 400 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8102 (mmtt) REVERT: L 418 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8117 (mt-10) REVERT: M 242 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: M 394 LYS cc_start: 0.6516 (ptpt) cc_final: 0.6199 (pttm) REVERT: M 410 LYS cc_start: 0.8919 (tptt) cc_final: 0.8636 (tptt) REVERT: N 242 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: O 242 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: O 410 LYS cc_start: 0.8973 (tptt) cc_final: 0.8749 (tptt) REVERT: O 418 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8056 (mt-10) REVERT: P 246 GLN cc_start: 0.9327 (pt0) cc_final: 0.9103 (pt0) REVERT: Q 400 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8247 (mmtt) REVERT: Q 418 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8057 (mt-10) REVERT: R 242 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: S 242 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: S 418 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8011 (mt-10) REVERT: T 242 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: T 410 LYS cc_start: 0.9016 (tptt) cc_final: 0.8804 (tptt) REVERT: U 242 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: V 267 THR cc_start: 0.9077 (m) cc_final: 0.8804 (p) REVERT: V 302 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7360 (tm-30) REVERT: V 376 LYS cc_start: 0.8541 (tmtt) cc_final: 0.8283 (ttmm) REVERT: V 410 LYS cc_start: 0.9005 (tptt) cc_final: 0.8767 (tptt) REVERT: V 418 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7985 (mt-10) REVERT: V 430 LEU cc_start: 0.8979 (tp) cc_final: 0.8642 (tt) REVERT: W 242 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: W 256 ILE cc_start: 0.8952 (mm) cc_final: 0.8713 (mm) REVERT: W 383 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7805 (mt-10) REVERT: W 418 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8037 (mt-10) REVERT: X 242 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: X 302 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7055 (tm-30) REVERT: X 377 MET cc_start: 0.8124 (mmm) cc_final: 0.7911 (tpt) REVERT: X 418 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8061 (mt-10) REVERT: Y 242 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: Y 302 GLU cc_start: 0.7338 (tm-30) cc_final: 0.7032 (tm-30) REVERT: Y 394 LYS cc_start: 0.7220 (pttm) cc_final: 0.6845 (pttm) REVERT: Z 299 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7602 (m-40) REVERT: Z 376 LYS cc_start: 0.8665 (tptp) cc_final: 0.8396 (tppp) REVERT: Z 377 MET cc_start: 0.7951 (mmm) cc_final: 0.7630 (mmm) REVERT: a 242 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: a 246 GLN cc_start: 0.9263 (pt0) cc_final: 0.9001 (pt0) REVERT: a 377 MET cc_start: 0.8143 (mmm) cc_final: 0.7740 (tpp) REVERT: b 418 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8080 (mt-10) REVERT: c 242 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: c 400 LYS cc_start: 0.8373 (mmtm) cc_final: 0.8138 (mmtt) REVERT: c 418 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8144 (mt-10) REVERT: d 242 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: d 394 LYS cc_start: 0.6497 (ptpt) cc_final: 0.6187 (pttm) REVERT: d 410 LYS cc_start: 0.8919 (tptt) cc_final: 0.8634 (tptt) REVERT: e 242 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: e 376 LYS cc_start: 0.8528 (tmtt) cc_final: 0.8317 (tptp) REVERT: f 242 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: f 400 LYS cc_start: 0.8617 (mmtm) cc_final: 0.8252 (mmtt) REVERT: f 410 LYS cc_start: 0.8929 (tptt) cc_final: 0.8656 (tptt) REVERT: f 418 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8026 (mt-10) REVERT: g 246 GLN cc_start: 0.9324 (pt0) cc_final: 0.9098 (pt0) REVERT: g 418 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8123 (mt-10) REVERT: h 246 GLN cc_start: 0.9227 (pt0) cc_final: 0.9018 (pt0) outliers start: 192 outliers final: 130 residues processed: 1222 average time/residue: 0.5833 time to fit residues: 1127.8710 Evaluate side-chains 1165 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1008 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 274 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 242 GLU Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 413 GLU Chi-restraints excluded: chain Q residue 230 LEU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 230 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 396 LEU Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 361 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 242 GLU Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 408 GLN Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 230 LEU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 396 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 7 optimal weight: 0.0570 chunk 367 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 420 optimal weight: 10.0000 chunk 340 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 442 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 408 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43146 Z= 0.206 Angle : 0.579 7.959 58174 Z= 0.292 Chirality : 0.039 0.160 6698 Planarity : 0.003 0.025 7786 Dihedral : 5.387 35.199 6026 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 4.15 % Allowed : 24.30 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 5202 helix: 3.03 (0.14), residues: 1428 sheet: -0.82 (0.11), residues: 2550 loop : -1.38 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS L 281 PHE 0.025 0.001 PHE P 422 TYR 0.006 0.001 TYR V 366 ARG 0.004 0.000 ARG F 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1118 time to evaluate : 4.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: B 242 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: B 418 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7037 (mm-30) REVERT: C 246 GLN cc_start: 0.9035 (pt0) cc_final: 0.8647 (pm20) REVERT: C 274 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7614 (t0) REVERT: C 418 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7563 (mm-30) REVERT: D 242 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: E 302 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7204 (tm-30) REVERT: E 418 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7974 (mt-10) REVERT: E 428 ASP cc_start: 0.7686 (m-30) cc_final: 0.7093 (m-30) REVERT: F 242 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: F 256 ILE cc_start: 0.8949 (mm) cc_final: 0.8737 (mm) REVERT: F 383 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7833 (mt-10) REVERT: F 418 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7971 (mt-10) REVERT: G 242 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: G 267 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8801 (p) REVERT: G 410 LYS cc_start: 0.8905 (tptt) cc_final: 0.8690 (tptt) REVERT: G 418 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8047 (mt-10) REVERT: H 242 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: H 281 HIS cc_start: 0.7525 (t70) cc_final: 0.7273 (t70) REVERT: H 410 LYS cc_start: 0.8930 (tptt) cc_final: 0.8673 (tptt) REVERT: I 299 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7578 (m-40) REVERT: I 376 LYS cc_start: 0.8641 (tptp) cc_final: 0.8399 (tppp) REVERT: I 377 MET cc_start: 0.7981 (mmm) cc_final: 0.7702 (mmm) REVERT: J 242 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: J 246 GLN cc_start: 0.9265 (pt0) cc_final: 0.9031 (pt0) REVERT: J 377 MET cc_start: 0.8214 (mmm) cc_final: 0.7788 (tpp) REVERT: K 418 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8025 (mt-10) REVERT: L 242 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: L 274 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7545 (t0) REVERT: L 400 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8140 (mmtt) REVERT: L 418 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8021 (mt-10) REVERT: M 267 THR cc_start: 0.9099 (m) cc_final: 0.8817 (p) REVERT: M 394 LYS cc_start: 0.6418 (ptpt) cc_final: 0.6167 (pttm) REVERT: N 242 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: N 302 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: N 410 LYS cc_start: 0.8908 (tptt) cc_final: 0.8599 (tptt) REVERT: N 418 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7581 (mm-30) REVERT: O 242 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: O 418 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8077 (mt-10) REVERT: P 246 GLN cc_start: 0.9328 (pt0) cc_final: 0.9102 (pt0) REVERT: Q 242 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: Q 246 GLN cc_start: 0.9052 (pt0) cc_final: 0.8790 (pt0) REVERT: Q 400 LYS cc_start: 0.8324 (mmtm) cc_final: 0.8087 (mmtt) REVERT: Q 418 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7945 (mt-10) REVERT: R 242 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: S 242 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: S 418 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7989 (mt-10) REVERT: T 242 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: T 246 GLN cc_start: 0.9039 (pt0) cc_final: 0.8631 (pm20) REVERT: T 418 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7441 (mm-30) REVERT: T 430 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8306 (tt) REVERT: U 242 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6882 (mp0) REVERT: V 267 THR cc_start: 0.9079 (m) cc_final: 0.8779 (p) REVERT: V 280 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7006 (tm-30) REVERT: V 302 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7289 (tm-30) REVERT: V 376 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8374 (ttmm) REVERT: V 400 LYS cc_start: 0.8321 (mmtm) cc_final: 0.8100 (mmtm) REVERT: V 410 LYS cc_start: 0.8997 (tptt) cc_final: 0.8663 (tptt) REVERT: V 418 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7979 (mt-10) REVERT: W 242 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: W 383 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7816 (mt-10) REVERT: W 410 LYS cc_start: 0.8772 (tptt) cc_final: 0.8129 (tptt) REVERT: W 412 ILE cc_start: 0.9423 (mm) cc_final: 0.9094 (mt) REVERT: W 418 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8038 (mt-10) REVERT: X 242 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: X 418 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8025 (mt-10) REVERT: Y 242 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: Y 281 HIS cc_start: 0.7510 (t70) cc_final: 0.7264 (t70) REVERT: Z 299 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7584 (m-40) REVERT: Z 376 LYS cc_start: 0.8643 (tptp) cc_final: 0.8397 (tppp) REVERT: Z 377 MET cc_start: 0.7984 (mmm) cc_final: 0.7705 (mmm) REVERT: a 242 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6654 (mp0) REVERT: a 246 GLN cc_start: 0.9264 (pt0) cc_final: 0.9026 (pt0) REVERT: a 377 MET cc_start: 0.8217 (mmm) cc_final: 0.7787 (tpp) REVERT: b 418 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8027 (mt-10) REVERT: c 242 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: c 274 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7536 (t0) REVERT: c 400 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8140 (mmtt) REVERT: c 418 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8019 (mt-10) REVERT: d 267 THR cc_start: 0.9102 (m) cc_final: 0.8827 (p) REVERT: d 394 LYS cc_start: 0.6409 (ptpt) cc_final: 0.6093 (pttm) REVERT: d 402 LEU cc_start: 0.8773 (tp) cc_final: 0.8480 (tp) REVERT: e 242 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: e 302 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: e 376 LYS cc_start: 0.8453 (tmtt) cc_final: 0.8240 (tptp) REVERT: e 410 LYS cc_start: 0.8889 (tptt) cc_final: 0.8583 (tptt) REVERT: e 418 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7118 (mm-30) REVERT: f 242 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: f 280 GLU cc_start: 0.7626 (tt0) cc_final: 0.7243 (tm-30) REVERT: f 418 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8071 (mt-10) REVERT: g 246 GLN cc_start: 0.9318 (pt0) cc_final: 0.9105 (pt0) REVERT: g 418 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8109 (mt-10) REVERT: h 242 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: h 418 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7825 (mm-30) outliers start: 199 outliers final: 135 residues processed: 1253 average time/residue: 0.5672 time to fit residues: 1124.3054 Evaluate side-chains 1172 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1005 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 413 GLU Chi-restraints excluded: chain Q residue 230 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 396 LEU Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 361 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 302 GLU Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 367 GLU Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain h residue 230 LEU Chi-restraints excluded: chain h residue 242 GLU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 424 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 10.0000 chunk 443 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 289 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 493 optimal weight: 0.8980 chunk 409 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 259 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 408 GLN Q 246 GLN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 GLN ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 411 GLN ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 408 GLN ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43146 Z= 0.229 Angle : 0.593 10.611 58174 Z= 0.297 Chirality : 0.039 0.246 6698 Planarity : 0.003 0.028 7786 Dihedral : 5.437 37.401 6026 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.69 % Allowed : 25.03 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.13), residues: 5202 helix: 3.06 (0.14), residues: 1428 sheet: -0.63 (0.11), residues: 2448 loop : -1.27 (0.19), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS L 281 PHE 0.028 0.001 PHE Z 422 TYR 0.007 0.001 TYR V 366 ARG 0.007 0.000 ARG P 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1292 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1067 time to evaluate : 5.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 242 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: B 394 LYS cc_start: 0.7249 (pttm) cc_final: 0.6996 (pttm) REVERT: C 242 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7393 (mp0) REVERT: C 246 GLN cc_start: 0.9074 (pt0) cc_final: 0.8645 (pm20) REVERT: C 274 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7623 (t0) REVERT: C 418 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7912 (mt-10) REVERT: D 242 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: D 410 LYS cc_start: 0.9139 (tptt) cc_final: 0.8899 (tptt) REVERT: E 418 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7915 (mt-10) REVERT: E 428 ASP cc_start: 0.7510 (m-30) cc_final: 0.7065 (m-30) REVERT: F 242 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: F 256 ILE cc_start: 0.8962 (mm) cc_final: 0.8758 (mm) REVERT: F 383 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7876 (mt-10) REVERT: F 418 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7964 (mt-10) REVERT: G 242 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: G 267 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8810 (p) REVERT: G 418 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8003 (mt-10) REVERT: H 242 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: H 281 HIS cc_start: 0.7522 (t70) cc_final: 0.7290 (t70) REVERT: H 410 LYS cc_start: 0.8972 (tptt) cc_final: 0.8649 (tptt) REVERT: H 430 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8658 (tt) REVERT: I 299 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7623 (m-40) REVERT: I 376 LYS cc_start: 0.8648 (tptp) cc_final: 0.8380 (tppp) REVERT: I 377 MET cc_start: 0.8094 (mmm) cc_final: 0.7850 (mmm) REVERT: J 242 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: J 377 MET cc_start: 0.8213 (mmm) cc_final: 0.7742 (tpp) REVERT: J 418 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7841 (tt0) REVERT: K 418 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8073 (mt-10) REVERT: L 242 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: L 418 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8022 (mt-10) REVERT: M 267 THR cc_start: 0.9106 (m) cc_final: 0.8870 (p) REVERT: M 280 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7140 (tm-30) REVERT: N 240 ASP cc_start: 0.9129 (t0) cc_final: 0.8867 (t0) REVERT: N 242 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: N 302 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: N 424 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8642 (p0) REVERT: O 242 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: O 418 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8068 (mt-10) REVERT: P 246 GLN cc_start: 0.9335 (pt0) cc_final: 0.9134 (pt0) REVERT: Q 242 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: Q 410 LYS cc_start: 0.8734 (tptt) cc_final: 0.8424 (tptt) REVERT: Q 418 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7852 (mt-10) REVERT: R 242 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: S 242 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: S 394 LYS cc_start: 0.7228 (pttm) cc_final: 0.6971 (pttm) REVERT: T 242 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: T 246 GLN cc_start: 0.9069 (pt0) cc_final: 0.8625 (pm20) REVERT: U 242 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: U 410 LYS cc_start: 0.9096 (tptt) cc_final: 0.8847 (tptt) REVERT: V 267 THR cc_start: 0.9098 (m) cc_final: 0.8846 (p) REVERT: V 280 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7074 (tm-30) REVERT: V 302 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7220 (tm-30) REVERT: V 394 LYS cc_start: 0.6719 (pttm) cc_final: 0.6518 (pttm) REVERT: V 418 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7937 (mt-10) REVERT: W 242 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: W 383 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7851 (mt-10) REVERT: W 400 LYS cc_start: 0.8627 (mmtm) cc_final: 0.8363 (mmtt) REVERT: W 412 ILE cc_start: 0.9413 (mm) cc_final: 0.9135 (mt) REVERT: W 418 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8005 (mt-10) REVERT: X 242 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: X 267 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8808 (p) REVERT: X 302 GLU cc_start: 0.7857 (mp0) cc_final: 0.7623 (mp0) REVERT: X 410 LYS cc_start: 0.8899 (tptt) cc_final: 0.8669 (tptt) REVERT: X 418 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7995 (mt-10) REVERT: Y 242 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: Y 281 HIS cc_start: 0.7510 (t70) cc_final: 0.7280 (t70) REVERT: Y 302 GLU cc_start: 0.7299 (tm-30) cc_final: 0.7033 (tm-30) REVERT: Z 299 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7631 (m-40) REVERT: Z 376 LYS cc_start: 0.8648 (tptp) cc_final: 0.8377 (tppp) REVERT: Z 377 MET cc_start: 0.8088 (mmm) cc_final: 0.7848 (mmm) REVERT: a 242 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6727 (mp0) REVERT: a 253 LEU cc_start: 0.8750 (mt) cc_final: 0.8545 (mt) REVERT: a 377 MET cc_start: 0.8215 (mmm) cc_final: 0.7745 (tpp) REVERT: a 410 LYS cc_start: 0.8718 (tptt) cc_final: 0.8492 (tptt) REVERT: b 418 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8077 (mt-10) REVERT: c 242 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: c 418 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8042 (mt-10) REVERT: d 267 THR cc_start: 0.9121 (m) cc_final: 0.8892 (p) REVERT: d 280 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7140 (tm-30) REVERT: d 402 LEU cc_start: 0.8684 (tp) cc_final: 0.8388 (tp) REVERT: e 242 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: e 302 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7018 (mm-30) REVERT: e 410 LYS cc_start: 0.8974 (tptt) cc_final: 0.8686 (tptt) REVERT: f 242 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: f 280 GLU cc_start: 0.7662 (tt0) cc_final: 0.7327 (tm-30) REVERT: f 410 LYS cc_start: 0.8987 (tptt) cc_final: 0.8741 (tptt) REVERT: f 418 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7975 (mt-10) REVERT: g 246 GLN cc_start: 0.9325 (pt0) cc_final: 0.9118 (pt0) REVERT: g 418 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8084 (mt-10) REVERT: g 430 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8484 (tt) REVERT: h 242 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: h 410 LYS cc_start: 0.8703 (tptt) cc_final: 0.8300 (tptt) REVERT: h 418 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7955 (mm-30) outliers start: 225 outliers final: 152 residues processed: 1224 average time/residue: 0.5560 time to fit residues: 1084.2783 Evaluate side-chains 1182 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 997 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 430 LEU Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 424 ASP Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 408 GLN Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 302 GLU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 430 LEU Chi-restraints excluded: chain Q residue 230 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 299 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 396 LEU Chi-restraints excluded: chain T residue 402 LEU Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Y residue 430 LEU Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 361 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 424 ASP Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 302 GLU Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 367 GLU Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 302 GLU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 430 LEU Chi-restraints excluded: chain h residue 230 LEU Chi-restraints excluded: chain h residue 242 GLU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 424 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 10.0000 chunk 55 optimal weight: 0.0980 chunk 281 optimal weight: 1.9990 chunk 360 optimal weight: 7.9990 chunk 279 optimal weight: 0.8980 chunk 415 optimal weight: 10.0000 chunk 275 optimal weight: 0.8980 chunk 491 optimal weight: 4.9990 chunk 307 optimal weight: 0.1980 chunk 299 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 411 GLN ** K 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 411 GLN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43146 Z= 0.184 Angle : 0.592 9.874 58174 Z= 0.295 Chirality : 0.040 0.248 6698 Planarity : 0.003 0.024 7786 Dihedral : 5.129 33.250 6026 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 4.48 % Allowed : 25.34 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.13), residues: 5202 helix: 3.31 (0.14), residues: 1462 sheet: -0.61 (0.11), residues: 2550 loop : -0.95 (0.20), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS c 281 PHE 0.031 0.001 PHE Z 422 TYR 0.005 0.001 TYR T 366 ARG 0.005 0.000 ARG P 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1119 time to evaluate : 5.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: A 410 LYS cc_start: 0.9036 (tptt) cc_final: 0.8825 (tptt) REVERT: B 242 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6589 (mt-10) REVERT: B 246 GLN cc_start: 0.9125 (pt0) cc_final: 0.8805 (pm20) REVERT: B 394 LYS cc_start: 0.7194 (pttm) cc_final: 0.6986 (pttm) REVERT: C 394 LYS cc_start: 0.7113 (ptpp) cc_final: 0.6829 (ptpp) REVERT: D 242 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: D 410 LYS cc_start: 0.9167 (tptt) cc_final: 0.8800 (tptt) REVERT: E 410 LYS cc_start: 0.8412 (tptp) cc_final: 0.8204 (tptt) REVERT: E 418 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7896 (mt-10) REVERT: F 242 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: F 376 LYS cc_start: 0.8713 (tptp) cc_final: 0.8426 (tppp) REVERT: F 377 MET cc_start: 0.8295 (tpt) cc_final: 0.8062 (tpt) REVERT: F 383 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7861 (mt-10) REVERT: F 412 ILE cc_start: 0.9408 (mm) cc_final: 0.8975 (mt) REVERT: F 418 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7978 (mt-10) REVERT: G 242 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: G 267 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8820 (p) REVERT: G 376 LYS cc_start: 0.8654 (tptp) cc_final: 0.8377 (tppp) REVERT: G 377 MET cc_start: 0.8373 (tpp) cc_final: 0.7935 (tpt) REVERT: G 410 LYS cc_start: 0.8911 (tptt) cc_final: 0.8688 (tptt) REVERT: G 418 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7971 (mt-10) REVERT: H 242 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: H 410 LYS cc_start: 0.9030 (tptt) cc_final: 0.8507 (tptt) REVERT: H 422 PHE cc_start: 0.8286 (t80) cc_final: 0.8069 (t80) REVERT: I 299 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7578 (m-40) REVERT: I 376 LYS cc_start: 0.8635 (tptp) cc_final: 0.8397 (tppp) REVERT: J 242 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6678 (mp0) REVERT: J 377 MET cc_start: 0.8220 (mmm) cc_final: 0.7739 (tpp) REVERT: J 418 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7850 (tt0) REVERT: K 376 LYS cc_start: 0.8567 (tptp) cc_final: 0.8350 (tppp) REVERT: K 377 MET cc_start: 0.8262 (mmm) cc_final: 0.7631 (tpp) REVERT: K 418 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8044 (mt-10) REVERT: K 425 LYS cc_start: 0.9536 (mtpp) cc_final: 0.9330 (mtmm) REVERT: L 242 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: L 274 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7427 (t0) REVERT: L 418 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7936 (mt-10) REVERT: M 267 THR cc_start: 0.9117 (m) cc_final: 0.8875 (p) REVERT: M 280 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7012 (tm-30) REVERT: N 240 ASP cc_start: 0.9118 (t0) cc_final: 0.8852 (t0) REVERT: N 242 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: N 302 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: O 242 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: O 302 GLU cc_start: 0.7578 (tm-30) cc_final: 0.6927 (tm-30) REVERT: O 376 LYS cc_start: 0.8710 (tptp) cc_final: 0.8339 (tppp) REVERT: P 246 GLN cc_start: 0.9325 (pt0) cc_final: 0.9094 (pt0) REVERT: P 418 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8005 (mt-10) REVERT: Q 242 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: Q 418 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7857 (mt-10) REVERT: R 242 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: R 246 GLN cc_start: 0.9205 (pt0) cc_final: 0.8907 (pm20) REVERT: S 242 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6604 (mt-10) REVERT: S 246 GLN cc_start: 0.9142 (pt0) cc_final: 0.8853 (pm20) REVERT: S 394 LYS cc_start: 0.7175 (pttm) cc_final: 0.6964 (pttm) REVERT: T 242 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: T 246 GLN cc_start: 0.9072 (pt0) cc_final: 0.8654 (pm20) REVERT: U 242 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6791 (mp0) REVERT: U 410 LYS cc_start: 0.9143 (tptt) cc_final: 0.8917 (tptt) REVERT: V 280 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7075 (tm-30) REVERT: V 400 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8321 (mmtm) REVERT: V 418 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7898 (mt-10) REVERT: W 242 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: W 376 LYS cc_start: 0.8713 (tptp) cc_final: 0.8431 (tppp) REVERT: W 377 MET cc_start: 0.8314 (tpt) cc_final: 0.8074 (tpt) REVERT: W 383 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7860 (mt-10) REVERT: W 400 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8348 (mmtt) REVERT: W 410 LYS cc_start: 0.8213 (tptt) cc_final: 0.7944 (tptt) REVERT: W 418 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8014 (mt-10) REVERT: X 242 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: X 376 LYS cc_start: 0.8661 (tptp) cc_final: 0.8386 (tppp) REVERT: X 377 MET cc_start: 0.8363 (tpp) cc_final: 0.7918 (tpt) REVERT: X 418 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7948 (mt-10) REVERT: Y 242 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: Y 302 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7106 (tm-30) REVERT: Y 420 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8639 (ptm) REVERT: Z 299 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7591 (m-40) REVERT: Z 376 LYS cc_start: 0.8634 (tptp) cc_final: 0.8393 (tppp) REVERT: a 242 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: a 377 MET cc_start: 0.8221 (mmm) cc_final: 0.7734 (tpp) REVERT: a 418 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7906 (tt0) REVERT: b 376 LYS cc_start: 0.8597 (tptp) cc_final: 0.8339 (tppp) REVERT: b 377 MET cc_start: 0.8258 (mmm) cc_final: 0.7637 (tpp) REVERT: b 418 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8047 (mt-10) REVERT: c 242 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6964 (mp0) REVERT: c 274 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7418 (t0) REVERT: c 418 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7960 (mt-10) REVERT: d 267 THR cc_start: 0.9120 (m) cc_final: 0.8883 (p) REVERT: d 280 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7005 (tm-30) REVERT: e 242 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: e 302 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7053 (mm-30) REVERT: e 410 LYS cc_start: 0.8934 (tptt) cc_final: 0.8641 (tptt) REVERT: e 418 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7847 (mm-30) REVERT: f 242 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: f 280 GLU cc_start: 0.7528 (tt0) cc_final: 0.7304 (tm-30) REVERT: f 376 LYS cc_start: 0.8710 (tptp) cc_final: 0.8370 (tppp) REVERT: f 410 LYS cc_start: 0.8982 (tptt) cc_final: 0.8626 (tptt) REVERT: f 418 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7991 (mt-10) REVERT: g 246 GLN cc_start: 0.9310 (pt0) cc_final: 0.9104 (pt0) REVERT: g 418 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8024 (mt-10) REVERT: h 242 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: h 246 GLN cc_start: 0.9167 (pt0) cc_final: 0.8806 (pt0) REVERT: h 418 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8022 (mm-30) outliers start: 215 outliers final: 141 residues processed: 1261 average time/residue: 0.5621 time to fit residues: 1124.8934 Evaluate side-chains 1210 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1038 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 408 GLN Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 299 ASN Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 424 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 299 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 408 GLN Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 230 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 424 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 420 MET Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 299 ASN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 430 LEU Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 243 SER Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 415 LEU Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 361 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 299 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 424 ASP Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 302 GLU Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 367 GLU Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 230 LEU Chi-restraints excluded: chain h residue 242 GLU Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 424 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 293 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 96 optimal weight: 0.0470 chunk 95 optimal weight: 0.5980 chunk 312 optimal weight: 0.8980 chunk 334 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 386 optimal weight: 4.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN ** C 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 411 GLN g 239 ASN ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43146 Z= 0.180 Angle : 0.614 9.369 58174 Z= 0.300 Chirality : 0.040 0.229 6698 Planarity : 0.003 0.024 7786 Dihedral : 4.959 33.842 6018 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 4.34 % Allowed : 26.39 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.13), residues: 5202 helix: 3.24 (0.14), residues: 1462 sheet: -0.46 (0.11), residues: 2550 loop : -0.80 (0.20), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS c 281 PHE 0.035 0.002 PHE Z 422 TYR 0.004 0.001 TYR G 366 ARG 0.007 0.000 ARG F 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1152 time to evaluate : 4.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: A 246 GLN cc_start: 0.9159 (pt0) cc_final: 0.8848 (pm20) REVERT: A 410 LYS cc_start: 0.9101 (tptt) cc_final: 0.8867 (tptt) REVERT: B 242 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: B 394 LYS cc_start: 0.7193 (pttm) cc_final: 0.6988 (pttm) REVERT: C 242 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: C 274 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7575 (t0) REVERT: C 410 LYS cc_start: 0.8662 (tptt) cc_final: 0.8368 (tptt) REVERT: C 420 MET cc_start: 0.8668 (ptm) cc_final: 0.8310 (tmm) REVERT: D 232 ASP cc_start: 0.8149 (m-30) cc_final: 0.7875 (m-30) REVERT: D 242 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: E 410 LYS cc_start: 0.8376 (tptp) cc_final: 0.8090 (tptt) REVERT: E 418 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7871 (mt-10) REVERT: E 428 ASP cc_start: 0.7482 (m-30) cc_final: 0.7022 (m-30) REVERT: F 242 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6504 (mp0) REVERT: F 376 LYS cc_start: 0.8671 (tptp) cc_final: 0.8375 (tppp) REVERT: F 418 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8011 (mt-10) REVERT: G 242 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: G 376 LYS cc_start: 0.8748 (tptp) cc_final: 0.8450 (tppp) REVERT: G 377 MET cc_start: 0.8357 (tpp) cc_final: 0.7922 (tpt) REVERT: G 410 LYS cc_start: 0.8912 (tptt) cc_final: 0.8676 (tptt) REVERT: G 418 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7966 (mt-10) REVERT: H 242 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: I 376 LYS cc_start: 0.8696 (tptp) cc_final: 0.8413 (tppp) REVERT: I 410 LYS cc_start: 0.8820 (tptt) cc_final: 0.8551 (tptt) REVERT: J 240 ASP cc_start: 0.8981 (t0) cc_final: 0.8729 (t0) REVERT: J 242 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: J 377 MET cc_start: 0.8225 (mmm) cc_final: 0.7840 (tpp) REVERT: J 418 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7964 (tt0) REVERT: K 246 GLN cc_start: 0.9172 (pt0) cc_final: 0.8920 (pm20) REVERT: K 376 LYS cc_start: 0.8677 (tptp) cc_final: 0.8348 (tppp) REVERT: K 418 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7942 (mt-10) REVERT: L 242 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: L 274 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7412 (t0) REVERT: L 418 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8048 (mt-10) REVERT: M 267 THR cc_start: 0.9115 (m) cc_final: 0.8894 (p) REVERT: M 280 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6988 (tm-30) REVERT: M 394 LYS cc_start: 0.6783 (pttm) cc_final: 0.6582 (pttm) REVERT: N 242 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: O 242 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6696 (mp0) REVERT: O 302 GLU cc_start: 0.7525 (tm-30) cc_final: 0.6831 (tm-30) REVERT: O 376 LYS cc_start: 0.8699 (tptp) cc_final: 0.8338 (tppp) REVERT: P 246 GLN cc_start: 0.9323 (pt0) cc_final: 0.9108 (pt0) REVERT: Q 242 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: Q 246 GLN cc_start: 0.9115 (pt0) cc_final: 0.8669 (pm20) REVERT: Q 410 LYS cc_start: 0.8676 (tptt) cc_final: 0.8411 (tptt) REVERT: Q 418 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7817 (mt-10) REVERT: R 242 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: S 242 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6719 (mp0) REVERT: S 394 LYS cc_start: 0.7160 (pttm) cc_final: 0.6917 (pttm) REVERT: T 232 ASP cc_start: 0.8015 (m-30) cc_final: 0.7653 (m-30) REVERT: T 242 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6790 (mp0) REVERT: T 246 GLN cc_start: 0.9065 (pt0) cc_final: 0.8850 (pt0) REVERT: T 394 LYS cc_start: 0.6884 (ptpp) cc_final: 0.6649 (pttm) REVERT: T 410 LYS cc_start: 0.8544 (tptt) cc_final: 0.7539 (tptt) REVERT: T 414 ASP cc_start: 0.8230 (m-30) cc_final: 0.7398 (m-30) REVERT: U 242 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: U 410 LYS cc_start: 0.9111 (tptt) cc_final: 0.8610 (tptt) REVERT: V 280 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6969 (tm-30) REVERT: V 413 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8334 (tm-30) REVERT: V 418 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7903 (mt-10) REVERT: W 242 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6527 (mt-10) REVERT: W 376 LYS cc_start: 0.8669 (tptp) cc_final: 0.8383 (tppp) REVERT: W 383 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7847 (mt-10) REVERT: W 400 LYS cc_start: 0.8644 (mmtm) cc_final: 0.8391 (mmtt) REVERT: W 410 LYS cc_start: 0.8194 (tptt) cc_final: 0.7894 (tptt) REVERT: W 418 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7977 (mt-10) REVERT: X 242 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: X 376 LYS cc_start: 0.8744 (tptp) cc_final: 0.8454 (tppp) REVERT: X 377 MET cc_start: 0.8368 (tpp) cc_final: 0.7930 (tpt) REVERT: X 410 LYS cc_start: 0.8890 (tptt) cc_final: 0.8689 (tptt) REVERT: X 418 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7940 (mt-10) REVERT: Y 242 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: Y 420 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8577 (ptm) REVERT: Z 376 LYS cc_start: 0.8694 (tptp) cc_final: 0.8412 (tppp) REVERT: Z 410 LYS cc_start: 0.8878 (tptt) cc_final: 0.8574 (tptt) REVERT: a 242 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: a 418 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7830 (tt0) REVERT: b 246 GLN cc_start: 0.9151 (pt0) cc_final: 0.8909 (pm20) REVERT: b 376 LYS cc_start: 0.8677 (tptp) cc_final: 0.8343 (tppp) REVERT: b 418 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7923 (mt-10) REVERT: c 242 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: c 274 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7372 (t0) REVERT: c 418 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8022 (mt-10) REVERT: d 267 THR cc_start: 0.9087 (m) cc_final: 0.8883 (p) REVERT: d 280 GLU cc_start: 0.7588 (tm-30) cc_final: 0.6987 (tm-30) REVERT: d 418 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8079 (tt0) REVERT: e 240 ASP cc_start: 0.9086 (t0) cc_final: 0.8840 (t0) REVERT: e 242 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: f 242 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: f 376 LYS cc_start: 0.8704 (tptp) cc_final: 0.8385 (tppp) REVERT: f 410 LYS cc_start: 0.9010 (tptt) cc_final: 0.8725 (tptt) REVERT: f 418 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7911 (mt-10) REVERT: g 246 GLN cc_start: 0.9309 (pt0) cc_final: 0.9082 (pt0) REVERT: g 418 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7998 (mt-10) REVERT: h 242 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: h 246 GLN cc_start: 0.9203 (pt0) cc_final: 0.8895 (pt0) outliers start: 208 outliers final: 129 residues processed: 1284 average time/residue: 0.5543 time to fit residues: 1137.2000 Evaluate side-chains 1254 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1097 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 408 GLN Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 408 GLN Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 230 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 235 LEU Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain V residue 230 LEU Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 420 MET Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 361 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 424 ASP Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 367 GLU Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 230 LEU Chi-restraints excluded: chain h residue 242 GLU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 430 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 7.9990 chunk 470 optimal weight: 3.9990 chunk 429 optimal weight: 0.9980 chunk 458 optimal weight: 6.9990 chunk 275 optimal weight: 0.0060 chunk 199 optimal weight: 1.9990 chunk 359 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 413 optimal weight: 2.9990 chunk 433 optimal weight: 2.9990 chunk 456 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 GLN ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 411 GLN ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 43146 Z= 0.246 Angle : 0.661 10.634 58174 Z= 0.323 Chirality : 0.040 0.296 6698 Planarity : 0.003 0.042 7786 Dihedral : 5.274 36.671 6004 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.94 % Allowed : 27.62 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 5202 helix: 2.94 (0.14), residues: 1428 sheet: -0.51 (0.11), residues: 2550 loop : -0.89 (0.20), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 281 PHE 0.033 0.002 PHE I 422 TYR 0.007 0.001 TYR E 366 ARG 0.013 0.000 ARG a 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1356 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1167 time to evaluate : 5.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: A 246 GLN cc_start: 0.9189 (pt0) cc_final: 0.8899 (pm20) REVERT: A 410 LYS cc_start: 0.9083 (tptt) cc_final: 0.8190 (tptt) REVERT: A 414 ASP cc_start: 0.8524 (m-30) cc_final: 0.7661 (m-30) REVERT: B 242 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: B 246 GLN cc_start: 0.9142 (pt0) cc_final: 0.8763 (pm20) REVERT: C 242 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.6588 (mp0) REVERT: C 246 GLN cc_start: 0.9041 (pt0) cc_final: 0.8462 (pm20) REVERT: C 274 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7614 (t0) REVERT: C 410 LYS cc_start: 0.8564 (tptt) cc_final: 0.8344 (tptt) REVERT: D 232 ASP cc_start: 0.8086 (m-30) cc_final: 0.7809 (m-30) REVERT: D 242 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: D 422 PHE cc_start: 0.8327 (t80) cc_final: 0.7583 (t80) REVERT: E 246 GLN cc_start: 0.9203 (pt0) cc_final: 0.8579 (pm20) REVERT: E 280 GLU cc_start: 0.7432 (tt0) cc_final: 0.7059 (tm-30) REVERT: E 418 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7872 (mt-10) REVERT: E 428 ASP cc_start: 0.7477 (m-30) cc_final: 0.7021 (m-30) REVERT: F 242 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: F 376 LYS cc_start: 0.8666 (tptp) cc_final: 0.8367 (tppp) REVERT: F 377 MET cc_start: 0.8376 (tpt) cc_final: 0.8094 (tpp) REVERT: F 418 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8066 (mt-10) REVERT: G 242 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6628 (mp0) REVERT: G 377 MET cc_start: 0.8388 (tpp) cc_final: 0.8139 (tpt) REVERT: G 410 LYS cc_start: 0.8899 (tptt) cc_final: 0.8671 (tptt) REVERT: G 418 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7942 (mt-10) REVERT: H 242 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: I 376 LYS cc_start: 0.8610 (tptp) cc_final: 0.8382 (tppp) REVERT: I 410 LYS cc_start: 0.8774 (tptt) cc_final: 0.7925 (tptt) REVERT: I 414 ASP cc_start: 0.8470 (m-30) cc_final: 0.7534 (m-30) REVERT: J 242 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: J 418 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7969 (tt0) REVERT: K 246 GLN cc_start: 0.9206 (pt0) cc_final: 0.8944 (pm20) REVERT: K 418 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7930 (mt-10) REVERT: L 242 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: L 410 LYS cc_start: 0.8565 (tptt) cc_final: 0.7680 (tptt) REVERT: L 414 ASP cc_start: 0.8349 (m-30) cc_final: 0.7614 (m-30) REVERT: L 418 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7990 (mt-10) REVERT: M 280 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7054 (tm-30) REVERT: M 394 LYS cc_start: 0.7124 (pttm) cc_final: 0.6648 (pttm) REVERT: M 418 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8038 (tt0) REVERT: N 242 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: N 302 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7036 (mm-30) REVERT: O 242 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: O 302 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6903 (tm-30) REVERT: O 410 LYS cc_start: 0.8711 (tptp) cc_final: 0.8371 (tptt) REVERT: P 246 GLN cc_start: 0.9331 (pt0) cc_final: 0.9103 (pt0) REVERT: Q 242 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: Q 383 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7973 (mt-10) REVERT: Q 410 LYS cc_start: 0.8731 (tptt) cc_final: 0.8333 (tptt) REVERT: Q 418 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7870 (mt-10) REVERT: R 242 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: R 246 GLN cc_start: 0.9215 (pt0) cc_final: 0.8941 (pm20) REVERT: S 242 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: S 246 GLN cc_start: 0.9135 (pt0) cc_final: 0.8765 (pm20) REVERT: S 418 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7881 (mt-10) REVERT: T 232 ASP cc_start: 0.8022 (m-30) cc_final: 0.7672 (m-30) REVERT: T 242 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: T 246 GLN cc_start: 0.9075 (pt0) cc_final: 0.8829 (pt0) REVERT: T 394 LYS cc_start: 0.6917 (ptpp) cc_final: 0.6514 (pttm) REVERT: T 410 LYS cc_start: 0.8537 (tptt) cc_final: 0.7570 (tptt) REVERT: T 414 ASP cc_start: 0.8172 (m-30) cc_final: 0.7420 (m-30) REVERT: U 232 ASP cc_start: 0.8099 (m-30) cc_final: 0.7842 (m-30) REVERT: U 242 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: V 267 THR cc_start: 0.9115 (m) cc_final: 0.8845 (p) REVERT: V 280 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7032 (tm-30) REVERT: V 418 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7941 (mt-10) REVERT: W 242 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: W 376 LYS cc_start: 0.8674 (tptp) cc_final: 0.8397 (tppp) REVERT: W 377 MET cc_start: 0.8386 (tpt) cc_final: 0.8115 (tpp) REVERT: W 410 LYS cc_start: 0.8417 (tptt) cc_final: 0.8176 (tptt) REVERT: W 418 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8057 (mt-10) REVERT: X 242 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: X 377 MET cc_start: 0.8400 (tpp) cc_final: 0.8125 (tpt) REVERT: X 410 LYS cc_start: 0.8884 (tptt) cc_final: 0.8672 (tptt) REVERT: X 418 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7960 (mt-10) REVERT: Y 242 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: Y 418 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7934 (tt0) REVERT: Z 376 LYS cc_start: 0.8641 (tptp) cc_final: 0.8415 (tppp) REVERT: Z 410 LYS cc_start: 0.8909 (tptt) cc_final: 0.8094 (tptt) REVERT: Z 414 ASP cc_start: 0.8433 (m-30) cc_final: 0.7467 (m-30) REVERT: a 242 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: a 418 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8039 (mt-10) REVERT: b 246 GLN cc_start: 0.9203 (pt0) cc_final: 0.8940 (pm20) REVERT: b 418 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7929 (mt-10) REVERT: c 242 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: c 414 ASP cc_start: 0.8195 (m-30) cc_final: 0.7598 (m-30) REVERT: c 418 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8162 (mt-10) REVERT: d 232 ASP cc_start: 0.7960 (m-30) cc_final: 0.7680 (m-30) REVERT: d 280 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7128 (tm-30) REVERT: d 418 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7908 (tt0) REVERT: d 424 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8365 (p0) REVERT: e 242 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: e 302 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7012 (mm-30) REVERT: f 242 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: f 410 LYS cc_start: 0.8972 (tptt) cc_final: 0.8760 (tptt) REVERT: f 418 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7960 (mt-10) REVERT: g 239 ASN cc_start: 0.9105 (t0) cc_final: 0.8887 (t0) REVERT: g 246 GLN cc_start: 0.9330 (pt0) cc_final: 0.9094 (pt0) REVERT: g 418 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7892 (mt-10) REVERT: h 242 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6500 (mp0) REVERT: h 246 GLN cc_start: 0.9233 (pt0) cc_final: 0.8997 (pt0) outliers start: 189 outliers final: 140 residues processed: 1291 average time/residue: 0.5882 time to fit residues: 1224.0775 Evaluate side-chains 1255 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1087 time to evaluate : 5.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 274 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 408 GLN Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 243 SER Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 302 GLU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 230 LEU Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 430 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain U residue 424 ASP Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 361 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 420 MET Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 424 ASP Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 302 GLU Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 408 GLN Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 420 MET Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 302 GLU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 230 LEU Chi-restraints excluded: chain h residue 242 GLU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 4.9990 chunk 484 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 336 optimal weight: 0.4980 chunk 508 optimal weight: 0.9990 chunk 467 optimal weight: 1.9990 chunk 404 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 312 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 43146 Z= 0.246 Angle : 0.687 10.986 58174 Z= 0.336 Chirality : 0.041 0.246 6698 Planarity : 0.003 0.050 7786 Dihedral : 5.276 37.254 6004 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.75 % Allowed : 28.01 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.13), residues: 5202 helix: 3.04 (0.14), residues: 1462 sheet: -0.50 (0.11), residues: 2550 loop : -0.70 (0.21), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 281 PHE 0.033 0.002 PHE T 422 TYR 0.007 0.001 TYR E 366 ARG 0.012 0.000 ARG a 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1146 time to evaluate : 5.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: A 418 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7857 (mt-10) REVERT: B 242 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: B 246 GLN cc_start: 0.9135 (pt0) cc_final: 0.8808 (pm20) REVERT: C 242 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6807 (mp0) REVERT: C 274 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7563 (t0) REVERT: C 410 LYS cc_start: 0.8569 (tptt) cc_final: 0.8363 (tptt) REVERT: D 232 ASP cc_start: 0.8112 (m-30) cc_final: 0.7845 (m-30) REVERT: D 242 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: D 428 ASP cc_start: 0.7448 (m-30) cc_final: 0.6544 (m-30) REVERT: E 280 GLU cc_start: 0.7438 (tt0) cc_final: 0.7044 (tm-30) REVERT: E 418 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7895 (mt-10) REVERT: E 428 ASP cc_start: 0.7480 (m-30) cc_final: 0.7039 (m-30) REVERT: F 242 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: F 376 LYS cc_start: 0.8702 (tptp) cc_final: 0.8418 (tppp) REVERT: F 418 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8043 (mt-10) REVERT: G 232 ASP cc_start: 0.8009 (m-30) cc_final: 0.7675 (m-30) REVERT: G 242 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: G 377 MET cc_start: 0.8362 (tpp) cc_final: 0.8110 (tpt) REVERT: G 409 MET cc_start: 0.8130 (tpp) cc_final: 0.7895 (tpt) REVERT: G 418 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7927 (mt-10) REVERT: H 242 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: I 376 LYS cc_start: 0.8637 (tptp) cc_final: 0.8406 (tppp) REVERT: I 410 LYS cc_start: 0.8806 (tptt) cc_final: 0.7949 (tptt) REVERT: I 414 ASP cc_start: 0.8480 (m-30) cc_final: 0.7537 (m-30) REVERT: I 425 LYS cc_start: 0.9480 (mtmm) cc_final: 0.9073 (mtmt) REVERT: J 240 ASP cc_start: 0.8903 (t0) cc_final: 0.8684 (t0) REVERT: J 242 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: J 418 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7756 (tt0) REVERT: K 242 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: K 418 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7991 (mt-10) REVERT: L 242 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: L 410 LYS cc_start: 0.8652 (tptt) cc_final: 0.7801 (tptt) REVERT: L 411 GLN cc_start: 0.8919 (pt0) cc_final: 0.8597 (pt0) REVERT: L 414 ASP cc_start: 0.8350 (m-30) cc_final: 0.7603 (m-30) REVERT: L 418 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7996 (mt-10) REVERT: M 280 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7018 (tm-30) REVERT: M 394 LYS cc_start: 0.7109 (pttm) cc_final: 0.6642 (pttm) REVERT: M 410 LYS cc_start: 0.8548 (tptp) cc_final: 0.8155 (tptt) REVERT: M 418 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8128 (tt0) REVERT: N 242 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: N 302 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: O 242 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: O 410 LYS cc_start: 0.8735 (tptp) cc_final: 0.8306 (tptt) REVERT: O 418 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7593 (tt0) REVERT: P 246 GLN cc_start: 0.9337 (pt0) cc_final: 0.9118 (pt0) REVERT: P 414 ASP cc_start: 0.8447 (t0) cc_final: 0.8116 (t0) REVERT: P 428 ASP cc_start: 0.7504 (m-30) cc_final: 0.7256 (m-30) REVERT: P 429 THR cc_start: 0.7772 (p) cc_final: 0.7550 (t) REVERT: Q 242 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: Q 410 LYS cc_start: 0.8640 (tptt) cc_final: 0.8325 (tptt) REVERT: Q 418 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7872 (mt-10) REVERT: R 242 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: R 246 GLN cc_start: 0.9187 (pt0) cc_final: 0.8910 (pm20) REVERT: S 242 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6595 (mp0) REVERT: S 246 GLN cc_start: 0.9166 (pt0) cc_final: 0.8777 (pm20) REVERT: S 410 LYS cc_start: 0.8211 (tptp) cc_final: 0.7889 (tptt) REVERT: T 232 ASP cc_start: 0.8007 (m-30) cc_final: 0.7650 (m-30) REVERT: T 242 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: T 246 GLN cc_start: 0.9102 (pt0) cc_final: 0.8897 (pt0) REVERT: T 376 LYS cc_start: 0.8593 (tppp) cc_final: 0.8323 (tptp) REVERT: T 394 LYS cc_start: 0.7022 (ptpp) cc_final: 0.6805 (pttm) REVERT: U 232 ASP cc_start: 0.8111 (m-30) cc_final: 0.7859 (m-30) REVERT: U 242 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: U 428 ASP cc_start: 0.7495 (m-30) cc_final: 0.6695 (m-30) REVERT: V 267 THR cc_start: 0.9100 (m) cc_final: 0.8827 (p) REVERT: V 280 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6948 (tm-30) REVERT: V 418 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8045 (mt-10) REVERT: W 242 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: W 376 LYS cc_start: 0.8689 (tptp) cc_final: 0.8434 (tppp) REVERT: W 377 MET cc_start: 0.8406 (tpt) cc_final: 0.8122 (tpp) REVERT: W 418 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8035 (mt-10) REVERT: X 232 ASP cc_start: 0.8026 (m-30) cc_final: 0.7686 (m-30) REVERT: X 242 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: X 377 MET cc_start: 0.8361 (tpp) cc_final: 0.8102 (tpt) REVERT: X 409 MET cc_start: 0.8076 (tpp) cc_final: 0.7870 (tpt) REVERT: X 418 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7957 (mt-10) REVERT: Y 242 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: Y 418 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8028 (tt0) REVERT: Z 376 LYS cc_start: 0.8632 (tptp) cc_final: 0.8395 (tppp) REVERT: Z 410 LYS cc_start: 0.8874 (tptt) cc_final: 0.8066 (tptt) REVERT: Z 414 ASP cc_start: 0.8389 (m-30) cc_final: 0.7393 (m-30) REVERT: Z 425 LYS cc_start: 0.9436 (mtmm) cc_final: 0.9108 (mtmt) REVERT: a 242 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: a 414 ASP cc_start: 0.8789 (t0) cc_final: 0.8563 (t0) REVERT: a 418 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7968 (mt-10) REVERT: b 242 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: b 267 THR cc_start: 0.9047 (m) cc_final: 0.8703 (p) REVERT: b 418 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7994 (mt-10) REVERT: c 242 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: c 414 ASP cc_start: 0.8231 (m-30) cc_final: 0.7637 (m-30) REVERT: c 418 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8009 (mt-10) REVERT: c 428 ASP cc_start: 0.7534 (m-30) cc_final: 0.7173 (m-30) REVERT: d 232 ASP cc_start: 0.7935 (m-30) cc_final: 0.7653 (m-30) REVERT: d 280 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7074 (tm-30) REVERT: d 418 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7928 (tt0) REVERT: e 242 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: e 302 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7018 (mm-30) REVERT: e 418 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7719 (mm-30) REVERT: f 242 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: f 376 LYS cc_start: 0.8776 (tptp) cc_final: 0.8490 (tppp) REVERT: f 410 LYS cc_start: 0.9000 (tptt) cc_final: 0.8721 (tptt) REVERT: f 418 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8032 (mt-10) REVERT: g 246 GLN cc_start: 0.9333 (pt0) cc_final: 0.9089 (pt0) REVERT: g 409 MET cc_start: 0.8369 (mmt) cc_final: 0.8132 (tpt) REVERT: g 414 ASP cc_start: 0.8138 (t0) cc_final: 0.7307 (t0) REVERT: g 418 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7845 (mt-10) REVERT: h 242 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: h 246 GLN cc_start: 0.9229 (pt0) cc_final: 0.8982 (pt0) REVERT: h 383 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7925 (mt-10) outliers start: 180 outliers final: 139 residues processed: 1262 average time/residue: 0.5542 time to fit residues: 1117.6879 Evaluate side-chains 1242 residues out of total 4794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1074 time to evaluate : 5.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 274 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 274 ASN Chi-restraints excluded: chain D residue 299 ASN Chi-restraints excluded: chain D residue 361 ASN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 274 ASN Chi-restraints excluded: chain E residue 299 ASN Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 299 ASN Chi-restraints excluded: chain F residue 361 ASN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 274 ASN Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 242 GLU Chi-restraints excluded: chain H residue 274 ASN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain I residue 274 ASN Chi-restraints excluded: chain I residue 287 ASP Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 242 GLU Chi-restraints excluded: chain J residue 274 ASN Chi-restraints excluded: chain J residue 299 ASN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 299 ASN Chi-restraints excluded: chain K residue 361 ASN Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 420 MET Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 274 ASN Chi-restraints excluded: chain L residue 361 ASN Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 230 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 361 ASN Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 242 GLU Chi-restraints excluded: chain N residue 274 ASN Chi-restraints excluded: chain N residue 302 GLU Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain O residue 274 ASN Chi-restraints excluded: chain O residue 361 ASN Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 274 ASN Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 302 GLU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 274 ASN Chi-restraints excluded: chain Q residue 361 ASN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 242 GLU Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 274 ASN Chi-restraints excluded: chain S residue 299 ASN Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 430 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 242 GLU Chi-restraints excluded: chain T residue 274 ASN Chi-restraints excluded: chain T residue 361 ASN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 242 GLU Chi-restraints excluded: chain U residue 274 ASN Chi-restraints excluded: chain U residue 299 ASN Chi-restraints excluded: chain U residue 361 ASN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain V residue 274 ASN Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 361 ASN Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 242 GLU Chi-restraints excluded: chain W residue 274 ASN Chi-restraints excluded: chain W residue 299 ASN Chi-restraints excluded: chain W residue 361 ASN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain W residue 430 LEU Chi-restraints excluded: chain X residue 242 GLU Chi-restraints excluded: chain X residue 274 ASN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 242 GLU Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 420 MET Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 274 ASN Chi-restraints excluded: chain Z residue 287 ASP Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 242 GLU Chi-restraints excluded: chain a residue 274 ASN Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain b residue 242 GLU Chi-restraints excluded: chain b residue 243 SER Chi-restraints excluded: chain b residue 274 ASN Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 361 ASN Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 420 MET Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain c residue 242 GLU Chi-restraints excluded: chain c residue 274 ASN Chi-restraints excluded: chain c residue 361 ASN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain d residue 235 LEU Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 361 ASN Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 242 GLU Chi-restraints excluded: chain e residue 274 ASN Chi-restraints excluded: chain e residue 302 GLU Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 408 GLN Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 274 ASN Chi-restraints excluded: chain f residue 361 ASN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 420 MET Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 274 ASN Chi-restraints excluded: chain g residue 299 ASN Chi-restraints excluded: chain g residue 302 GLU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 230 LEU Chi-restraints excluded: chain h residue 242 GLU Chi-restraints excluded: chain h residue 274 ASN Chi-restraints excluded: chain h residue 361 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 430 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 0.1980 chunk 430 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 373 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 416 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 411 GLN ** K 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 239 ASN ** L 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN ** Q 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 411 GLN X 411 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.165698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.114079 restraints weight = 78534.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.117844 restraints weight = 27316.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.120003 restraints weight = 14539.602| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 43146 Z= 0.194 Angle : 0.681 10.891 58174 Z= 0.333 Chirality : 0.041 0.250 6698 Planarity : 0.003 0.049 7786 Dihedral : 4.876 35.594 6004 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.53 % Allowed : 28.54 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.13), residues: 5202 helix: 2.96 (0.14), residues: 1462 sheet: -0.34 (0.11), residues: 2550 loop : -0.66 (0.21), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS L 281 PHE 0.031 0.002 PHE Q 422 TYR 0.004 0.001 TYR G 393 ARG 0.012 0.000 ARG a 244 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15699.38 seconds wall clock time: 280 minutes 1.15 seconds (16801.15 seconds total)