Starting phenix.real_space_refine on Sat Jan 20 03:03:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zdh_6917/01_2024/5zdh_6917_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zdh_6917/01_2024/5zdh_6917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zdh_6917/01_2024/5zdh_6917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zdh_6917/01_2024/5zdh_6917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zdh_6917/01_2024/5zdh_6917_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zdh_6917/01_2024/5zdh_6917_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 315 5.16 5 C 41070 2.51 5 N 11640 2.21 5 O 13020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 520": "NH1" <-> "NH2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 581": "NH1" <-> "NH2" Residue "A ARG 597": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 637": "NH1" <-> "NH2" Residue "B ARG 520": "NH1" <-> "NH2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "B ARG 581": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "C ARG 520": "NH1" <-> "NH2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C ARG 581": "NH1" <-> "NH2" Residue "C ARG 597": "NH1" <-> "NH2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "D ARG 520": "NH1" <-> "NH2" Residue "D ARG 574": "NH1" <-> "NH2" Residue "D ARG 581": "NH1" <-> "NH2" Residue "D ARG 597": "NH1" <-> "NH2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "E ARG 520": "NH1" <-> "NH2" Residue "E ARG 574": "NH1" <-> "NH2" Residue "E ARG 581": "NH1" <-> "NH2" Residue "E ARG 597": "NH1" <-> "NH2" Residue "E ARG 603": "NH1" <-> "NH2" Residue "E ARG 637": "NH1" <-> "NH2" Residue "F ARG 520": "NH1" <-> "NH2" Residue "F ARG 574": "NH1" <-> "NH2" Residue "F ARG 581": "NH1" <-> "NH2" Residue "F ARG 597": "NH1" <-> "NH2" Residue "F ARG 603": "NH1" <-> "NH2" Residue "F ARG 637": "NH1" <-> "NH2" Residue "G ARG 520": "NH1" <-> "NH2" Residue "G ARG 574": "NH1" <-> "NH2" Residue "G ARG 581": "NH1" <-> "NH2" Residue "G ARG 597": "NH1" <-> "NH2" Residue "G ARG 603": "NH1" <-> "NH2" Residue "G ARG 637": "NH1" <-> "NH2" Residue "H ARG 520": "NH1" <-> "NH2" Residue "H ARG 574": "NH1" <-> "NH2" Residue "H ARG 581": "NH1" <-> "NH2" Residue "H ARG 597": "NH1" <-> "NH2" Residue "H ARG 603": "NH1" <-> "NH2" Residue "H ARG 637": "NH1" <-> "NH2" Residue "I ARG 520": "NH1" <-> "NH2" Residue "I ARG 574": "NH1" <-> "NH2" Residue "I ARG 581": "NH1" <-> "NH2" Residue "I ARG 597": "NH1" <-> "NH2" Residue "I ARG 603": "NH1" <-> "NH2" Residue "I ARG 637": "NH1" <-> "NH2" Residue "J ARG 520": "NH1" <-> "NH2" Residue "J ARG 574": "NH1" <-> "NH2" Residue "J ARG 581": "NH1" <-> "NH2" Residue "J ARG 597": "NH1" <-> "NH2" Residue "J ARG 603": "NH1" <-> "NH2" Residue "J ARG 637": "NH1" <-> "NH2" Residue "K ARG 520": "NH1" <-> "NH2" Residue "K ARG 574": "NH1" <-> "NH2" Residue "K ARG 581": "NH1" <-> "NH2" Residue "K ARG 597": "NH1" <-> "NH2" Residue "K ARG 603": "NH1" <-> "NH2" Residue "K ARG 637": "NH1" <-> "NH2" Residue "L ARG 520": "NH1" <-> "NH2" Residue "L ARG 574": "NH1" <-> "NH2" Residue "L ARG 581": "NH1" <-> "NH2" Residue "L ARG 597": "NH1" <-> "NH2" Residue "L ARG 603": "NH1" <-> "NH2" Residue "L ARG 637": "NH1" <-> "NH2" Residue "M ARG 520": "NH1" <-> "NH2" Residue "M ARG 574": "NH1" <-> "NH2" Residue "M ARG 581": "NH1" <-> "NH2" Residue "M ARG 597": "NH1" <-> "NH2" Residue "M ARG 603": "NH1" <-> "NH2" Residue "M ARG 637": "NH1" <-> "NH2" Residue "N ARG 520": "NH1" <-> "NH2" Residue "N ARG 574": "NH1" <-> "NH2" Residue "N ARG 581": "NH1" <-> "NH2" Residue "N ARG 597": "NH1" <-> "NH2" Residue "N ARG 603": "NH1" <-> "NH2" Residue "N ARG 637": "NH1" <-> "NH2" Residue "O ARG 520": "NH1" <-> "NH2" Residue "O ARG 574": "NH1" <-> "NH2" Residue "O ARG 581": "NH1" <-> "NH2" Residue "O ARG 597": "NH1" <-> "NH2" Residue "O ARG 603": "NH1" <-> "NH2" Residue "O ARG 637": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 66045 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "B" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "C" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "D" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "E" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "F" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "G" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "H" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "I" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "J" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "K" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "L" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "M" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "N" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "O" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3762 Classifications: {'peptide': 497} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 4 Chain: "P" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "U" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 641 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 25.36, per 1000 atoms: 0.38 Number of scatterers: 66045 At special positions: 0 Unit cell: (209.88, 208.56, 196.68, 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 315 16.00 O 13020 8.00 N 11640 7.00 C 41070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS P 70 " - pdb=" SG CYS P 107 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 70 " - pdb=" SG CYS Q 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 70 " - pdb=" SG CYS R 107 " distance=2.02 Simple disulfide: pdb=" SG CYS S 70 " - pdb=" SG CYS S 107 " distance=2.02 Simple disulfide: pdb=" SG CYS T 70 " - pdb=" SG CYS T 107 " distance=2.02 Simple disulfide: pdb=" SG CYS U 70 " - pdb=" SG CYS U 107 " distance=2.02 Simple disulfide: pdb=" SG CYS V 70 " - pdb=" SG CYS V 107 " distance=2.02 Simple disulfide: pdb=" SG CYS W 70 " - pdb=" SG CYS W 107 " distance=2.02 Simple disulfide: pdb=" SG CYS X 70 " - pdb=" SG CYS X 107 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 70 " - pdb=" SG CYS Y 107 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 70 " - pdb=" SG CYS Z 107 " distance=2.02 Simple disulfide: pdb=" SG CYS a 70 " - pdb=" SG CYS a 107 " distance=2.02 Simple disulfide: pdb=" SG CYS b 70 " - pdb=" SG CYS b 107 " distance=2.02 Simple disulfide: pdb=" SG CYS c 70 " - pdb=" SG CYS c 107 " distance=2.02 Simple disulfide: pdb=" SG CYS d 70 " - pdb=" SG CYS d 107 " distance=2.02 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: 19.66 Conformation dependent library (CDL) restraints added in 9.1 seconds 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16290 Finding SS restraints... Secondary structure from input PDB file: 225 helices and 150 sheets defined 31.2% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.60 Creating SS restraints... Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 removed outlier: 3.647A pdb=" N ILE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 160 " --> pdb=" O THR A 156 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 371 removed outlier: 3.581A pdb=" N ALA A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 removed outlier: 3.954A pdb=" N ASN A 562 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 604 " --> pdb=" O ASN A 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 612 " --> pdb=" O TYR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.595A pdb=" N ALA A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.808A pdb=" N ILE B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 160 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 166 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 235 removed outlier: 3.523A pdb=" N LYS B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 315 " --> pdb=" O SER B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA B 368 " --> pdb=" O THR B 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU B 403 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.744A pdb=" N ASP B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 564 removed outlier: 3.955A pdb=" N ASN B 562 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 599 " --> pdb=" O SER B 595 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 604 " --> pdb=" O ASN B 600 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 612 " --> pdb=" O TYR B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 643 removed outlier: 3.595A pdb=" N ALA B 638 " --> pdb=" O PRO B 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 639 " --> pdb=" O GLU B 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 640 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 128 " --> pdb=" O GLN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 166 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.630A pdb=" N GLU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 235 removed outlier: 3.523A pdb=" N LYS C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 267 removed outlier: 3.935A pdb=" N VAL C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN C 307 " --> pdb=" O GLN C 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 311 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 315 " --> pdb=" O SER C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA C 368 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU C 403 " --> pdb=" O THR C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 564 removed outlier: 3.956A pdb=" N ASN C 562 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL C 594 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 597 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 599 " --> pdb=" O SER C 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 604 " --> pdb=" O ASN C 600 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 608 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 612 " --> pdb=" O TYR C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 643 removed outlier: 3.596A pdb=" N ALA C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 639 " --> pdb=" O GLU C 635 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 640 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 641 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY C 643 " --> pdb=" O PHE C 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 166 removed outlier: 3.647A pdb=" N ILE D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN D 307 " --> pdb=" O GLN D 303 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D 311 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA D 368 " --> pdb=" O THR D 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER D 370 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU D 403 " --> pdb=" O THR D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 564 removed outlier: 3.955A pdb=" N ASN D 562 " --> pdb=" O LEU D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 612 removed outlier: 3.611A pdb=" N VAL D 594 " --> pdb=" O ALA D 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG D 597 " --> pdb=" O GLY D 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 599 " --> pdb=" O SER D 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 604 " --> pdb=" O ASN D 600 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 612 " --> pdb=" O TYR D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 643 removed outlier: 3.595A pdb=" N ALA D 638 " --> pdb=" O PRO D 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 639 " --> pdb=" O GLU D 635 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 640 " --> pdb=" O VAL D 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN D 641 " --> pdb=" O ARG D 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 643 " --> pdb=" O PHE D 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 removed outlier: 3.808A pdb=" N ILE E 126 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER E 128 " --> pdb=" O GLN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 160 " --> pdb=" O THR E 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS E 164 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY E 166 " --> pdb=" O VAL E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 264 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN E 307 " --> pdb=" O GLN E 303 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER E 311 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 315 " --> pdb=" O SER E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA E 368 " --> pdb=" O THR E 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU E 403 " --> pdb=" O THR E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP E 556 " --> pdb=" O LEU E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 564 removed outlier: 3.954A pdb=" N ASN E 562 " --> pdb=" O LEU E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL E 594 " --> pdb=" O ALA E 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 597 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR E 599 " --> pdb=" O SER E 595 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA E 604 " --> pdb=" O ASN E 600 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR E 608 " --> pdb=" O ALA E 604 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN E 612 " --> pdb=" O TYR E 608 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA E 638 " --> pdb=" O PRO E 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE E 639 " --> pdb=" O GLU E 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU E 640 " --> pdb=" O VAL E 636 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN E 641 " --> pdb=" O ARG E 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E 643 " --> pdb=" O PHE E 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 removed outlier: 3.808A pdb=" N ILE F 126 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER F 128 " --> pdb=" O GLN F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS F 164 " --> pdb=" O GLN F 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY F 166 " --> pdb=" O VAL F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG F 232 " --> pdb=" O ARG F 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 264 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN F 307 " --> pdb=" O GLN F 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER F 311 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN F 315 " --> pdb=" O SER F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA F 368 " --> pdb=" O THR F 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 370 " --> pdb=" O GLY F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU F 403 " --> pdb=" O THR F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 557 removed outlier: 3.744A pdb=" N ASP F 556 " --> pdb=" O LEU F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 564 removed outlier: 3.955A pdb=" N ASN F 562 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 612 removed outlier: 3.611A pdb=" N VAL F 594 " --> pdb=" O ALA F 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG F 597 " --> pdb=" O GLY F 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR F 599 " --> pdb=" O SER F 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 604 " --> pdb=" O ASN F 600 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 608 " --> pdb=" O ALA F 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 612 " --> pdb=" O TYR F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA F 638 " --> pdb=" O PRO F 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 639 " --> pdb=" O GLU F 635 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 640 " --> pdb=" O VAL F 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN F 641 " --> pdb=" O ARG F 637 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY F 643 " --> pdb=" O PHE F 639 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 130 removed outlier: 3.808A pdb=" N ILE G 126 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER G 128 " --> pdb=" O GLN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE G 159 " --> pdb=" O LEU G 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS G 164 " --> pdb=" O GLN G 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY G 166 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG G 233 " --> pdb=" O ARG G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 267 removed outlier: 3.937A pdb=" N VAL G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 264 " --> pdb=" O VAL G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN G 307 " --> pdb=" O GLN G 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER G 311 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN G 315 " --> pdb=" O SER G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA G 368 " --> pdb=" O THR G 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER G 370 " --> pdb=" O GLY G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 404 removed outlier: 3.564A pdb=" N LEU G 403 " --> pdb=" O THR G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP G 556 " --> pdb=" O LEU G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 564 removed outlier: 3.955A pdb=" N ASN G 562 " --> pdb=" O LEU G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL G 594 " --> pdb=" O ALA G 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG G 597 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR G 599 " --> pdb=" O SER G 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA G 604 " --> pdb=" O ASN G 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR G 608 " --> pdb=" O ALA G 604 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN G 612 " --> pdb=" O TYR G 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA G 638 " --> pdb=" O PRO G 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE G 639 " --> pdb=" O GLU G 635 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU G 640 " --> pdb=" O VAL G 636 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN G 641 " --> pdb=" O ARG G 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY G 643 " --> pdb=" O PHE G 639 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER H 128 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 166 removed outlier: 3.647A pdb=" N ILE H 159 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN H 160 " --> pdb=" O THR H 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS H 164 " --> pdb=" O GLN H 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY H 166 " --> pdb=" O VAL H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG H 232 " --> pdb=" O ARG H 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 233 " --> pdb=" O ARG H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 267 removed outlier: 3.937A pdb=" N VAL H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 317 removed outlier: 3.578A pdb=" N GLN H 307 " --> pdb=" O GLN H 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER H 311 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN H 315 " --> pdb=" O SER H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA H 368 " --> pdb=" O THR H 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER H 370 " --> pdb=" O GLY H 366 " (cutoff:3.500A) Processing helix chain 'H' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU H 403 " --> pdb=" O THR H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP H 556 " --> pdb=" O LEU H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 564 removed outlier: 3.955A pdb=" N ASN H 562 " --> pdb=" O LEU H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL H 594 " --> pdb=" O ALA H 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG H 597 " --> pdb=" O GLY H 593 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR H 599 " --> pdb=" O SER H 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 604 " --> pdb=" O ASN H 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR H 608 " --> pdb=" O ALA H 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN H 612 " --> pdb=" O TYR H 608 " (cutoff:3.500A) Processing helix chain 'H' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA H 638 " --> pdb=" O PRO H 634 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE H 639 " --> pdb=" O GLU H 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 640 " --> pdb=" O VAL H 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN H 641 " --> pdb=" O ARG H 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY H 643 " --> pdb=" O PHE H 639 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE I 126 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 166 removed outlier: 3.647A pdb=" N ILE I 159 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN I 160 " --> pdb=" O THR I 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS I 164 " --> pdb=" O GLN I 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY I 166 " --> pdb=" O VAL I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU I 188 " --> pdb=" O ALA I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS I 226 " --> pdb=" O ALA I 222 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG I 232 " --> pdb=" O ARG I 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG I 233 " --> pdb=" O ARG I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN I 307 " --> pdb=" O GLN I 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER I 311 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN I 315 " --> pdb=" O SER I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA I 368 " --> pdb=" O THR I 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 404 removed outlier: 3.564A pdb=" N LEU I 403 " --> pdb=" O THR I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP I 556 " --> pdb=" O LEU I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 564 removed outlier: 3.956A pdb=" N ASN I 562 " --> pdb=" O LEU I 559 " (cutoff:3.500A) Processing helix chain 'I' and resid 590 through 612 removed outlier: 3.611A pdb=" N VAL I 594 " --> pdb=" O ALA I 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG I 597 " --> pdb=" O GLY I 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR I 599 " --> pdb=" O SER I 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA I 604 " --> pdb=" O ASN I 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR I 608 " --> pdb=" O ALA I 604 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN I 612 " --> pdb=" O TYR I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA I 638 " --> pdb=" O PRO I 634 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 639 " --> pdb=" O GLU I 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU I 640 " --> pdb=" O VAL I 636 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN I 641 " --> pdb=" O ARG I 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY I 643 " --> pdb=" O PHE I 639 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 130 removed outlier: 3.808A pdb=" N ILE J 126 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER J 128 " --> pdb=" O GLN J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 166 removed outlier: 3.647A pdb=" N ILE J 159 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN J 160 " --> pdb=" O THR J 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS J 164 " --> pdb=" O GLN J 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY J 166 " --> pdb=" O VAL J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU J 188 " --> pdb=" O ALA J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 235 removed outlier: 3.523A pdb=" N LYS J 226 " --> pdb=" O ALA J 222 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG J 232 " --> pdb=" O ARG J 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL J 264 " --> pdb=" O VAL J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN J 307 " --> pdb=" O GLN J 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER J 311 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN J 315 " --> pdb=" O SER J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA J 368 " --> pdb=" O THR J 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER J 370 " --> pdb=" O GLY J 366 " (cutoff:3.500A) Processing helix chain 'J' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU J 403 " --> pdb=" O THR J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP J 556 " --> pdb=" O LEU J 553 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 564 removed outlier: 3.954A pdb=" N ASN J 562 " --> pdb=" O LEU J 559 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL J 594 " --> pdb=" O ALA J 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG J 597 " --> pdb=" O GLY J 593 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR J 599 " --> pdb=" O SER J 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA J 604 " --> pdb=" O ASN J 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR J 608 " --> pdb=" O ALA J 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN J 612 " --> pdb=" O TYR J 608 " (cutoff:3.500A) Processing helix chain 'J' and resid 633 through 643 removed outlier: 3.595A pdb=" N ALA J 638 " --> pdb=" O PRO J 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE J 639 " --> pdb=" O GLU J 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU J 640 " --> pdb=" O VAL J 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN J 641 " --> pdb=" O ARG J 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY J 643 " --> pdb=" O PHE J 639 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE K 126 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER K 128 " --> pdb=" O GLN K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN K 160 " --> pdb=" O THR K 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY K 166 " --> pdb=" O VAL K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS K 226 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG K 228 " --> pdb=" O ARG K 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG K 232 " --> pdb=" O ARG K 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 267 removed outlier: 3.935A pdb=" N VAL K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 317 removed outlier: 3.578A pdb=" N GLN K 307 " --> pdb=" O GLN K 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER K 311 " --> pdb=" O GLN K 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 371 removed outlier: 3.579A pdb=" N ALA K 368 " --> pdb=" O THR K 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER K 370 " --> pdb=" O GLY K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU K 403 " --> pdb=" O THR K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 552 through 557 removed outlier: 3.746A pdb=" N ASP K 556 " --> pdb=" O LEU K 553 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 564 removed outlier: 3.955A pdb=" N ASN K 562 " --> pdb=" O LEU K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 590 through 612 removed outlier: 3.611A pdb=" N VAL K 594 " --> pdb=" O ALA K 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG K 597 " --> pdb=" O GLY K 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR K 599 " --> pdb=" O SER K 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA K 604 " --> pdb=" O ASN K 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR K 608 " --> pdb=" O ALA K 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN K 612 " --> pdb=" O TYR K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA K 638 " --> pdb=" O PRO K 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE K 639 " --> pdb=" O GLU K 635 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU K 640 " --> pdb=" O VAL K 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN K 641 " --> pdb=" O ARG K 637 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY K 643 " --> pdb=" O PHE K 639 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE L 126 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE L 159 " --> pdb=" O LEU L 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN L 160 " --> pdb=" O THR L 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS L 164 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY L 166 " --> pdb=" O VAL L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 235 removed outlier: 3.525A pdb=" N LYS L 226 " --> pdb=" O ALA L 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG L 228 " --> pdb=" O ARG L 224 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG L 232 " --> pdb=" O ARG L 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN L 307 " --> pdb=" O GLN L 303 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER L 311 " --> pdb=" O GLN L 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN L 315 " --> pdb=" O SER L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA L 368 " --> pdb=" O THR L 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER L 370 " --> pdb=" O GLY L 366 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU L 403 " --> pdb=" O THR L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP L 556 " --> pdb=" O LEU L 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 559 through 564 removed outlier: 3.954A pdb=" N ASN L 562 " --> pdb=" O LEU L 559 " (cutoff:3.500A) Processing helix chain 'L' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL L 594 " --> pdb=" O ALA L 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG L 597 " --> pdb=" O GLY L 593 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR L 599 " --> pdb=" O SER L 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA L 604 " --> pdb=" O ASN L 600 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR L 608 " --> pdb=" O ALA L 604 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN L 612 " --> pdb=" O TYR L 608 " (cutoff:3.500A) Processing helix chain 'L' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA L 638 " --> pdb=" O PRO L 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE L 639 " --> pdb=" O GLU L 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU L 640 " --> pdb=" O VAL L 636 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN L 641 " --> pdb=" O ARG L 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY L 643 " --> pdb=" O PHE L 639 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE M 126 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP M 127 " --> pdb=" O ARG M 123 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER M 128 " --> pdb=" O GLN M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE M 159 " --> pdb=" O LEU M 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN M 160 " --> pdb=" O THR M 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS M 164 " --> pdb=" O GLN M 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY M 166 " --> pdb=" O VAL M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 190 removed outlier: 3.630A pdb=" N GLU M 188 " --> pdb=" O ALA M 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS M 226 " --> pdb=" O ALA M 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG M 228 " --> pdb=" O ARG M 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG M 232 " --> pdb=" O ARG M 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG M 233 " --> pdb=" O ARG M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 267 removed outlier: 3.935A pdb=" N VAL M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL M 264 " --> pdb=" O VAL M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 317 removed outlier: 3.578A pdb=" N GLN M 307 " --> pdb=" O GLN M 303 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER M 311 " --> pdb=" O GLN M 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA M 368 " --> pdb=" O THR M 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER M 370 " --> pdb=" O GLY M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU M 403 " --> pdb=" O THR M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 552 through 557 removed outlier: 3.744A pdb=" N ASP M 556 " --> pdb=" O LEU M 553 " (cutoff:3.500A) Processing helix chain 'M' and resid 559 through 564 removed outlier: 3.954A pdb=" N ASN M 562 " --> pdb=" O LEU M 559 " (cutoff:3.500A) Processing helix chain 'M' and resid 590 through 612 removed outlier: 3.611A pdb=" N VAL M 594 " --> pdb=" O ALA M 590 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG M 597 " --> pdb=" O GLY M 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR M 599 " --> pdb=" O SER M 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA M 604 " --> pdb=" O ASN M 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR M 608 " --> pdb=" O ALA M 604 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN M 612 " --> pdb=" O TYR M 608 " (cutoff:3.500A) Processing helix chain 'M' and resid 633 through 643 removed outlier: 3.595A pdb=" N ALA M 638 " --> pdb=" O PRO M 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE M 639 " --> pdb=" O GLU M 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU M 640 " --> pdb=" O VAL M 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN M 641 " --> pdb=" O ARG M 637 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY M 643 " --> pdb=" O PHE M 639 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 130 removed outlier: 3.809A pdb=" N ILE N 126 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP N 127 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER N 128 " --> pdb=" O GLN N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 166 removed outlier: 3.646A pdb=" N ILE N 159 " --> pdb=" O LEU N 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN N 160 " --> pdb=" O THR N 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS N 164 " --> pdb=" O GLN N 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY N 166 " --> pdb=" O VAL N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU N 188 " --> pdb=" O ALA N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS N 226 " --> pdb=" O ALA N 222 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG N 228 " --> pdb=" O ARG N 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG N 232 " --> pdb=" O ARG N 228 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG N 233 " --> pdb=" O ARG N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 267 removed outlier: 3.936A pdb=" N VAL N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL N 264 " --> pdb=" O VAL N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN N 307 " --> pdb=" O GLN N 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER N 311 " --> pdb=" O GLN N 307 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN N 315 " --> pdb=" O SER N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 361 through 371 removed outlier: 3.580A pdb=" N ALA N 368 " --> pdb=" O THR N 364 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER N 370 " --> pdb=" O GLY N 366 " (cutoff:3.500A) Processing helix chain 'N' and resid 399 through 404 removed outlier: 3.565A pdb=" N LEU N 403 " --> pdb=" O THR N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 552 through 557 removed outlier: 3.745A pdb=" N ASP N 556 " --> pdb=" O LEU N 553 " (cutoff:3.500A) Processing helix chain 'N' and resid 559 through 564 removed outlier: 3.955A pdb=" N ASN N 562 " --> pdb=" O LEU N 559 " (cutoff:3.500A) Processing helix chain 'N' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL N 594 " --> pdb=" O ALA N 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG N 597 " --> pdb=" O GLY N 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR N 599 " --> pdb=" O SER N 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA N 604 " --> pdb=" O ASN N 600 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR N 608 " --> pdb=" O ALA N 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN N 612 " --> pdb=" O TYR N 608 " (cutoff:3.500A) Processing helix chain 'N' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA N 638 " --> pdb=" O PRO N 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE N 639 " --> pdb=" O GLU N 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU N 640 " --> pdb=" O VAL N 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN N 641 " --> pdb=" O ARG N 637 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY N 643 " --> pdb=" O PHE N 639 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 130 removed outlier: 3.808A pdb=" N ILE O 126 " --> pdb=" O LEU O 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP O 127 " --> pdb=" O ARG O 123 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER O 128 " --> pdb=" O GLN O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 166 removed outlier: 3.647A pdb=" N ILE O 159 " --> pdb=" O LEU O 155 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN O 160 " --> pdb=" O THR O 156 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N HIS O 164 " --> pdb=" O GLN O 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY O 166 " --> pdb=" O VAL O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 190 removed outlier: 3.629A pdb=" N GLU O 188 " --> pdb=" O ALA O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 222 through 235 removed outlier: 3.524A pdb=" N LYS O 226 " --> pdb=" O ALA O 222 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG O 228 " --> pdb=" O ARG O 224 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG O 232 " --> pdb=" O ARG O 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG O 233 " --> pdb=" O ARG O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 267 removed outlier: 3.935A pdb=" N VAL O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL O 264 " --> pdb=" O VAL O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 317 removed outlier: 3.579A pdb=" N GLN O 307 " --> pdb=" O GLN O 303 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER O 311 " --> pdb=" O GLN O 307 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN O 315 " --> pdb=" O SER O 311 " (cutoff:3.500A) Processing helix chain 'O' and resid 361 through 371 removed outlier: 3.581A pdb=" N ALA O 368 " --> pdb=" O THR O 364 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER O 370 " --> pdb=" O GLY O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 399 through 404 removed outlier: 3.564A pdb=" N LEU O 403 " --> pdb=" O THR O 399 " (cutoff:3.500A) Processing helix chain 'O' and resid 552 through 557 removed outlier: 3.744A pdb=" N ASP O 556 " --> pdb=" O LEU O 553 " (cutoff:3.500A) Processing helix chain 'O' and resid 559 through 564 removed outlier: 3.955A pdb=" N ASN O 562 " --> pdb=" O LEU O 559 " (cutoff:3.500A) Processing helix chain 'O' and resid 590 through 612 removed outlier: 3.610A pdb=" N VAL O 594 " --> pdb=" O ALA O 590 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG O 597 " --> pdb=" O GLY O 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR O 599 " --> pdb=" O SER O 595 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA O 604 " --> pdb=" O ASN O 600 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR O 608 " --> pdb=" O ALA O 604 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN O 612 " --> pdb=" O TYR O 608 " (cutoff:3.500A) Processing helix chain 'O' and resid 633 through 643 removed outlier: 3.594A pdb=" N ALA O 638 " --> pdb=" O PRO O 634 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE O 639 " --> pdb=" O GLU O 635 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU O 640 " --> pdb=" O VAL O 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN O 641 " --> pdb=" O ARG O 637 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY O 643 " --> pdb=" O PHE O 639 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA P 16 " --> pdb=" O ALA P 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN P 21 " --> pdb=" O GLN P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR P 63 " --> pdb=" O ASP P 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN P 68 " --> pdb=" O SER P 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET P 69 " --> pdb=" O TYR P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 79 Processing helix chain 'Q' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN Q 21 " --> pdb=" O GLN Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR Q 63 " --> pdb=" O ASP Q 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN Q 68 " --> pdb=" O SER Q 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET Q 69 " --> pdb=" O TYR Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 79 Processing helix chain 'R' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN R 21 " --> pdb=" O GLN R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR R 63 " --> pdb=" O ASP R 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN R 68 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 79 Processing helix chain 'S' and resid 9 through 21 removed outlier: 3.624A pdb=" N ALA S 16 " --> pdb=" O ALA S 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN S 21 " --> pdb=" O GLN S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR S 63 " --> pdb=" O ASP S 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN S 68 " --> pdb=" O SER S 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 Processing helix chain 'T' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA T 16 " --> pdb=" O ALA T 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN T 21 " --> pdb=" O GLN T 17 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 72 removed outlier: 3.934A pdb=" N THR T 63 " --> pdb=" O ASP T 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN T 68 " --> pdb=" O SER T 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET T 69 " --> pdb=" O TYR T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 79 Processing helix chain 'U' and resid 9 through 21 removed outlier: 3.624A pdb=" N ALA U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN U 21 " --> pdb=" O GLN U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR U 63 " --> pdb=" O ASP U 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN U 68 " --> pdb=" O SER U 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET U 69 " --> pdb=" O TYR U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 79 Processing helix chain 'V' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA V 16 " --> pdb=" O ALA V 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN V 21 " --> pdb=" O GLN V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 72 removed outlier: 3.934A pdb=" N THR V 63 " --> pdb=" O ASP V 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN V 68 " --> pdb=" O SER V 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET V 69 " --> pdb=" O TYR V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 79 Processing helix chain 'W' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA W 16 " --> pdb=" O ALA W 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN W 21 " --> pdb=" O GLN W 17 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 72 removed outlier: 3.934A pdb=" N THR W 63 " --> pdb=" O ASP W 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN W 68 " --> pdb=" O SER W 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET W 69 " --> pdb=" O TYR W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 74 through 79 Processing helix chain 'X' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA X 16 " --> pdb=" O ALA X 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN X 21 " --> pdb=" O GLN X 17 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR X 63 " --> pdb=" O ASP X 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN X 68 " --> pdb=" O SER X 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET X 69 " --> pdb=" O TYR X 65 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 79 Processing helix chain 'Y' and resid 9 through 21 removed outlier: 3.624A pdb=" N ALA Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN Y 21 " --> pdb=" O GLN Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR Y 63 " --> pdb=" O ASP Y 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN Y 68 " --> pdb=" O SER Y 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET Y 69 " --> pdb=" O TYR Y 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 74 through 79 Processing helix chain 'Z' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA Z 16 " --> pdb=" O ALA Z 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN Z 21 " --> pdb=" O GLN Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR Z 63 " --> pdb=" O ASP Z 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN Z 68 " --> pdb=" O SER Z 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET Z 69 " --> pdb=" O TYR Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 79 Processing helix chain 'a' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA a 16 " --> pdb=" O ALA a 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN a 21 " --> pdb=" O GLN a 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR a 63 " --> pdb=" O ASP a 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN a 68 " --> pdb=" O SER a 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET a 69 " --> pdb=" O TYR a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 79 Processing helix chain 'b' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA b 16 " --> pdb=" O ALA b 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN b 21 " --> pdb=" O GLN b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR b 63 " --> pdb=" O ASP b 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN b 68 " --> pdb=" O SER b 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET b 69 " --> pdb=" O TYR b 65 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 79 Processing helix chain 'c' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA c 16 " --> pdb=" O ALA c 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN c 21 " --> pdb=" O GLN c 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR c 63 " --> pdb=" O ASP c 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN c 68 " --> pdb=" O SER c 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET c 69 " --> pdb=" O TYR c 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 74 through 79 Processing helix chain 'd' and resid 9 through 21 removed outlier: 3.623A pdb=" N ALA d 16 " --> pdb=" O ALA d 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN d 21 " --> pdb=" O GLN d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 59 through 72 removed outlier: 3.933A pdb=" N THR d 63 " --> pdb=" O ASP d 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN d 68 " --> pdb=" O SER d 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET d 69 " --> pdb=" O TYR d 65 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 79 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR A 169 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 248 Processing sheet with id=AA4, first strand: chain 'A' and resid 584 through 585 removed outlier: 3.578A pdb=" N TRP A 419 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 436 Processing sheet with id=AA6, first strand: chain 'A' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA A 568 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A 572 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP A 542 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A 574 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET A 540 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU A 576 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY A 538 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 578 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 458 removed outlier: 12.780A pdb=" N LYS A 479 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N VAL A 507 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 481 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 505 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 516 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 34 through 38 Processing sheet with id=AB1, first strand: chain 'V' and resid 86 through 89 Processing sheet with id=AB2, first strand: chain 'B' and resid 103 through 109 removed outlier: 3.600A pdb=" N VAL B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR B 169 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 244 through 248 Processing sheet with id=AB5, first strand: chain 'B' and resid 584 through 585 removed outlier: 3.579A pdb=" N TRP B 419 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 434 through 436 Processing sheet with id=AB7, first strand: chain 'B' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA B 568 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU B 572 " --> pdb=" O ASP B 542 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP B 542 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG B 574 " --> pdb=" O MET B 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET B 540 " --> pdb=" O ARG B 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 576 " --> pdb=" O GLY B 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY B 538 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL B 578 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 351 through 352 Processing sheet with id=AB9, first strand: chain 'B' and resid 448 through 458 removed outlier: 12.780A pdb=" N LYS B 479 " --> pdb=" O VAL B 507 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL B 507 " --> pdb=" O LYS B 479 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY B 481 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 505 " --> pdb=" O GLY B 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 516 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 34 through 38 Processing sheet with id=AC2, first strand: chain 'W' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'C' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR C 169 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 244 through 248 Processing sheet with id=AC6, first strand: chain 'C' and resid 584 through 585 removed outlier: 3.578A pdb=" N TRP C 419 " --> pdb=" O LYS C 416 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 434 through 436 Processing sheet with id=AC8, first strand: chain 'C' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA C 568 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU C 572 " --> pdb=" O ASP C 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP C 542 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG C 574 " --> pdb=" O MET C 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET C 540 " --> pdb=" O ARG C 574 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU C 576 " --> pdb=" O GLY C 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY C 538 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 578 " --> pdb=" O LEU C 536 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 351 through 352 Processing sheet with id=AD1, first strand: chain 'C' and resid 448 through 458 removed outlier: 12.780A pdb=" N LYS C 479 " --> pdb=" O VAL C 507 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL C 507 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY C 481 " --> pdb=" O SER C 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 505 " --> pdb=" O GLY C 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 516 " --> pdb=" O GLU C 508 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 34 through 38 Processing sheet with id=AD3, first strand: chain 'X' and resid 86 through 89 Processing sheet with id=AD4, first strand: chain 'D' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 169 through 174 removed outlier: 3.716A pdb=" N THR D 169 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 244 through 248 Processing sheet with id=AD7, first strand: chain 'D' and resid 584 through 585 removed outlier: 3.578A pdb=" N TRP D 419 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 434 through 436 Processing sheet with id=AD9, first strand: chain 'D' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA D 568 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU D 572 " --> pdb=" O ASP D 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP D 542 " --> pdb=" O GLU D 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG D 574 " --> pdb=" O MET D 540 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET D 540 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 576 " --> pdb=" O GLY D 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY D 538 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 578 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 351 through 352 Processing sheet with id=AE2, first strand: chain 'D' and resid 448 through 458 removed outlier: 12.779A pdb=" N LYS D 479 " --> pdb=" O VAL D 507 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL D 507 " --> pdb=" O LYS D 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY D 481 " --> pdb=" O SER D 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 505 " --> pdb=" O GLY D 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 516 " --> pdb=" O GLU D 508 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 34 through 38 Processing sheet with id=AE4, first strand: chain 'X' and resid 86 through 89 Processing sheet with id=AE5, first strand: chain 'E' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL E 142 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR E 169 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 244 through 248 Processing sheet with id=AE8, first strand: chain 'E' and resid 584 through 585 removed outlier: 3.579A pdb=" N TRP E 419 " --> pdb=" O LYS E 416 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 434 through 436 Processing sheet with id=AF1, first strand: chain 'E' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA E 568 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU E 572 " --> pdb=" O ASP E 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP E 542 " --> pdb=" O GLU E 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG E 574 " --> pdb=" O MET E 540 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET E 540 " --> pdb=" O ARG E 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU E 576 " --> pdb=" O GLY E 538 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY E 538 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL E 578 " --> pdb=" O LEU E 536 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 351 through 352 Processing sheet with id=AF3, first strand: chain 'E' and resid 448 through 458 removed outlier: 12.780A pdb=" N LYS E 479 " --> pdb=" O VAL E 507 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL E 507 " --> pdb=" O LYS E 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY E 481 " --> pdb=" O SER E 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER E 505 " --> pdb=" O GLY E 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL E 516 " --> pdb=" O GLU E 508 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AF5, first strand: chain 'Z' and resid 86 through 89 Processing sheet with id=AF6, first strand: chain 'F' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR F 169 " --> pdb=" O GLY F 219 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 244 through 248 Processing sheet with id=AF9, first strand: chain 'F' and resid 584 through 585 removed outlier: 3.579A pdb=" N TRP F 419 " --> pdb=" O LYS F 416 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 434 through 436 Processing sheet with id=AG2, first strand: chain 'F' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA F 568 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU F 572 " --> pdb=" O ASP F 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP F 542 " --> pdb=" O GLU F 572 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG F 574 " --> pdb=" O MET F 540 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET F 540 " --> pdb=" O ARG F 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 576 " --> pdb=" O GLY F 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY F 538 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL F 578 " --> pdb=" O LEU F 536 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 351 through 352 Processing sheet with id=AG4, first strand: chain 'F' and resid 448 through 458 removed outlier: 12.780A pdb=" N LYS F 479 " --> pdb=" O VAL F 507 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL F 507 " --> pdb=" O LYS F 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY F 481 " --> pdb=" O SER F 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 505 " --> pdb=" O GLY F 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL F 516 " --> pdb=" O GLU F 508 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 34 through 38 Processing sheet with id=AG6, first strand: chain 'a' and resid 86 through 89 Processing sheet with id=AG7, first strand: chain 'G' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL G 142 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR G 169 " --> pdb=" O GLY G 219 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 244 through 248 Processing sheet with id=AH1, first strand: chain 'G' and resid 584 through 585 removed outlier: 3.579A pdb=" N TRP G 419 " --> pdb=" O LYS G 416 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 434 through 436 Processing sheet with id=AH3, first strand: chain 'G' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA G 568 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU G 572 " --> pdb=" O ASP G 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP G 542 " --> pdb=" O GLU G 572 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG G 574 " --> pdb=" O MET G 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET G 540 " --> pdb=" O ARG G 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU G 576 " --> pdb=" O GLY G 538 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY G 538 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL G 578 " --> pdb=" O LEU G 536 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 351 through 352 Processing sheet with id=AH5, first strand: chain 'G' and resid 448 through 458 removed outlier: 12.779A pdb=" N LYS G 479 " --> pdb=" O VAL G 507 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL G 507 " --> pdb=" O LYS G 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY G 481 " --> pdb=" O SER G 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER G 505 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 516 " --> pdb=" O GLU G 508 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 34 through 38 Processing sheet with id=AH7, first strand: chain 'b' and resid 86 through 89 Processing sheet with id=AH8, first strand: chain 'H' and resid 103 through 109 removed outlier: 3.600A pdb=" N VAL H 142 " --> pdb=" O ASP H 138 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR H 169 " --> pdb=" O GLY H 219 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 244 through 248 Processing sheet with id=AI2, first strand: chain 'H' and resid 584 through 585 removed outlier: 3.579A pdb=" N TRP H 419 " --> pdb=" O LYS H 416 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 434 through 436 Processing sheet with id=AI4, first strand: chain 'H' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA H 568 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU H 572 " --> pdb=" O ASP H 542 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP H 542 " --> pdb=" O GLU H 572 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG H 574 " --> pdb=" O MET H 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET H 540 " --> pdb=" O ARG H 574 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU H 576 " --> pdb=" O GLY H 538 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY H 538 " --> pdb=" O LEU H 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL H 578 " --> pdb=" O LEU H 536 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 351 through 352 Processing sheet with id=AI6, first strand: chain 'H' and resid 448 through 458 removed outlier: 12.781A pdb=" N LYS H 479 " --> pdb=" O VAL H 507 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL H 507 " --> pdb=" O LYS H 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY H 481 " --> pdb=" O SER H 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER H 505 " --> pdb=" O GLY H 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL H 516 " --> pdb=" O GLU H 508 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'c' and resid 34 through 38 Processing sheet with id=AI8, first strand: chain 'c' and resid 86 through 89 Processing sheet with id=AI9, first strand: chain 'I' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL I 142 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR I 169 " --> pdb=" O GLY I 219 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 244 through 248 Processing sheet with id=AJ3, first strand: chain 'I' and resid 584 through 585 removed outlier: 3.578A pdb=" N TRP I 419 " --> pdb=" O LYS I 416 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'I' and resid 434 through 436 Processing sheet with id=AJ5, first strand: chain 'I' and resid 546 through 547 removed outlier: 3.605A pdb=" N ALA I 568 " --> pdb=" O SER I 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU I 572 " --> pdb=" O ASP I 542 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP I 542 " --> pdb=" O GLU I 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG I 574 " --> pdb=" O MET I 540 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET I 540 " --> pdb=" O ARG I 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU I 576 " --> pdb=" O GLY I 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY I 538 " --> pdb=" O LEU I 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL I 578 " --> pdb=" O LEU I 536 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'I' and resid 351 through 352 Processing sheet with id=AJ7, first strand: chain 'I' and resid 448 through 458 removed outlier: 12.781A pdb=" N LYS I 479 " --> pdb=" O VAL I 507 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL I 507 " --> pdb=" O LYS I 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY I 481 " --> pdb=" O SER I 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER I 505 " --> pdb=" O GLY I 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL I 516 " --> pdb=" O GLU I 508 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'd' and resid 34 through 38 Processing sheet with id=AJ9, first strand: chain 'd' and resid 86 through 89 Processing sheet with id=AK1, first strand: chain 'J' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL J 142 " --> pdb=" O ASP J 138 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'J' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR J 169 " --> pdb=" O GLY J 219 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J' and resid 244 through 248 Processing sheet with id=AK4, first strand: chain 'J' and resid 584 through 585 removed outlier: 3.578A pdb=" N TRP J 419 " --> pdb=" O LYS J 416 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'J' and resid 434 through 436 Processing sheet with id=AK6, first strand: chain 'J' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA J 568 " --> pdb=" O SER J 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU J 572 " --> pdb=" O ASP J 542 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP J 542 " --> pdb=" O GLU J 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG J 574 " --> pdb=" O MET J 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET J 540 " --> pdb=" O ARG J 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU J 576 " --> pdb=" O GLY J 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY J 538 " --> pdb=" O LEU J 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL J 578 " --> pdb=" O LEU J 536 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'J' and resid 351 through 352 Processing sheet with id=AK8, first strand: chain 'J' and resid 448 through 458 removed outlier: 12.781A pdb=" N LYS J 479 " --> pdb=" O VAL J 507 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL J 507 " --> pdb=" O LYS J 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY J 481 " --> pdb=" O SER J 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER J 505 " --> pdb=" O GLY J 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL J 516 " --> pdb=" O GLU J 508 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'P' and resid 34 through 38 Processing sheet with id=AL1, first strand: chain 'P' and resid 86 through 89 Processing sheet with id=AL2, first strand: chain 'K' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL K 142 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'K' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR K 169 " --> pdb=" O GLY K 219 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'K' and resid 244 through 248 Processing sheet with id=AL5, first strand: chain 'K' and resid 584 through 585 removed outlier: 3.578A pdb=" N TRP K 419 " --> pdb=" O LYS K 416 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'K' and resid 434 through 436 Processing sheet with id=AL7, first strand: chain 'K' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA K 568 " --> pdb=" O SER K 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU K 572 " --> pdb=" O ASP K 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP K 542 " --> pdb=" O GLU K 572 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG K 574 " --> pdb=" O MET K 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET K 540 " --> pdb=" O ARG K 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU K 576 " --> pdb=" O GLY K 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY K 538 " --> pdb=" O LEU K 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL K 578 " --> pdb=" O LEU K 536 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'K' and resid 351 through 352 Processing sheet with id=AL9, first strand: chain 'K' and resid 448 through 458 removed outlier: 12.780A pdb=" N LYS K 479 " --> pdb=" O VAL K 507 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL K 507 " --> pdb=" O LYS K 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY K 481 " --> pdb=" O SER K 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER K 505 " --> pdb=" O GLY K 481 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 516 " --> pdb=" O GLU K 508 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Q' and resid 34 through 38 Processing sheet with id=AM2, first strand: chain 'Q' and resid 86 through 89 Processing sheet with id=AM3, first strand: chain 'L' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL L 142 " --> pdb=" O ASP L 138 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'L' and resid 169 through 174 removed outlier: 3.716A pdb=" N THR L 169 " --> pdb=" O GLY L 219 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'L' and resid 244 through 248 Processing sheet with id=AM6, first strand: chain 'L' and resid 584 through 585 removed outlier: 3.579A pdb=" N TRP L 419 " --> pdb=" O LYS L 416 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'L' and resid 434 through 436 Processing sheet with id=AM8, first strand: chain 'L' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA L 568 " --> pdb=" O SER L 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU L 572 " --> pdb=" O ASP L 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP L 542 " --> pdb=" O GLU L 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG L 574 " --> pdb=" O MET L 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET L 540 " --> pdb=" O ARG L 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU L 576 " --> pdb=" O GLY L 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY L 538 " --> pdb=" O LEU L 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL L 578 " --> pdb=" O LEU L 536 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'L' and resid 351 through 352 Processing sheet with id=AN1, first strand: chain 'L' and resid 448 through 458 removed outlier: 12.781A pdb=" N LYS L 479 " --> pdb=" O VAL L 507 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL L 507 " --> pdb=" O LYS L 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY L 481 " --> pdb=" O SER L 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER L 505 " --> pdb=" O GLY L 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL L 516 " --> pdb=" O GLU L 508 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'R' and resid 34 through 38 Processing sheet with id=AN3, first strand: chain 'R' and resid 86 through 89 Processing sheet with id=AN4, first strand: chain 'M' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL M 142 " --> pdb=" O ASP M 138 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'M' and resid 169 through 174 removed outlier: 3.715A pdb=" N THR M 169 " --> pdb=" O GLY M 219 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'M' and resid 244 through 248 Processing sheet with id=AN7, first strand: chain 'M' and resid 584 through 585 removed outlier: 3.579A pdb=" N TRP M 419 " --> pdb=" O LYS M 416 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'M' and resid 434 through 436 Processing sheet with id=AN9, first strand: chain 'M' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA M 568 " --> pdb=" O SER M 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU M 572 " --> pdb=" O ASP M 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP M 542 " --> pdb=" O GLU M 572 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG M 574 " --> pdb=" O MET M 540 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET M 540 " --> pdb=" O ARG M 574 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU M 576 " --> pdb=" O GLY M 538 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY M 538 " --> pdb=" O LEU M 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL M 578 " --> pdb=" O LEU M 536 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'M' and resid 351 through 352 Processing sheet with id=AO2, first strand: chain 'M' and resid 448 through 458 removed outlier: 12.780A pdb=" N LYS M 479 " --> pdb=" O VAL M 507 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL M 507 " --> pdb=" O LYS M 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY M 481 " --> pdb=" O SER M 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER M 505 " --> pdb=" O GLY M 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL M 516 " --> pdb=" O GLU M 508 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'S' and resid 34 through 38 Processing sheet with id=AO4, first strand: chain 'S' and resid 86 through 89 Processing sheet with id=AO5, first strand: chain 'N' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL N 142 " --> pdb=" O ASP N 138 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'N' and resid 169 through 174 removed outlier: 3.716A pdb=" N THR N 169 " --> pdb=" O GLY N 219 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'N' and resid 244 through 248 Processing sheet with id=AO8, first strand: chain 'N' and resid 584 through 585 removed outlier: 3.578A pdb=" N TRP N 419 " --> pdb=" O LYS N 416 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'N' and resid 434 through 436 Processing sheet with id=AP1, first strand: chain 'N' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA N 568 " --> pdb=" O SER N 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU N 572 " --> pdb=" O ASP N 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP N 542 " --> pdb=" O GLU N 572 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG N 574 " --> pdb=" O MET N 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET N 540 " --> pdb=" O ARG N 574 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU N 576 " --> pdb=" O GLY N 538 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY N 538 " --> pdb=" O LEU N 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL N 578 " --> pdb=" O LEU N 536 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'N' and resid 351 through 352 Processing sheet with id=AP3, first strand: chain 'N' and resid 448 through 458 removed outlier: 12.781A pdb=" N LYS N 479 " --> pdb=" O VAL N 507 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL N 507 " --> pdb=" O LYS N 479 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY N 481 " --> pdb=" O SER N 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER N 505 " --> pdb=" O GLY N 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL N 516 " --> pdb=" O GLU N 508 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'T' and resid 34 through 38 Processing sheet with id=AP5, first strand: chain 'T' and resid 86 through 89 Processing sheet with id=AP6, first strand: chain 'O' and resid 103 through 109 removed outlier: 3.599A pdb=" N VAL O 142 " --> pdb=" O ASP O 138 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'O' and resid 169 through 174 removed outlier: 3.716A pdb=" N THR O 169 " --> pdb=" O GLY O 219 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'O' and resid 244 through 248 Processing sheet with id=AP9, first strand: chain 'O' and resid 584 through 585 removed outlier: 3.578A pdb=" N TRP O 419 " --> pdb=" O LYS O 416 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'O' and resid 434 through 436 Processing sheet with id=AQ2, first strand: chain 'O' and resid 546 through 547 removed outlier: 3.606A pdb=" N ALA O 568 " --> pdb=" O SER O 547 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU O 572 " --> pdb=" O ASP O 542 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP O 542 " --> pdb=" O GLU O 572 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG O 574 " --> pdb=" O MET O 540 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET O 540 " --> pdb=" O ARG O 574 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU O 576 " --> pdb=" O GLY O 538 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY O 538 " --> pdb=" O LEU O 576 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL O 578 " --> pdb=" O LEU O 536 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'O' and resid 351 through 352 Processing sheet with id=AQ4, first strand: chain 'O' and resid 448 through 458 removed outlier: 12.781A pdb=" N LYS O 479 " --> pdb=" O VAL O 507 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N VAL O 507 " --> pdb=" O LYS O 479 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY O 481 " --> pdb=" O SER O 505 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER O 505 " --> pdb=" O GLY O 481 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL O 516 " --> pdb=" O GLU O 508 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'U' and resid 34 through 38 Processing sheet with id=AQ6, first strand: chain 'U' and resid 86 through 89 3075 hydrogen bonds defined for protein. 8370 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: 26.19 Time building geometry restraints manager: 21.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19823 1.33 - 1.45: 10227 1.45 - 1.57: 36025 1.57 - 1.70: 0 1.70 - 1.82: 600 Bond restraints: 66675 Sorted by residual: bond pdb=" CA VAL M 551 " pdb=" CB VAL M 551 " ideal model delta sigma weight residual 1.537 1.460 0.077 1.29e-02 6.01e+03 3.58e+01 bond pdb=" CA VAL F 551 " pdb=" CB VAL F 551 " ideal model delta sigma weight residual 1.537 1.460 0.077 1.29e-02 6.01e+03 3.58e+01 bond pdb=" CA VAL B 551 " pdb=" CB VAL B 551 " ideal model delta sigma weight residual 1.537 1.460 0.077 1.29e-02 6.01e+03 3.56e+01 bond pdb=" CA VAL N 551 " pdb=" CB VAL N 551 " ideal model delta sigma weight residual 1.537 1.460 0.077 1.29e-02 6.01e+03 3.55e+01 bond pdb=" CA VAL A 551 " pdb=" CB VAL A 551 " ideal model delta sigma weight residual 1.537 1.460 0.077 1.29e-02 6.01e+03 3.55e+01 ... (remaining 66670 not shown) Histogram of bond angle deviations from ideal: 93.87 - 105.12: 1470 105.12 - 116.37: 45249 116.37 - 127.62: 43026 127.62 - 138.86: 450 138.86 - 150.11: 15 Bond angle restraints: 90210 Sorted by residual: angle pdb=" C VAL J 551 " pdb=" N PRO J 552 " pdb=" CA PRO J 552 " ideal model delta sigma weight residual 127.00 150.11 -23.11 2.40e+00 1.74e-01 9.27e+01 angle pdb=" C VAL B 551 " pdb=" N PRO B 552 " pdb=" CA PRO B 552 " ideal model delta sigma weight residual 127.00 150.07 -23.07 2.40e+00 1.74e-01 9.24e+01 angle pdb=" C VAL L 551 " pdb=" N PRO L 552 " pdb=" CA PRO L 552 " ideal model delta sigma weight residual 127.00 150.06 -23.06 2.40e+00 1.74e-01 9.23e+01 angle pdb=" C VAL D 551 " pdb=" N PRO D 552 " pdb=" CA PRO D 552 " ideal model delta sigma weight residual 127.00 150.06 -23.06 2.40e+00 1.74e-01 9.23e+01 angle pdb=" C VAL K 551 " pdb=" N PRO K 552 " pdb=" CA PRO K 552 " ideal model delta sigma weight residual 127.00 150.04 -23.04 2.40e+00 1.74e-01 9.22e+01 ... (remaining 90205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 39540 16.86 - 33.72: 1500 33.72 - 50.59: 285 50.59 - 67.45: 105 67.45 - 84.31: 30 Dihedral angle restraints: 41460 sinusoidal: 16455 harmonic: 25005 Sorted by residual: dihedral pdb=" CA LEU O 459 " pdb=" C LEU O 459 " pdb=" N THR O 460 " pdb=" CA THR O 460 " ideal model delta harmonic sigma weight residual 0.00 -40.35 40.35 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA LEU G 459 " pdb=" C LEU G 459 " pdb=" N THR G 460 " pdb=" CA THR G 460 " ideal model delta harmonic sigma weight residual 0.00 -40.33 40.33 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA LEU J 459 " pdb=" C LEU J 459 " pdb=" N THR J 460 " pdb=" CA THR J 460 " ideal model delta harmonic sigma weight residual 0.00 -40.30 40.30 0 5.00e+00 4.00e-02 6.50e+01 ... (remaining 41457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 8172 0.074 - 0.147: 2471 0.147 - 0.221: 248 0.221 - 0.295: 44 0.295 - 0.369: 30 Chirality restraints: 10965 Sorted by residual: chirality pdb=" CA VAL M 551 " pdb=" N VAL M 551 " pdb=" C VAL M 551 " pdb=" CB VAL M 551 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA VAL F 551 " pdb=" N VAL F 551 " pdb=" C VAL F 551 " pdb=" CB VAL F 551 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA VAL N 551 " pdb=" N VAL N 551 " pdb=" C VAL N 551 " pdb=" CB VAL N 551 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 10962 not shown) Planarity restraints: 11745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 301 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO A 302 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 301 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO K 302 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO K 302 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 302 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 301 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO F 302 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 302 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 302 " -0.032 5.00e-02 4.00e+02 ... (remaining 11742 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 180 2.26 - 2.92: 30180 2.92 - 3.58: 91224 3.58 - 4.24: 148357 4.24 - 4.90: 256642 Nonbonded interactions: 526583 Sorted by model distance: nonbonded pdb=" O ASN c 7 " pdb=" O ALA c 8 " model vdw 1.598 3.040 nonbonded pdb=" O ASN V 7 " pdb=" O ALA V 8 " model vdw 1.598 3.040 nonbonded pdb=" O ASN Z 7 " pdb=" O ALA Z 8 " model vdw 1.598 3.040 nonbonded pdb=" O ASN d 7 " pdb=" O ALA d 8 " model vdw 1.598 3.040 nonbonded pdb=" O ASN b 7 " pdb=" O ALA b 8 " model vdw 1.598 3.040 ... (remaining 526578 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' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 9.120 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 133.670 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 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 : 0.016 0.105 66675 Z= 1.069 Angle : 1.321 23.110 90210 Z= 0.694 Chirality : 0.067 0.369 10965 Planarity : 0.006 0.058 11745 Dihedral : 10.623 84.309 25125 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 1.60 % Allowed : 6.19 % Favored : 92.21 % Rotamer: Outliers : 1.42 % Allowed : 2.24 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: -4.98 (0.07), residues: 8445 helix: -4.62 (0.05), residues: 2415 sheet: -2.24 (0.07), residues: 3450 loop : -2.89 (0.10), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP E 419 HIS 0.004 0.001 HIS C 164 PHE 0.026 0.004 PHE I 517 TYR 0.019 0.003 TYR T 85 ARG 0.012 0.002 ARG D 520 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1366 time to evaluate : 5.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 334 GLU cc_start: 0.6858 (tt0) cc_final: 0.6642 (tt0) REVERT: D 562 ASN cc_start: 0.8305 (m-40) cc_final: 0.8037 (m110) REVERT: F 400 LEU cc_start: 0.8303 (tp) cc_final: 0.8083 (tp) REVERT: G 420 MET cc_start: 0.6415 (ptp) cc_final: 0.6112 (ptp) REVERT: H 541 ASP cc_start: 0.7514 (t0) cc_final: 0.7209 (t0) REVERT: J 540 MET cc_start: 0.6842 (mmt) cc_final: 0.6472 (mmt) REVERT: K 540 MET cc_start: 0.7004 (mmt) cc_final: 0.6702 (mmt) REVERT: L 257 LEU cc_start: 0.8492 (mt) cc_final: 0.8273 (mt) REVERT: M 540 MET cc_start: 0.6893 (mmt) cc_final: 0.6493 (mmt) REVERT: Q 85 TYR cc_start: 0.6300 (t80) cc_final: 0.6056 (t80) REVERT: R 7 ASN cc_start: 0.5912 (OUTLIER) cc_final: 0.5631 (p0) REVERT: R 44 MET cc_start: 0.6969 (mtp) cc_final: 0.6646 (mtt) REVERT: U 6 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6493 (mm-30) REVERT: V 6 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: W 19 ILE cc_start: 0.8308 (mt) cc_final: 0.8014 (mt) REVERT: X 6 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: Y 6 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6504 (mm-30) REVERT: Y 85 TYR cc_start: 0.6472 (t80) cc_final: 0.6155 (t80) REVERT: Z 19 ILE cc_start: 0.8600 (mt) cc_final: 0.8245 (mt) REVERT: a 6 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6428 (mm-30) REVERT: b 6 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6748 (mm-30) REVERT: d 6 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6838 (mm-30) outliers start: 105 outliers final: 34 residues processed: 1471 average time/residue: 0.6337 time to fit residues: 1553.7175 Evaluate side-chains 976 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 934 time to evaluate : 4.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 442 THR Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain Q residue 7 ASN Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 6 GLU Chi-restraints excluded: chain T residue 7 ASN Chi-restraints excluded: chain T residue 34 LEU Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain V residue 6 GLU Chi-restraints excluded: chain W residue 7 ASN Chi-restraints excluded: chain X residue 6 GLU Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain Y residue 6 GLU Chi-restraints excluded: chain Z residue 7 ASN Chi-restraints excluded: chain a residue 6 GLU Chi-restraints excluded: chain a residue 7 ASN Chi-restraints excluded: chain b residue 6 GLU Chi-restraints excluded: chain b residue 7 ASN Chi-restraints excluded: chain d residue 6 GLU Chi-restraints excluded: chain d residue 7 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 721 optimal weight: 0.8980 chunk 648 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 437 optimal weight: 0.9990 chunk 346 optimal weight: 30.0000 chunk 670 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 407 optimal weight: 0.3980 chunk 498 optimal weight: 0.9990 chunk 776 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 303 GLN A 343 GLN A 445 ASN A 575 ASN A 596 GLN A 630 GLN B 243 ASN B 303 GLN B 343 GLN B 402 GLN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN B 596 GLN B 630 GLN C 243 ASN C 303 GLN C 343 GLN C 445 ASN C 575 ASN C 596 GLN C 630 GLN D 243 ASN D 303 GLN D 343 GLN D 445 ASN D 575 ASN D 630 GLN D 641 ASN E 243 ASN E 343 GLN ** E 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 ASN E 596 GLN E 630 GLN F 243 ASN F 343 GLN F 371 GLN F 445 ASN F 575 ASN F 630 GLN G 243 ASN G 343 GLN G 445 ASN ** G 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 ASN G 596 GLN G 630 GLN G 641 ASN H 243 ASN H 303 GLN H 343 GLN ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 445 ASN H 575 ASN H 596 GLN H 630 GLN I 205 GLN I 243 ASN I 303 GLN I 343 GLN ** I 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 575 ASN I 630 GLN J 205 GLN J 243 ASN J 343 GLN ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 402 GLN J 445 ASN J 575 ASN J 596 GLN J 630 GLN K 243 ASN K 343 GLN K 445 ASN K 562 ASN K 575 ASN K 596 GLN K 630 GLN L 205 GLN L 243 ASN L 303 GLN L 343 GLN ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 445 ASN ** L 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 575 ASN L 596 GLN L 630 GLN L 641 ASN M 205 GLN M 243 ASN M 343 GLN M 402 GLN ** M 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 575 ASN M 630 GLN N 205 GLN N 243 ASN N 303 GLN N 343 GLN ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 575 ASN N 596 GLN N 630 GLN O 243 ASN O 293 HIS O 303 GLN O 343 GLN O 445 ASN O 497 GLN O 575 ASN O 596 GLN O 630 GLN O 641 ASN P 21 GLN ** P 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 ASN Q 21 GLN Q 22 ASN Q 96 ASN R 21 GLN ** R 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN R 96 ASN S 21 GLN S 36 GLN S 96 ASN T 17 GLN T 21 GLN T 96 ASN U 21 GLN U 36 GLN U 96 ASN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 GLN V 36 GLN V 96 ASN W 21 GLN W 36 GLN W 96 ASN X 17 GLN X 21 GLN X 36 GLN X 96 ASN ** Y 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 21 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 96 ASN Z 21 GLN Z 36 GLN Z 96 ASN a 21 GLN a 22 ASN a 36 GLN a 96 ASN b 21 GLN b 22 ASN b 36 GLN b 96 ASN ** c 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 GLN c 36 GLN c 96 ASN d 21 GLN d 36 GLN d 96 ASN Total number of N/Q/H flips: 152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 66675 Z= 0.242 Angle : 0.833 12.283 90210 Z= 0.429 Chirality : 0.049 0.179 10965 Planarity : 0.005 0.047 11745 Dihedral : 7.409 95.825 9225 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 1.02 % Allowed : 4.51 % Favored : 94.47 % Rotamer: Outliers : 2.17 % Allowed : 7.25 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.07), residues: 8445 helix: -3.45 (0.06), residues: 2415 sheet: -1.74 (0.07), residues: 3435 loop : -2.53 (0.10), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 344 HIS 0.003 0.001 HIS K 324 PHE 0.013 0.001 PHE c 61 TYR 0.025 0.002 TYR Q 65 ARG 0.005 0.001 ARG C 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1104 time to evaluate : 5.510 Fit side-chains revert: symmetry clash REVERT: A 420 MET cc_start: 0.6568 (ptp) cc_final: 0.6316 (ptp) REVERT: B 232 ARG cc_start: 0.6907 (mmt-90) cc_final: 0.6285 (ttm-80) REVERT: B 596 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.6969 (mm110) REVERT: C 206 ILE cc_start: 0.8274 (mt) cc_final: 0.8068 (mt) REVERT: C 238 MET cc_start: 0.6460 (ptt) cc_final: 0.6173 (ptt) REVERT: C 454 GLN cc_start: 0.7904 (pt0) cc_final: 0.7646 (pt0) REVERT: D 562 ASN cc_start: 0.8047 (m-40) cc_final: 0.7789 (m110) REVERT: E 475 VAL cc_start: 0.7801 (t) cc_final: 0.7464 (t) REVERT: E 514 ASP cc_start: 0.7530 (m-30) cc_final: 0.7136 (m-30) REVERT: F 232 ARG cc_start: 0.6880 (tpp-160) cc_final: 0.6667 (tpp-160) REVERT: G 227 MET cc_start: 0.7274 (mtm) cc_final: 0.7065 (ttm) REVERT: G 420 MET cc_start: 0.6342 (ptp) cc_final: 0.6021 (ptp) REVERT: G 541 ASP cc_start: 0.7077 (t0) cc_final: 0.6828 (t0) REVERT: M 609 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7565 (mmt-90) REVERT: N 293 HIS cc_start: 0.6598 (p-80) cc_final: 0.6380 (p90) REVERT: N 454 GLN cc_start: 0.7936 (pt0) cc_final: 0.7581 (pt0) REVERT: O 103 MET cc_start: 0.3565 (tpp) cc_final: 0.3199 (tpt) REVERT: a 96 ASN cc_start: 0.4265 (OUTLIER) cc_final: 0.3997 (p0) outliers start: 160 outliers final: 77 residues processed: 1212 average time/residue: 0.6130 time to fit residues: 1263.9808 Evaluate side-chains 935 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 855 time to evaluate : 5.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 596 GLN Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 596 GLN Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 546 GLU Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 420 MET Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 557 ILE Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 447 GLU Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain M residue 252 SER Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 609 ARG Chi-restraints excluded: chain M residue 624 VAL Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 287 SER Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 442 THR Chi-restraints excluded: chain N residue 447 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain O residue 252 SER Chi-restraints excluded: chain O residue 287 SER Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain a residue 96 ASN Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain d residue 20 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 431 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 646 optimal weight: 9.9990 chunk 528 optimal weight: 3.9990 chunk 214 optimal weight: 0.6980 chunk 777 optimal weight: 0.0870 chunk 840 optimal weight: 3.9990 chunk 692 optimal weight: 10.0000 chunk 771 optimal weight: 1.9990 chunk 265 optimal weight: 0.5980 chunk 624 optimal weight: 0.9980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN D 205 GLN ** D 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 596 GLN F 303 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN F 502 GLN G 293 HIS G 303 GLN ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 502 GLN ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 205 GLN I 293 HIS ** I 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 ASN J 293 HIS J 303 GLN ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 HIS K 303 GLN ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 GLN L 293 HIS ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 371 GLN M 205 GLN M 303 GLN ** M 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 371 GLN M 402 GLN ** M 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 445 ASN O 293 HIS ** O 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 641 ASN Q 96 ASN R 22 ASN ** U 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 96 ASN ** Y 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 96 ASN ** c 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 66675 Z= 0.224 Angle : 0.748 15.755 90210 Z= 0.381 Chirality : 0.046 0.194 10965 Planarity : 0.005 0.051 11745 Dihedral : 6.029 49.822 9166 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.89 % Allowed : 5.22 % Favored : 93.89 % Rotamer: Outliers : 2.85 % Allowed : 9.27 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.08), residues: 8445 helix: -2.06 (0.08), residues: 2505 sheet: -1.25 (0.08), residues: 3405 loop : -2.15 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 419 HIS 0.002 0.001 HIS K 293 PHE 0.010 0.001 PHE M 517 TYR 0.023 0.002 TYR U 85 ARG 0.005 0.000 ARG G 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1157 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 947 time to evaluate : 5.635 Fit side-chains revert: symmetry clash REVERT: A 360 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7526 (pt) REVERT: C 508 GLU cc_start: 0.6473 (pt0) cc_final: 0.6235 (pt0) REVERT: D 562 ASN cc_start: 0.7965 (m-40) cc_final: 0.7757 (m110) REVERT: E 232 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.7158 (mmp80) REVERT: E 437 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8401 (p) REVERT: E 514 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: F 232 ARG cc_start: 0.6963 (tpp-160) cc_final: 0.6745 (tpp-160) REVERT: G 420 MET cc_start: 0.6359 (ptp) cc_final: 0.6045 (ptp) REVERT: H 577 MET cc_start: 0.7509 (mmt) cc_final: 0.7183 (mmt) REVERT: I 261 LEU cc_start: 0.8199 (mt) cc_final: 0.7975 (mt) REVERT: I 360 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7961 (pt) REVERT: K 225 ASP cc_start: 0.7475 (t0) cc_final: 0.7274 (t0) REVERT: K 577 MET cc_start: 0.7838 (mmm) cc_final: 0.7358 (mmt) REVERT: L 360 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7750 (pt) REVERT: L 437 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8548 (p) REVERT: L 454 GLN cc_start: 0.8141 (pt0) cc_final: 0.7920 (pt0) REVERT: M 103 MET cc_start: 0.4459 (tpt) cc_final: 0.4227 (tpt) REVERT: M 125 MET cc_start: 0.2979 (mmm) cc_final: 0.2143 (mmm) REVERT: N 455 ASP cc_start: 0.6952 (t0) cc_final: 0.6709 (t0) REVERT: O 103 MET cc_start: 0.3536 (tpp) cc_final: 0.3093 (tpt) REVERT: S 23 LEU cc_start: 0.7389 (tt) cc_final: 0.7169 (tt) REVERT: X 78 MET cc_start: 0.3771 (tmm) cc_final: 0.3476 (mmt) outliers start: 210 outliers final: 127 residues processed: 1094 average time/residue: 0.6489 time to fit residues: 1240.2258 Evaluate side-chains 950 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 817 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 300 THR Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 624 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 310 GLN Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 551 VAL Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 351 LEU Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 573 LYS Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 535 VAL Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 206 ILE Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 234 LEU Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 360 ILE Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 447 GLU Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain L residue 551 VAL Chi-restraints excluded: chain L residue 595 SER Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 232 ARG Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 287 SER Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 442 THR Chi-restraints excluded: chain N residue 447 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 514 ASP Chi-restraints excluded: chain N residue 535 VAL Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain O residue 287 SER Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain T residue 18 ASN Chi-restraints excluded: chain X residue 20 SER Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain b residue 18 ASN Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain d residue 20 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 768 optimal weight: 3.9990 chunk 584 optimal weight: 1.9990 chunk 403 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 371 optimal weight: 0.7980 chunk 522 optimal weight: 0.9990 chunk 780 optimal weight: 3.9990 chunk 826 optimal weight: 6.9990 chunk 407 optimal weight: 0.9980 chunk 739 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 ASN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 445 ASN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 GLN ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 GLN H 630 GLN I 205 GLN I 293 HIS ** I 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 596 GLN L 205 GLN ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 402 GLN M 445 ASN ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 293 HIS O 359 GLN O 371 GLN ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 596 GLN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 96 ASN ** Y 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 66675 Z= 0.234 Angle : 0.720 16.462 90210 Z= 0.362 Chirality : 0.046 0.180 10965 Planarity : 0.005 0.053 11745 Dihedral : 5.764 54.684 9166 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.89 % Allowed : 5.75 % Favored : 93.36 % Rotamer: Outliers : 2.67 % Allowed : 11.44 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.23 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.25 (0.08), residues: 8445 helix: -1.21 (0.09), residues: 2640 sheet: -1.07 (0.08), residues: 3405 loop : -2.05 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 419 HIS 0.003 0.001 HIS I 293 PHE 0.010 0.001 PHE M 517 TYR 0.023 0.002 TYR P 85 ARG 0.009 0.000 ARG L 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 903 time to evaluate : 5.522 Fit side-chains REVERT: A 233 ARG cc_start: 0.7739 (tpp80) cc_final: 0.7505 (tpp80) REVERT: A 535 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8574 (p) REVERT: D 494 ASN cc_start: 0.5639 (m-40) cc_final: 0.5369 (m-40) REVERT: D 535 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8306 (p) REVERT: D 562 ASN cc_start: 0.8013 (m-40) cc_final: 0.7790 (m-40) REVERT: E 232 ARG cc_start: 0.7546 (mmt-90) cc_final: 0.7221 (mmp80) REVERT: E 514 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: E 541 ASP cc_start: 0.6982 (t0) cc_final: 0.6626 (t0) REVERT: F 232 ARG cc_start: 0.6978 (tpp-160) cc_final: 0.6743 (tpp-160) REVERT: G 229 ARG cc_start: 0.7342 (ttp80) cc_final: 0.7103 (tmm-80) REVERT: G 420 MET cc_start: 0.6308 (ptp) cc_final: 0.6075 (ptp) REVERT: H 125 MET cc_start: 0.3704 (mmm) cc_final: 0.3448 (mmm) REVERT: H 485 LYS cc_start: 0.8141 (ttpt) cc_final: 0.7873 (ttmm) REVERT: J 589 MET cc_start: 0.6488 (ttp) cc_final: 0.6186 (ttm) REVERT: K 577 MET cc_start: 0.7638 (mmm) cc_final: 0.7065 (mmt) REVERT: L 360 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7747 (pt) REVERT: L 437 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8530 (p) REVERT: N 589 MET cc_start: 0.6603 (ttm) cc_final: 0.6165 (ttm) REVERT: O 103 MET cc_start: 0.3448 (tpp) cc_final: 0.2984 (tpt) REVERT: S 23 LEU cc_start: 0.7491 (tt) cc_final: 0.7218 (tt) REVERT: S 36 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7270 (mm-40) REVERT: Z 36 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7302 (mm-40) outliers start: 197 outliers final: 145 residues processed: 1038 average time/residue: 0.6057 time to fit residues: 1088.8125 Evaluate side-chains 967 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 815 time to evaluate : 5.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 615 SER Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 607 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain H residue 287 SER Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 551 VAL Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 573 LYS Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 624 VAL Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 535 VAL Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 360 ILE Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 447 GLU Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain L residue 595 SER Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 420 MET Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 595 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 287 SER Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 447 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 514 ASP Chi-restraints excluded: chain N residue 515 VAL Chi-restraints excluded: chain N residue 533 LEU Chi-restraints excluded: chain N residue 535 VAL Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain S residue 36 GLN Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain d residue 20 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 688 optimal weight: 0.3980 chunk 469 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 615 optimal weight: 4.9990 chunk 340 optimal weight: 2.9990 chunk 705 optimal weight: 1.9990 chunk 571 optimal weight: 0.0970 chunk 0 optimal weight: 30.0000 chunk 422 optimal weight: 1.9990 chunk 741 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN B 596 GLN B 630 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 GLN E 630 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 630 GLN I 177 ASN ** I 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 497 GLN J 177 ASN ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 GLN ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 596 GLN L 205 GLN ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 630 GLN O 293 HIS O 371 GLN ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 ASN T 96 ASN U 21 GLN U 96 ASN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 GLN X 96 ASN Y 7 ASN Y 96 ASN a 21 GLN ** c 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 66675 Z= 0.277 Angle : 0.721 16.805 90210 Z= 0.360 Chirality : 0.047 0.208 10965 Planarity : 0.005 0.055 11745 Dihedral : 5.760 59.475 9165 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.11 % Favored : 93.00 % Rotamer: Outliers : 3.18 % Allowed : 11.99 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.09), residues: 8445 helix: -0.64 (0.09), residues: 2655 sheet: -1.09 (0.08), residues: 3390 loop : -1.99 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 419 HIS 0.003 0.001 HIS H 293 PHE 0.012 0.001 PHE M 517 TYR 0.023 0.002 TYR P 85 ARG 0.007 0.000 ARG L 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 868 time to evaluate : 5.585 Fit side-chains REVERT: A 498 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7833 (mmt) REVERT: A 535 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8621 (p) REVERT: A 577 MET cc_start: 0.7058 (mmp) cc_final: 0.6784 (mmt) REVERT: B 226 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7582 (ptpt) REVERT: B 498 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7194 (mmt) REVERT: C 498 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7400 (mmt) REVERT: D 125 MET cc_start: 0.3355 (mmm) cc_final: 0.2968 (mmm) REVERT: D 498 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7523 (mmt) REVERT: D 512 SER cc_start: 0.7576 (t) cc_final: 0.7196 (m) REVERT: D 562 ASN cc_start: 0.8026 (m-40) cc_final: 0.7811 (m-40) REVERT: E 226 LYS cc_start: 0.7710 (mtmt) cc_final: 0.7441 (mtpt) REVERT: E 232 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.7166 (mmp80) REVERT: E 437 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8445 (p) REVERT: E 514 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: E 541 ASP cc_start: 0.6923 (t0) cc_final: 0.6645 (t0) REVERT: F 498 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7432 (mmt) REVERT: G 420 MET cc_start: 0.6335 (ptp) cc_final: 0.6132 (ptp) REVERT: J 498 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7343 (mmt) REVERT: J 589 MET cc_start: 0.6485 (ttp) cc_final: 0.6181 (ttm) REVERT: K 225 ASP cc_start: 0.7560 (t0) cc_final: 0.7315 (t0) REVERT: K 577 MET cc_start: 0.7680 (mmm) cc_final: 0.7226 (mmt) REVERT: L 360 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7730 (pt) REVERT: L 437 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8596 (p) REVERT: N 103 MET cc_start: 0.4713 (tmm) cc_final: 0.4363 (tmm) REVERT: S 36 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7059 (mm-40) REVERT: T 89 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.5010 (mt) REVERT: T 96 ASN cc_start: 0.4330 (OUTLIER) cc_final: 0.4094 (p0) REVERT: W 36 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.6911 (mm-40) REVERT: Z 36 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7394 (mm-40) REVERT: b 36 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.7393 (mm-40) REVERT: b 69 MET cc_start: 0.5245 (mmp) cc_final: 0.4965 (mmp) outliers start: 235 outliers final: 162 residues processed: 1025 average time/residue: 0.5912 time to fit residues: 1050.2347 Evaluate side-chains 975 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 796 time to evaluate : 5.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 447 GLU Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 352 MET Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 519 GLU Chi-restraints excluded: chain G residue 573 LYS Chi-restraints excluded: chain G residue 607 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 551 VAL Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 573 LYS Chi-restraints excluded: chain J residue 176 ASP Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 498 MET Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 624 VAL Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain K residue 535 VAL Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain K residue 557 ILE Chi-restraints excluded: chain K residue 596 GLN Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 360 ILE Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain L residue 515 VAL Chi-restraints excluded: chain L residue 551 VAL Chi-restraints excluded: chain L residue 595 SER Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 420 MET Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 595 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 287 SER Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 442 THR Chi-restraints excluded: chain N residue 447 GLU Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 514 ASP Chi-restraints excluded: chain N residue 515 VAL Chi-restraints excluded: chain N residue 533 LEU Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain O residue 252 SER Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 36 GLN Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 96 ASN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain W residue 36 GLN Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain b residue 36 GLN Chi-restraints excluded: chain c residue 20 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 278 optimal weight: 0.9990 chunk 744 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 485 optimal weight: 1.9990 chunk 204 optimal weight: 6.9990 chunk 827 optimal weight: 8.9990 chunk 686 optimal weight: 10.0000 chunk 383 optimal weight: 0.0370 chunk 68 optimal weight: 3.9990 chunk 273 optimal weight: 0.3980 chunk 434 optimal weight: 2.9990 overall best weight: 1.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** C 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN ** F 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 630 GLN ** I 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 HIS ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 GLN ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 596 GLN ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 641 ASN ** M 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 445 ASN N 630 GLN O 293 HIS O 371 GLN ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 96 ASN U 21 GLN U 36 GLN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 GLN X 96 ASN Y 21 GLN a 21 GLN a 36 GLN c 7 ASN d 21 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 66675 Z= 0.246 Angle : 0.699 15.966 90210 Z= 0.347 Chirality : 0.046 0.217 10965 Planarity : 0.005 0.054 11745 Dihedral : 5.610 58.387 9165 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.07 % Favored : 93.04 % Rotamer: Outliers : 3.20 % Allowed : 12.59 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.24 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.09), residues: 8445 helix: -0.29 (0.10), residues: 2655 sheet: -1.08 (0.08), residues: 3390 loop : -1.93 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 419 HIS 0.003 0.001 HIS H 293 PHE 0.010 0.001 PHE M 517 TYR 0.021 0.002 TYR P 65 ARG 0.008 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 845 time to evaluate : 5.770 Fit side-chains revert: symmetry clash REVERT: A 498 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7809 (mmt) REVERT: A 535 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8620 (p) REVERT: A 577 MET cc_start: 0.6951 (mmp) cc_final: 0.6747 (mmt) REVERT: B 226 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7508 (ptpt) REVERT: B 498 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7242 (mmt) REVERT: C 498 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7415 (mmt) REVERT: D 226 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7267 (mtmt) REVERT: D 498 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7502 (mmt) REVERT: D 512 SER cc_start: 0.7461 (t) cc_final: 0.7164 (m) REVERT: D 562 ASN cc_start: 0.8038 (m-40) cc_final: 0.7816 (m-40) REVERT: E 232 ARG cc_start: 0.7532 (mmt-90) cc_final: 0.7181 (mmp80) REVERT: E 437 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8401 (p) REVERT: E 514 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: F 498 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7393 (mmt) REVERT: H 485 LYS cc_start: 0.8156 (ttpt) cc_final: 0.7905 (ttmm) REVERT: H 577 MET cc_start: 0.7557 (mmt) cc_final: 0.7165 (mmt) REVERT: J 498 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7347 (mmt) REVERT: J 589 MET cc_start: 0.6478 (ttp) cc_final: 0.6193 (ttm) REVERT: K 498 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7048 (mmt) REVERT: K 577 MET cc_start: 0.7674 (mmm) cc_final: 0.7262 (mmt) REVERT: K 596 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.7025 (mm110) REVERT: L 360 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7724 (pt) REVERT: L 437 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8591 (p) REVERT: M 494 ASN cc_start: 0.5980 (m-40) cc_final: 0.5769 (m-40) REVERT: N 103 MET cc_start: 0.4552 (tmm) cc_final: 0.4198 (tmm) REVERT: N 455 ASP cc_start: 0.6959 (t0) cc_final: 0.6758 (t0) REVERT: N 494 ASN cc_start: 0.6012 (m-40) cc_final: 0.5786 (m-40) REVERT: O 498 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7557 (mmt) REVERT: S 36 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7067 (mm-40) REVERT: W 36 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7007 (mm-40) REVERT: Z 36 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7507 (mm-40) REVERT: b 36 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: b 69 MET cc_start: 0.5197 (mmp) cc_final: 0.4908 (mmp) REVERT: d 36 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7202 (mm-40) outliers start: 236 outliers final: 162 residues processed: 1009 average time/residue: 0.5888 time to fit residues: 1034.5036 Evaluate side-chains 978 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 797 time to evaluate : 5.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 514 ASP Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 352 MET Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain G residue 447 GLU Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 514 ASP Chi-restraints excluded: chain G residue 519 GLU Chi-restraints excluded: chain G residue 607 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 513 LEU Chi-restraints excluded: chain H residue 551 VAL Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 573 LYS Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 498 MET Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 624 VAL Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 498 MET Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain K residue 535 VAL Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain K residue 557 ILE Chi-restraints excluded: chain K residue 596 GLN Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 360 ILE Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 442 THR Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain L residue 551 VAL Chi-restraints excluded: chain L residue 595 SER Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 420 MET Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 595 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 287 SER Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 514 ASP Chi-restraints excluded: chain N residue 533 LEU Chi-restraints excluded: chain N residue 535 VAL Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain O residue 498 MET Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain S residue 36 GLN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain W residue 36 GLN Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 36 GLN Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain a residue 36 GLN Chi-restraints excluded: chain b residue 36 GLN Chi-restraints excluded: chain d residue 36 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 797 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 471 optimal weight: 1.9990 chunk 604 optimal weight: 7.9990 chunk 468 optimal weight: 0.2980 chunk 696 optimal weight: 0.7980 chunk 461 optimal weight: 3.9990 chunk 824 optimal weight: 6.9990 chunk 515 optimal weight: 0.3980 chunk 502 optimal weight: 10.0000 chunk 380 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 359 GLN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 596 GLN E 630 GLN ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 GLN ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 ASN ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 ASN K 596 GLN ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 497 GLN M 307 GLN N 245 GLN ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 445 ASN N 630 GLN O 293 HIS ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN U 21 GLN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 22 ASN X 21 GLN X 96 ASN Y 21 GLN a 21 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 66675 Z= 0.199 Angle : 0.672 15.378 90210 Z= 0.334 Chirality : 0.045 0.207 10965 Planarity : 0.005 0.052 11745 Dihedral : 5.396 57.688 9165 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.71 % Allowed : 6.02 % Favored : 93.27 % Rotamer: Outliers : 2.68 % Allowed : 13.92 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.09), residues: 8445 helix: 0.05 (0.10), residues: 2655 sheet: -1.00 (0.08), residues: 3390 loop : -1.86 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 419 HIS 0.002 0.001 HIS H 293 PHE 0.009 0.001 PHE X 61 TYR 0.020 0.001 TYR P 65 ARG 0.009 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 859 time to evaluate : 5.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7742 (mmt) REVERT: A 535 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8605 (p) REVERT: C 498 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7320 (mmt) REVERT: C 577 MET cc_start: 0.7448 (mmm) cc_final: 0.6994 (mmt) REVERT: D 125 MET cc_start: 0.3511 (mmm) cc_final: 0.3047 (mmm) REVERT: D 226 LYS cc_start: 0.7562 (mtpt) cc_final: 0.7357 (mtmt) REVERT: D 498 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7560 (mmt) REVERT: D 562 ASN cc_start: 0.8021 (m-40) cc_final: 0.7802 (m-40) REVERT: E 188 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6839 (mp0) REVERT: E 232 ARG cc_start: 0.7498 (mmt-90) cc_final: 0.7117 (mmp80) REVERT: E 437 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8371 (p) REVERT: F 498 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: G 188 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6552 (mp0) REVERT: H 144 MET cc_start: 0.4216 (mmp) cc_final: 0.3968 (mmp) REVERT: H 485 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7896 (ttmm) REVERT: H 540 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6625 (mmt) REVERT: J 144 MET cc_start: 0.3897 (mmp) cc_final: 0.3636 (mmp) REVERT: J 498 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7252 (mmt) REVERT: J 589 MET cc_start: 0.6426 (ttp) cc_final: 0.6143 (ttm) REVERT: K 233 ARG cc_start: 0.7830 (tpp80) cc_final: 0.7527 (tpp80) REVERT: K 577 MET cc_start: 0.7509 (mmm) cc_final: 0.7125 (mmt) REVERT: L 360 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7840 (pt) REVERT: L 437 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8560 (p) REVERT: M 188 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6384 (mp0) REVERT: N 103 MET cc_start: 0.4356 (tmm) cc_final: 0.4078 (tmm) REVERT: N 455 ASP cc_start: 0.6982 (t0) cc_final: 0.6771 (t0) REVERT: O 498 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7599 (mmt) REVERT: S 36 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6860 (mm-40) REVERT: b 69 MET cc_start: 0.5002 (mmp) cc_final: 0.4752 (mmp) REVERT: d 36 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7130 (mm-40) outliers start: 198 outliers final: 159 residues processed: 992 average time/residue: 0.5914 time to fit residues: 1015.8219 Evaluate side-chains 973 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 801 time to evaluate : 5.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 352 MET Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 519 GLU Chi-restraints excluded: chain G residue 607 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 513 LEU Chi-restraints excluded: chain H residue 540 MET Chi-restraints excluded: chain H residue 551 VAL Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 573 LYS Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 498 MET Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 624 VAL Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 513 LEU Chi-restraints excluded: chain K residue 535 VAL Chi-restraints excluded: chain K residue 557 ILE Chi-restraints excluded: chain K residue 596 GLN Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 360 ILE Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain L residue 515 VAL Chi-restraints excluded: chain L residue 551 VAL Chi-restraints excluded: chain L residue 595 SER Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 259 ASP Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 420 MET Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 287 SER Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 442 THR Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 533 LEU Chi-restraints excluded: chain N residue 535 VAL Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain O residue 498 MET Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 589 MET Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain S residue 36 GLN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain X residue 96 ASN Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain d residue 36 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 509 optimal weight: 2.9990 chunk 329 optimal weight: 0.7980 chunk 492 optimal weight: 8.9990 chunk 248 optimal weight: 30.0000 chunk 161 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 523 optimal weight: 2.9990 chunk 561 optimal weight: 0.9980 chunk 407 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 647 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 445 ASN ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 GLN ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 HIS ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 596 GLN ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 177 ASN ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 445 ASN N 630 GLN O 177 ASN O 371 GLN ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 596 GLN O 630 GLN U 21 GLN U 96 ASN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 GLN V 96 ASN X 21 GLN X 96 ASN Y 21 GLN Y 96 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 66675 Z= 0.294 Angle : 0.718 15.529 90210 Z= 0.354 Chirality : 0.046 0.190 10965 Planarity : 0.005 0.054 11745 Dihedral : 5.609 58.354 9165 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.07 % Favored : 92.22 % Rotamer: Outliers : 2.87 % Allowed : 14.15 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.09), residues: 8445 helix: 0.10 (0.10), residues: 2655 sheet: -1.14 (0.08), residues: 3390 loop : -1.86 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 419 HIS 0.003 0.001 HIS L 164 PHE 0.011 0.001 PHE M 517 TYR 0.016 0.002 TYR P 65 ARG 0.009 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 815 time to evaluate : 5.560 Fit side-chains revert: symmetry clash REVERT: A 498 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7890 (mmt) REVERT: A 535 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8658 (p) REVERT: B 498 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7272 (mmt) REVERT: C 498 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7442 (mmt) REVERT: C 552 PRO cc_start: 0.6936 (OUTLIER) cc_final: 0.6679 (Cg_endo) REVERT: D 498 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7531 (mmt) REVERT: D 562 ASN cc_start: 0.8047 (m-40) cc_final: 0.7831 (m-40) REVERT: E 188 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6868 (mp0) REVERT: E 437 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8412 (p) REVERT: E 494 ASN cc_start: 0.6133 (m-40) cc_final: 0.5929 (m-40) REVERT: F 498 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7414 (mmt) REVERT: G 188 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6553 (mp0) REVERT: I 188 GLU cc_start: 0.7168 (mp0) cc_final: 0.6965 (mp0) REVERT: J 144 MET cc_start: 0.3994 (mmp) cc_final: 0.3736 (mmp) REVERT: J 494 ASN cc_start: 0.5665 (m-40) cc_final: 0.5464 (m-40) REVERT: J 498 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7354 (mmt) REVERT: J 589 MET cc_start: 0.6491 (ttp) cc_final: 0.6213 (ttm) REVERT: K 233 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7454 (tpp80) REVERT: K 498 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7128 (mmt) REVERT: K 577 MET cc_start: 0.7635 (mmm) cc_final: 0.7262 (mmt) REVERT: L 437 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8608 (p) REVERT: M 103 MET cc_start: 0.3595 (tpt) cc_final: 0.3276 (tpt) REVERT: M 188 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6405 (mp0) REVERT: N 455 ASP cc_start: 0.7022 (t0) cc_final: 0.6804 (t0) REVERT: O 498 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7629 (mmt) REVERT: S 36 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7106 (mm-40) REVERT: W 18 ASN cc_start: 0.8385 (t0) cc_final: 0.8121 (t0) REVERT: b 69 MET cc_start: 0.5067 (mmp) cc_final: 0.4811 (mmp) REVERT: d 36 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7207 (mm-40) outliers start: 212 outliers final: 172 residues processed: 956 average time/residue: 0.5986 time to fit residues: 991.3490 Evaluate side-chains 971 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 785 time to evaluate : 5.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 552 PRO Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 560 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 352 MET Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 519 GLU Chi-restraints excluded: chain G residue 607 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 487 THR Chi-restraints excluded: chain H residue 513 LEU Chi-restraints excluded: chain H residue 551 VAL Chi-restraints excluded: chain H residue 554 LEU Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 573 LYS Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 498 MET Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 624 VAL Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 498 MET Chi-restraints excluded: chain K residue 508 GLU Chi-restraints excluded: chain K residue 535 VAL Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain K residue 557 ILE Chi-restraints excluded: chain K residue 596 GLN Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 442 THR Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain L residue 515 VAL Chi-restraints excluded: chain L residue 551 VAL Chi-restraints excluded: chain L residue 595 SER Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 287 SER Chi-restraints excluded: chain M residue 420 MET Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 595 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 287 SER Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 442 THR Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 533 LEU Chi-restraints excluded: chain N residue 535 VAL Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain O residue 498 MET Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 589 MET Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain O residue 596 GLN Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain S residue 36 GLN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain d residue 36 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 749 optimal weight: 7.9990 chunk 789 optimal weight: 10.0000 chunk 720 optimal weight: 0.0470 chunk 767 optimal weight: 4.9990 chunk 462 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 603 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 693 optimal weight: 6.9990 chunk 726 optimal weight: 3.9990 chunk 765 optimal weight: 3.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 630 GLN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 293 HIS ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 502 GLN ** I 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 HIS ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 GLN ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 596 GLN ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 402 GLN ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 630 GLN ** O 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 630 GLN P 96 ASN U 21 GLN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 GLN W 21 GLN X 21 GLN Y 21 GLN Z 21 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 66675 Z= 0.356 Angle : 0.750 16.588 90210 Z= 0.370 Chirality : 0.047 0.226 10965 Planarity : 0.005 0.057 11745 Dihedral : 5.819 59.934 9165 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.42 % Favored : 91.87 % Rotamer: Outliers : 2.78 % Allowed : 14.72 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.09), residues: 8445 helix: 0.06 (0.10), residues: 2655 sheet: -1.27 (0.08), residues: 3345 loop : -1.98 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 419 HIS 0.003 0.001 HIS L 164 PHE 0.011 0.001 PHE M 517 TYR 0.015 0.002 TYR V 65 ARG 0.009 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 798 time to evaluate : 5.543 Fit side-chains revert: symmetry clash REVERT: A 498 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7927 (mmt) REVERT: A 535 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 554 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8298 (mp) REVERT: B 498 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7300 (mmt) REVERT: C 498 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7484 (mmt) REVERT: C 552 PRO cc_start: 0.7032 (OUTLIER) cc_final: 0.6809 (Cg_endo) REVERT: D 498 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7541 (mmt) REVERT: D 562 ASN cc_start: 0.8065 (m-40) cc_final: 0.7852 (m-40) REVERT: E 188 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6891 (mp0) REVERT: E 238 MET cc_start: 0.4585 (ptt) cc_final: 0.4250 (ptt) REVERT: E 437 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8445 (p) REVERT: E 494 ASN cc_start: 0.6014 (m-40) cc_final: 0.5772 (m-40) REVERT: F 498 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7480 (mmt) REVERT: G 188 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6549 (mp0) REVERT: H 577 MET cc_start: 0.7456 (mmt) cc_final: 0.7118 (mmt) REVERT: J 144 MET cc_start: 0.4079 (mmp) cc_final: 0.3820 (mmp) REVERT: J 498 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7394 (mmt) REVERT: K 498 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7133 (mmt) REVERT: K 577 MET cc_start: 0.7649 (mmm) cc_final: 0.7294 (mmt) REVERT: L 437 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8677 (p) REVERT: M 103 MET cc_start: 0.3818 (tpt) cc_final: 0.3414 (tpt) REVERT: N 103 MET cc_start: 0.4376 (tmm) cc_final: 0.4051 (tmm) REVERT: N 455 ASP cc_start: 0.7030 (t0) cc_final: 0.6822 (t0) REVERT: O 498 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7650 (mmt) REVERT: S 36 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7294 (mm-40) REVERT: W 18 ASN cc_start: 0.8345 (t0) cc_final: 0.8078 (t0) REVERT: b 69 MET cc_start: 0.5081 (mmp) cc_final: 0.4825 (mmp) REVERT: c 36 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7007 (mm-40) REVERT: d 36 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7296 (mm-40) outliers start: 205 outliers final: 168 residues processed: 932 average time/residue: 0.5873 time to fit residues: 948.3557 Evaluate side-chains 962 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 778 time to evaluate : 5.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 552 PRO Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 352 MET Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 447 GLU Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 352 MET Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain G residue 451 MET Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 519 GLU Chi-restraints excluded: chain G residue 607 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 487 THR Chi-restraints excluded: chain H residue 513 LEU Chi-restraints excluded: chain H residue 551 VAL Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 573 LYS Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 498 MET Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 624 VAL Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 352 MET Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 498 MET Chi-restraints excluded: chain K residue 508 GLU Chi-restraints excluded: chain K residue 535 VAL Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain K residue 557 ILE Chi-restraints excluded: chain K residue 570 LYS Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 442 THR Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain L residue 515 VAL Chi-restraints excluded: chain L residue 551 VAL Chi-restraints excluded: chain L residue 595 SER Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 420 MET Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 595 SER Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 287 SER Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 442 THR Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 533 LEU Chi-restraints excluded: chain N residue 535 VAL Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain O residue 498 MET Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 589 MET Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain S residue 36 GLN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain Z residue 19 ILE Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain d residue 36 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 504 optimal weight: 0.8980 chunk 812 optimal weight: 10.0000 chunk 495 optimal weight: 6.9990 chunk 385 optimal weight: 2.9990 chunk 564 optimal weight: 0.6980 chunk 851 optimal weight: 7.9990 chunk 783 optimal weight: 1.9990 chunk 678 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 523 optimal weight: 0.9980 chunk 415 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 630 GLN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 GLN ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 630 GLN ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 371 GLN ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 596 GLN O 630 GLN P 21 GLN P 96 ASN T 22 ASN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 GLN W 21 GLN X 21 GLN Y 21 GLN Z 21 GLN b 21 GLN c 21 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 66675 Z= 0.221 Angle : 0.692 16.733 90210 Z= 0.341 Chirality : 0.046 0.191 10965 Planarity : 0.005 0.052 11745 Dihedral : 5.516 58.913 9165 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.04 % Favored : 93.24 % Rotamer: Outliers : 2.51 % Allowed : 15.16 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.09), residues: 8445 helix: 0.24 (0.10), residues: 2670 sheet: -1.18 (0.08), residues: 3345 loop : -1.91 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 419 HIS 0.002 0.001 HIS D 293 PHE 0.009 0.001 PHE M 517 TYR 0.016 0.001 TYR P 65 ARG 0.009 0.000 ARG A 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16890 Ramachandran restraints generated. 8445 Oldfield, 0 Emsley, 8445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 821 time to evaluate : 5.672 Fit side-chains revert: symmetry clash REVERT: A 498 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7878 (mmt) REVERT: A 535 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8601 (p) REVERT: B 498 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7175 (mmt) REVERT: B 541 ASP cc_start: 0.7004 (t0) cc_final: 0.6790 (t70) REVERT: C 498 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7346 (mmt) REVERT: C 552 PRO cc_start: 0.6906 (OUTLIER) cc_final: 0.6645 (Cg_endo) REVERT: C 577 MET cc_start: 0.7450 (mmm) cc_final: 0.7027 (mmt) REVERT: D 144 MET cc_start: 0.2864 (mmm) cc_final: 0.2557 (mmp) REVERT: D 498 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7557 (mmt) REVERT: D 562 ASN cc_start: 0.8046 (m-40) cc_final: 0.7821 (m-40) REVERT: E 188 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6802 (mp0) REVERT: E 238 MET cc_start: 0.4408 (ptt) cc_final: 0.4133 (ptt) REVERT: E 437 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8440 (p) REVERT: E 577 MET cc_start: 0.7678 (mmt) cc_final: 0.7314 (mmt) REVERT: F 498 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7365 (mmt) REVERT: F 608 TYR cc_start: 0.8095 (t80) cc_final: 0.7893 (t80) REVERT: H 485 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7901 (ttmm) REVERT: I 188 GLU cc_start: 0.6992 (mp0) cc_final: 0.6708 (mp0) REVERT: I 494 ASN cc_start: 0.5868 (m-40) cc_final: 0.5665 (m-40) REVERT: I 577 MET cc_start: 0.7293 (mmt) cc_final: 0.6857 (mmt) REVERT: J 144 MET cc_start: 0.4025 (mmp) cc_final: 0.3767 (mmp) REVERT: J 498 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7506 (mmt) REVERT: J 589 MET cc_start: 0.6444 (ttp) cc_final: 0.6182 (ttm) REVERT: K 498 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7099 (mmt) REVERT: K 577 MET cc_start: 0.7423 (mmm) cc_final: 0.7063 (mmt) REVERT: L 437 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8592 (p) REVERT: M 103 MET cc_start: 0.3766 (tpt) cc_final: 0.3373 (tpt) REVERT: M 541 ASP cc_start: 0.7419 (t0) cc_final: 0.7093 (t70) REVERT: N 103 MET cc_start: 0.4547 (tmm) cc_final: 0.4218 (tmm) REVERT: N 455 ASP cc_start: 0.7006 (t0) cc_final: 0.6788 (t0) REVERT: O 498 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7612 (mmt) REVERT: P 96 ASN cc_start: 0.4629 (OUTLIER) cc_final: 0.4205 (p0) REVERT: S 36 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7279 (mm-40) REVERT: b 69 MET cc_start: 0.5060 (mmp) cc_final: 0.4788 (mmp) REVERT: c 36 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.6879 (mm-40) REVERT: d 36 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7173 (mm-40) outliers start: 185 outliers final: 159 residues processed: 943 average time/residue: 0.5844 time to fit residues: 953.5337 Evaluate side-chains 968 residues out of total 7425 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 793 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 498 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 447 GLU Chi-restraints excluded: chain B residue 498 MET Chi-restraints excluded: chain B residue 508 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 595 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 SER Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 498 MET Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 552 PRO Chi-restraints excluded: chain C residue 573 LYS Chi-restraints excluded: chain C residue 589 MET Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 498 MET Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 437 THR Chi-restraints excluded: chain E residue 442 THR Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 617 MET Chi-restraints excluded: chain F residue 176 ASP Chi-restraints excluded: chain F residue 206 ILE Chi-restraints excluded: chain F residue 352 MET Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 487 THR Chi-restraints excluded: chain F residue 498 MET Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 437 THR Chi-restraints excluded: chain G residue 442 THR Chi-restraints excluded: chain G residue 487 THR Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 519 GLU Chi-restraints excluded: chain G residue 607 ILE Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain H residue 176 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 ILE Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 442 THR Chi-restraints excluded: chain H residue 447 GLU Chi-restraints excluded: chain H residue 513 LEU Chi-restraints excluded: chain H residue 551 VAL Chi-restraints excluded: chain H residue 615 SER Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 257 LEU Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 437 THR Chi-restraints excluded: chain I residue 487 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 573 LYS Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 420 MET Chi-restraints excluded: chain J residue 437 THR Chi-restraints excluded: chain J residue 442 THR Chi-restraints excluded: chain J residue 447 GLU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 498 MET Chi-restraints excluded: chain J residue 515 VAL Chi-restraints excluded: chain J residue 535 VAL Chi-restraints excluded: chain J residue 554 LEU Chi-restraints excluded: chain J residue 624 VAL Chi-restraints excluded: chain K residue 176 ASP Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 252 SER Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 437 THR Chi-restraints excluded: chain K residue 442 THR Chi-restraints excluded: chain K residue 487 THR Chi-restraints excluded: chain K residue 498 MET Chi-restraints excluded: chain K residue 508 GLU Chi-restraints excluded: chain K residue 535 VAL Chi-restraints excluded: chain K residue 551 VAL Chi-restraints excluded: chain K residue 557 ILE Chi-restraints excluded: chain K residue 570 LYS Chi-restraints excluded: chain L residue 176 ASP Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 420 MET Chi-restraints excluded: chain L residue 437 THR Chi-restraints excluded: chain L residue 442 THR Chi-restraints excluded: chain L residue 487 THR Chi-restraints excluded: chain L residue 515 VAL Chi-restraints excluded: chain L residue 551 VAL Chi-restraints excluded: chain L residue 595 SER Chi-restraints excluded: chain M residue 176 ASP Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 215 VAL Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 420 MET Chi-restraints excluded: chain M residue 437 THR Chi-restraints excluded: chain M residue 442 THR Chi-restraints excluded: chain M residue 447 GLU Chi-restraints excluded: chain M residue 487 THR Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain M residue 533 LEU Chi-restraints excluded: chain M residue 535 VAL Chi-restraints excluded: chain M residue 551 VAL Chi-restraints excluded: chain M residue 595 SER Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 420 MET Chi-restraints excluded: chain N residue 437 THR Chi-restraints excluded: chain N residue 442 THR Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 533 LEU Chi-restraints excluded: chain N residue 535 VAL Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain O residue 420 MET Chi-restraints excluded: chain O residue 437 THR Chi-restraints excluded: chain O residue 442 THR Chi-restraints excluded: chain O residue 487 THR Chi-restraints excluded: chain O residue 498 MET Chi-restraints excluded: chain O residue 551 VAL Chi-restraints excluded: chain O residue 595 SER Chi-restraints excluded: chain O residue 596 GLN Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 96 ASN Chi-restraints excluded: chain S residue 36 GLN Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain d residue 36 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 855 random chunks: chunk 538 optimal weight: 6.9990 chunk 722 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 625 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 188 optimal weight: 1.9990 chunk 679 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 chunk 697 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN B 402 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 GLN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN ** G 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 630 GLN ** H 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 371 GLN ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 630 GLN ** J 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 630 GLN P 21 GLN T 22 ASN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 GLN W 21 GLN X 21 GLN Y 21 GLN Z 21 GLN b 21 GLN c 21 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.204726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.155043 restraints weight = 66631.641| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.59 r_work: 0.3508 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.264 66675 Z= 0.279 Angle : 0.787 59.199 90210 Z= 0.409 Chirality : 0.047 0.721 10965 Planarity : 0.005 0.080 11745 Dihedral : 5.512 58.891 9165 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.17 % Favored : 93.11 % Rotamer: Outliers : 2.38 % Allowed : 15.49 % Favored : 82.13 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.09), residues: 8445 helix: 0.24 (0.10), residues: 2670 sheet: -1.20 (0.08), residues: 3390 loop : -1.83 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 419 HIS 0.002 0.001 HIS D 293 PHE 0.009 0.001 PHE M 517 TYR 0.015 0.001 TYR V 65 ARG 0.008 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17279.64 seconds wall clock time: 307 minutes 19.14 seconds (18439.14 seconds total)