Starting phenix.real_space_refine on Sat Mar 16 13:17:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfs_25101/03_2024/7sfs_25101.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfs_25101/03_2024/7sfs_25101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfs_25101/03_2024/7sfs_25101.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfs_25101/03_2024/7sfs_25101.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfs_25101/03_2024/7sfs_25101.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sfs_25101/03_2024/7sfs_25101.pdb" } resolution = 2.76 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= 0.004 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 359 5.16 5 C 45871 2.51 5 N 12764 2.21 5 O 14227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M GLU 79": "OE1" <-> "OE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "M ASP 126": "OD1" <-> "OD2" Residue "M PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 239": "OD1" <-> "OD2" Residue "M ASP 423": "OD1" <-> "OD2" Residue "M GLU 575": "OE1" <-> "OE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 426": "OE1" <-> "OE2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ASP 126": "OD1" <-> "OD2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 362": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E ASP 126": "OD1" <-> "OD2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 239": "OD1" <-> "OD2" Residue "E PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 520": "OD1" <-> "OD2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F ASP 126": "OD1" <-> "OD2" Residue "F PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 575": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H GLU 79": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 119": "OE1" <-> "OE2" Residue "H ASP 127": "OD1" <-> "OD2" Residue "H TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 239": "OD1" <-> "OD2" Residue "H PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 426": "OE1" <-> "OE2" Residue "H ASP 520": "OD1" <-> "OD2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "I PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 520": "OD1" <-> "OD2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 423": "OD1" <-> "OD2" Residue "J GLU 575": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K GLU 98": "OE1" <-> "OE2" Residue "K GLU 119": "OE1" <-> "OE2" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 426": "OE1" <-> "OE2" Residue "N GLU 9": "OE1" <-> "OE2" Residue "N PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 30": "OE1" <-> "OE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O ASP 69": "OD1" <-> "OD2" Residue "O ASP 93": "OD1" <-> "OD2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "P GLU 9": "OE1" <-> "OE2" Residue "P PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 97": "OE1" <-> "OE2" Residue "Q PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "Q GLU 97": "OE1" <-> "OE2" Residue "R GLU 9": "OE1" <-> "OE2" Residue "R GLU 30": "OE1" <-> "OE2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S ASP 93": "OD1" <-> "OD2" Residue "S GLU 97": "OE1" <-> "OE2" Residue "T GLU 30": "OE1" <-> "OE2" Residue "T GLU 47": "OE1" <-> "OE2" Residue "T GLU 71": "OE1" <-> "OE2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "V ASP 28": "OD1" <-> "OD2" Residue "V GLU 71": "OE1" <-> "OE2" Residue "V GLU 97": "OE1" <-> "OE2" Residue "V TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 9": "OE1" <-> "OE2" Residue "W PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 28": "OD1" <-> "OD2" Residue "W GLU 47": "OE1" <-> "OE2" Residue "W ASP 93": "OD1" <-> "OD2" Residue "W GLU 97": "OE1" <-> "OE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "L ASP 93": "OD1" <-> "OD2" Residue "L GLU 97": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 73221 Number of models: 1 Model: "" Number of chains: 24 Chain: "M" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 4930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 4930 Classifications: {'peptide': 623} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "O" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "P" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "Q" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1147 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "R" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "S" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "T" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "U" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "V" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "W" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "L" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 10, 'TRANS': 139} Time building chain proxies: 27.62, per 1000 atoms: 0.38 Number of scatterers: 73221 At special positions: 0 Unit cell: (189.618, 189.618, 254.694, 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 359 16.00 O 14227 8.00 N 12764 7.00 C 45871 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.49 Conformation dependent library (CDL) restraints added in 9.4 seconds 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17416 Finding SS restraints... Secondary structure from input PDB file: 358 helices and 84 sheets defined 48.9% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'M' and resid 6 through 21 removed outlier: 3.900A pdb=" N ARG M 11 " --> pdb=" O LYS M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 39 removed outlier: 3.690A pdb=" N GLU M 28 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS M 29 " --> pdb=" O GLU M 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS M 30 " --> pdb=" O VAL M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 45 removed outlier: 3.598A pdb=" N TRP M 44 " --> pdb=" O GLY M 41 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU M 45 " --> pdb=" O GLY M 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 41 through 45' Processing helix chain 'M' and resid 70 through 83 removed outlier: 3.624A pdb=" N ASN M 83 " --> pdb=" O GLU M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 114 removed outlier: 3.680A pdb=" N ARG M 109 " --> pdb=" O ASN M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 131 Processing helix chain 'M' and resid 162 through 165 Processing helix chain 'M' and resid 191 through 198 removed outlier: 3.596A pdb=" N GLU M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 261 removed outlier: 4.000A pdb=" N GLU M 260 " --> pdb=" O SER M 256 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP M 261 " --> pdb=" O ASP M 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 256 through 261' Processing helix chain 'M' and resid 328 through 330 No H-bonds generated for 'chain 'M' and resid 328 through 330' Processing helix chain 'M' and resid 331 through 352 removed outlier: 3.706A pdb=" N LEU M 340 " --> pdb=" O ARG M 336 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP M 347 " --> pdb=" O SER M 343 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR M 348 " --> pdb=" O MET M 344 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP M 352 " --> pdb=" O THR M 348 " (cutoff:3.500A) Processing helix chain 'M' and resid 360 through 365 removed outlier: 3.795A pdb=" N ILE M 364 " --> pdb=" O GLY M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 373 removed outlier: 3.735A pdb=" N TRP M 371 " --> pdb=" O LEU M 367 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA M 373 " --> pdb=" O LYS M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 410 through 428 removed outlier: 3.702A pdb=" N ALA M 414 " --> pdb=" O ASN M 410 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN M 425 " --> pdb=" O SER M 421 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 455 removed outlier: 3.845A pdb=" N MET M 455 " --> pdb=" O ASN M 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 451 through 455' Processing helix chain 'M' and resid 457 through 484 removed outlier: 3.597A pdb=" N ALA M 465 " --> pdb=" O LEU M 461 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS M 466 " --> pdb=" O ASP M 462 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG M 470 " --> pdb=" O LYS M 466 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG M 480 " --> pdb=" O LEU M 476 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLU M 481 " --> pdb=" O SER M 477 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL M 482 " --> pdb=" O MET M 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 538 through 551 removed outlier: 3.601A pdb=" N ALA M 542 " --> pdb=" O ALA M 538 " (cutoff:3.500A) Processing helix chain 'M' and resid 559 through 571 removed outlier: 3.915A pdb=" N ALA M 563 " --> pdb=" O PRO M 559 " (cutoff:3.500A) Processing helix chain 'M' and resid 577 through 591 removed outlier: 3.506A pdb=" N SER M 591 " --> pdb=" O GLN M 587 " (cutoff:3.500A) Processing helix chain 'M' and resid 604 through 615 Processing helix chain 'M' and resid 616 through 623 Processing helix chain 'M' and resid 625 through 641 removed outlier: 4.142A pdb=" N ALA M 630 " --> pdb=" O GLN M 626 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN M 631 " --> pdb=" O MET M 627 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN M 639 " --> pdb=" O GLN M 635 " (cutoff:3.500A) Processing helix chain 'M' and resid 641 through 670 removed outlier: 3.931A pdb=" N GLN M 645 " --> pdb=" O THR M 641 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG M 670 " --> pdb=" O LEU M 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 21 removed outlier: 3.901A pdb=" N ARG A 11 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.671A pdb=" N GLU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.529A pdb=" N TRP A 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 45 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 45' Processing helix chain 'A' and resid 69 through 83 removed outlier: 4.381A pdb=" N LEU A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 114 removed outlier: 3.616A pdb=" N ARG A 109 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 131 Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 191 through 198 removed outlier: 3.701A pdb=" N GLU A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.982A pdb=" N GLU A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 261' Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.795A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 348 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.751A pdb=" N ILE A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.686A pdb=" N TRP A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 428 removed outlier: 3.609A pdb=" N ALA A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.950A pdb=" N MET A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 455' Processing helix chain 'A' and resid 457 through 484 removed outlier: 3.680A pdb=" N ALA A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 551 removed outlier: 3.609A pdb=" N ALA A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.855A pdb=" N ALA A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.517A pdb=" N SER A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'A' and resid 615 through 623 removed outlier: 4.419A pdb=" N GLU A 619 " --> pdb=" O GLN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 641 removed outlier: 4.042A pdb=" N ALA A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 631 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN A 639 " --> pdb=" O GLN A 635 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 669 removed outlier: 3.932A pdb=" N GLN A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 21 removed outlier: 3.782A pdb=" N ARG B 11 " --> pdb=" O LYS B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 39 removed outlier: 3.643A pdb=" N GLU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.537A pdb=" N TRP B 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 45 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 45' Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.601A pdb=" N ASN B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 114 removed outlier: 3.626A pdb=" N ARG B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 131 Processing helix chain 'B' and resid 162 through 165 Processing helix chain 'B' and resid 191 through 198 removed outlier: 3.632A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.854A pdb=" N GLU B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 261' Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 352 removed outlier: 3.722A pdb=" N LEU B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP B 347 " --> pdb=" O SER B 343 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 348 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP B 352 " --> pdb=" O THR B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 365 removed outlier: 3.697A pdb=" N ILE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 373 removed outlier: 3.698A pdb=" N TRP B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 428 removed outlier: 3.713A pdb=" N ALA B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.947A pdb=" N MET B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 455' Processing helix chain 'B' and resid 457 through 484 removed outlier: 3.585A pdb=" N ALA B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 551 removed outlier: 3.584A pdb=" N ALA B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.998A pdb=" N ALA B 563 " --> pdb=" O PRO B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 591 removed outlier: 3.606A pdb=" N SER B 591 " --> pdb=" O GLN B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 615 through 623 removed outlier: 4.352A pdb=" N GLU B 619 " --> pdb=" O GLN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 641 removed outlier: 4.061A pdb=" N ALA B 630 " --> pdb=" O GLN B 626 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 631 " --> pdb=" O MET B 627 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B 639 " --> pdb=" O GLN B 635 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 670 removed outlier: 3.943A pdb=" N GLN B 645 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 21 removed outlier: 3.900A pdb=" N ARG C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 39 removed outlier: 3.687A pdb=" N GLU C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.596A pdb=" N TRP C 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 45 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 45' Processing helix chain 'C' and resid 70 through 83 removed outlier: 3.606A pdb=" N ASN C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 114 removed outlier: 3.681A pdb=" N ARG C 109 " --> pdb=" O ASN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 191 through 198 removed outlier: 3.595A pdb=" N GLU C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 4.004A pdb=" N GLU C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP C 261 " --> pdb=" O ASP C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'C' and resid 331 through 352 removed outlier: 3.705A pdb=" N LEU C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 348 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 365 removed outlier: 3.806A pdb=" N ILE C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.732A pdb=" N TRP C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 373 " --> pdb=" O LYS C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 428 removed outlier: 3.702A pdb=" N ALA C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 3.844A pdb=" N MET C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 451 through 455' Processing helix chain 'C' and resid 457 through 484 removed outlier: 3.593A pdb=" N ALA C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 466 " --> pdb=" O ASP C 462 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 551 removed outlier: 3.605A pdb=" N ALA C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 removed outlier: 3.915A pdb=" N ALA C 563 " --> pdb=" O PRO C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 591 removed outlier: 3.507A pdb=" N SER C 591 " --> pdb=" O GLN C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 615 Processing helix chain 'C' and resid 615 through 623 removed outlier: 4.400A pdb=" N GLU C 619 " --> pdb=" O GLN C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 641 removed outlier: 4.069A pdb=" N ALA C 630 " --> pdb=" O GLN C 626 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN C 639 " --> pdb=" O GLN C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 669 removed outlier: 3.931A pdb=" N GLN C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 21 removed outlier: 3.901A pdb=" N ARG D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 39 removed outlier: 3.705A pdb=" N GLU D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 45 removed outlier: 3.529A pdb=" N TRP D 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU D 45 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 45' Processing helix chain 'D' and resid 69 through 83 removed outlier: 4.386A pdb=" N LEU D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 114 removed outlier: 3.616A pdb=" N ARG D 109 " --> pdb=" O ASN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 131 Processing helix chain 'D' and resid 162 through 165 Processing helix chain 'D' and resid 191 through 198 removed outlier: 3.726A pdb=" N GLU D 198 " --> pdb=" O LYS D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 3.986A pdb=" N GLU D 260 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP D 261 " --> pdb=" O ASP D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 261' Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'D' and resid 331 through 352 removed outlier: 3.785A pdb=" N LEU D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP D 347 " --> pdb=" O SER D 343 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 348 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP D 352 " --> pdb=" O THR D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 365 removed outlier: 3.745A pdb=" N ILE D 364 " --> pdb=" O GLY D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 373 removed outlier: 3.697A pdb=" N TRP D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 428 removed outlier: 3.605A pdb=" N ALA D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 455 removed outlier: 3.951A pdb=" N MET D 455 " --> pdb=" O ASN D 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 451 through 455' Processing helix chain 'D' and resid 457 through 484 removed outlier: 3.677A pdb=" N ALA D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU D 481 " --> pdb=" O SER D 477 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 482 " --> pdb=" O MET D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 551 removed outlier: 3.610A pdb=" N ALA D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 removed outlier: 3.820A pdb=" N ALA D 563 " --> pdb=" O PRO D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 591 removed outlier: 3.521A pdb=" N SER D 591 " --> pdb=" O GLN D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 615 through 623 removed outlier: 4.417A pdb=" N GLU D 619 " --> pdb=" O GLN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 641 removed outlier: 4.040A pdb=" N ALA D 630 " --> pdb=" O GLN D 626 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 631 " --> pdb=" O MET D 627 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN D 639 " --> pdb=" O GLN D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 669 removed outlier: 3.932A pdb=" N GLN D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 21 removed outlier: 3.824A pdb=" N ARG E 11 " --> pdb=" O LYS E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 39 removed outlier: 3.659A pdb=" N GLU E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 45 removed outlier: 3.536A pdb=" N TRP E 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 45 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 45' Processing helix chain 'E' and resid 70 through 83 removed outlier: 3.611A pdb=" N ASN E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 114 removed outlier: 3.625A pdb=" N ARG E 109 " --> pdb=" O ASN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 131 Processing helix chain 'E' and resid 162 through 165 Processing helix chain 'E' and resid 191 through 198 removed outlier: 3.633A pdb=" N GLU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 3.853A pdb=" N GLU E 260 " --> pdb=" O SER E 256 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP E 261 " --> pdb=" O ASP E 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 256 through 261' Processing helix chain 'E' and resid 328 through 330 No H-bonds generated for 'chain 'E' and resid 328 through 330' Processing helix chain 'E' and resid 331 through 352 removed outlier: 3.716A pdb=" N LEU E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP E 347 " --> pdb=" O SER E 343 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 348 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP E 352 " --> pdb=" O THR E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 365 removed outlier: 3.698A pdb=" N ILE E 364 " --> pdb=" O GLY E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.693A pdb=" N TRP E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 428 removed outlier: 3.714A pdb=" N ALA E 414 " --> pdb=" O ASN E 410 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN E 425 " --> pdb=" O SER E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 455 removed outlier: 3.947A pdb=" N MET E 455 " --> pdb=" O ASN E 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 451 through 455' Processing helix chain 'E' and resid 457 through 484 removed outlier: 3.586A pdb=" N ALA E 465 " --> pdb=" O LEU E 461 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 470 " --> pdb=" O LYS E 466 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLU E 481 " --> pdb=" O SER E 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 551 removed outlier: 3.582A pdb=" N ALA E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 571 removed outlier: 4.104A pdb=" N ALA E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 591 removed outlier: 3.603A pdb=" N SER E 591 " --> pdb=" O GLN E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 615 Processing helix chain 'E' and resid 615 through 623 removed outlier: 4.352A pdb=" N GLU E 619 " --> pdb=" O GLN E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 641 removed outlier: 4.059A pdb=" N ALA E 630 " --> pdb=" O GLN E 626 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN E 631 " --> pdb=" O MET E 627 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN E 639 " --> pdb=" O GLN E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 670 removed outlier: 3.950A pdb=" N GLN E 645 " --> pdb=" O THR E 641 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG E 670 " --> pdb=" O LEU E 666 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 21 removed outlier: 3.905A pdb=" N ARG F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 39 removed outlier: 3.678A pdb=" N GLU F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.597A pdb=" N TRP F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU F 45 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 45' Processing helix chain 'F' and resid 70 through 83 removed outlier: 3.616A pdb=" N ASN F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 114 removed outlier: 3.681A pdb=" N ARG F 109 " --> pdb=" O ASN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 131 Processing helix chain 'F' and resid 162 through 165 Processing helix chain 'F' and resid 191 through 198 removed outlier: 3.596A pdb=" N GLU F 198 " --> pdb=" O LYS F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 4.041A pdb=" N GLU F 260 " --> pdb=" O SER F 256 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP F 261 " --> pdb=" O ASP F 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 256 through 261' Processing helix chain 'F' and resid 328 through 330 No H-bonds generated for 'chain 'F' and resid 328 through 330' Processing helix chain 'F' and resid 331 through 352 removed outlier: 3.704A pdb=" N LEU F 340 " --> pdb=" O ARG F 336 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP F 347 " --> pdb=" O SER F 343 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR F 348 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP F 352 " --> pdb=" O THR F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 365 removed outlier: 3.793A pdb=" N ILE F 364 " --> pdb=" O GLY F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.730A pdb=" N TRP F 371 " --> pdb=" O LEU F 367 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 373 " --> pdb=" O LYS F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 428 removed outlier: 3.655A pdb=" N ALA F 414 " --> pdb=" O ASN F 410 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN F 425 " --> pdb=" O SER F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 455 removed outlier: 3.848A pdb=" N MET F 455 " --> pdb=" O ASN F 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 451 through 455' Processing helix chain 'F' and resid 457 through 484 removed outlier: 3.593A pdb=" N ALA F 465 " --> pdb=" O LEU F 461 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG F 480 " --> pdb=" O LEU F 476 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU F 481 " --> pdb=" O SER F 477 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 482 " --> pdb=" O MET F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 551 removed outlier: 3.601A pdb=" N ALA F 542 " --> pdb=" O ALA F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 571 removed outlier: 3.920A pdb=" N ALA F 563 " --> pdb=" O PRO F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 577 through 591 removed outlier: 3.556A pdb=" N SER F 591 " --> pdb=" O GLN F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 615 Processing helix chain 'F' and resid 615 through 623 removed outlier: 4.445A pdb=" N GLU F 619 " --> pdb=" O GLN F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 625 through 641 removed outlier: 4.110A pdb=" N ALA F 630 " --> pdb=" O GLN F 626 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN F 631 " --> pdb=" O MET F 627 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN F 639 " --> pdb=" O GLN F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 670 removed outlier: 3.933A pdb=" N GLN F 645 " --> pdb=" O THR F 641 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG F 670 " --> pdb=" O LEU F 666 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 21 removed outlier: 3.905A pdb=" N ARG G 11 " --> pdb=" O LYS G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 39 removed outlier: 3.663A pdb=" N GLU G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 45 removed outlier: 3.529A pdb=" N TRP G 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU G 45 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 45' Processing helix chain 'G' and resid 69 through 83 removed outlier: 4.387A pdb=" N LEU G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 114 removed outlier: 3.615A pdb=" N ARG G 109 " --> pdb=" O ASN G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 131 Processing helix chain 'G' and resid 162 through 165 Processing helix chain 'G' and resid 191 through 198 removed outlier: 3.701A pdb=" N GLU G 198 " --> pdb=" O LYS G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 261 removed outlier: 3.986A pdb=" N GLU G 260 " --> pdb=" O SER G 256 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP G 261 " --> pdb=" O ASP G 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 256 through 261' Processing helix chain 'G' and resid 328 through 330 No H-bonds generated for 'chain 'G' and resid 328 through 330' Processing helix chain 'G' and resid 331 through 352 removed outlier: 3.788A pdb=" N LEU G 340 " --> pdb=" O ARG G 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP G 347 " --> pdb=" O SER G 343 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP G 352 " --> pdb=" O THR G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 365 removed outlier: 3.742A pdb=" N ILE G 364 " --> pdb=" O GLY G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 373 removed outlier: 3.686A pdb=" N TRP G 371 " --> pdb=" O LEU G 367 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA G 373 " --> pdb=" O LYS G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 428 removed outlier: 3.608A pdb=" N ALA G 414 " --> pdb=" O ASN G 410 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN G 425 " --> pdb=" O SER G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 484 removed outlier: 3.676A pdb=" N ALA G 465 " --> pdb=" O LEU G 461 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS G 466 " --> pdb=" O ASP G 462 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG G 470 " --> pdb=" O LYS G 466 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 480 " --> pdb=" O LEU G 476 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU G 481 " --> pdb=" O SER G 477 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 551 removed outlier: 3.610A pdb=" N ALA G 542 " --> pdb=" O ALA G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 571 removed outlier: 3.851A pdb=" N ALA G 563 " --> pdb=" O PRO G 559 " (cutoff:3.500A) Processing helix chain 'G' and resid 577 through 591 removed outlier: 3.517A pdb=" N SER G 591 " --> pdb=" O GLN G 587 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 615 Processing helix chain 'G' and resid 615 through 623 removed outlier: 4.420A pdb=" N GLU G 619 " --> pdb=" O GLN G 615 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 641 removed outlier: 4.040A pdb=" N ALA G 630 " --> pdb=" O GLN G 626 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 631 " --> pdb=" O MET G 627 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN G 639 " --> pdb=" O GLN G 635 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR G 641 " --> pdb=" O ALA G 637 " (cutoff:3.500A) Processing helix chain 'G' and resid 641 through 669 removed outlier: 3.932A pdb=" N GLN G 645 " --> pdb=" O THR G 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 21 removed outlier: 3.781A pdb=" N ARG H 11 " --> pdb=" O LYS H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 39 removed outlier: 3.643A pdb=" N GLU H 28 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS H 30 " --> pdb=" O VAL H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 45 removed outlier: 3.550A pdb=" N TRP H 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU H 45 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 45' Processing helix chain 'H' and resid 70 through 83 removed outlier: 3.611A pdb=" N ASN H 83 " --> pdb=" O GLU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 114 removed outlier: 3.625A pdb=" N ARG H 109 " --> pdb=" O ASN H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 131 Processing helix chain 'H' and resid 162 through 165 Processing helix chain 'H' and resid 191 through 198 removed outlier: 3.794A pdb=" N GLU H 198 " --> pdb=" O LYS H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 261 removed outlier: 3.778A pdb=" N GLU H 260 " --> pdb=" O SER H 256 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP H 261 " --> pdb=" O ASP H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 256 through 261' Processing helix chain 'H' and resid 328 through 330 No H-bonds generated for 'chain 'H' and resid 328 through 330' Processing helix chain 'H' and resid 331 through 352 removed outlier: 3.726A pdb=" N LEU H 340 " --> pdb=" O ARG H 336 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP H 347 " --> pdb=" O SER H 343 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR H 348 " --> pdb=" O MET H 344 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP H 352 " --> pdb=" O THR H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 365 removed outlier: 3.700A pdb=" N ILE H 364 " --> pdb=" O GLY H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.700A pdb=" N TRP H 371 " --> pdb=" O LEU H 367 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA H 373 " --> pdb=" O LYS H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 428 removed outlier: 3.693A pdb=" N ALA H 414 " --> pdb=" O ASN H 410 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN H 425 " --> pdb=" O SER H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 455 removed outlier: 3.961A pdb=" N MET H 455 " --> pdb=" O ASN H 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 451 through 455' Processing helix chain 'H' and resid 457 through 484 removed outlier: 3.587A pdb=" N ALA H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS H 466 " --> pdb=" O ASP H 462 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG H 470 " --> pdb=" O LYS H 466 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG H 480 " --> pdb=" O LEU H 476 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU H 481 " --> pdb=" O SER H 477 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL H 482 " --> pdb=" O MET H 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 551 removed outlier: 3.582A pdb=" N ALA H 542 " --> pdb=" O ALA H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 571 removed outlier: 4.060A pdb=" N ALA H 563 " --> pdb=" O PRO H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 577 through 591 removed outlier: 3.606A pdb=" N SER H 591 " --> pdb=" O GLN H 587 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 615 Processing helix chain 'H' and resid 615 through 623 removed outlier: 4.391A pdb=" N GLU H 619 " --> pdb=" O GLN H 615 " (cutoff:3.500A) Processing helix chain 'H' and resid 625 through 641 removed outlier: 4.110A pdb=" N ALA H 630 " --> pdb=" O GLN H 626 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN H 631 " --> pdb=" O MET H 627 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN H 639 " --> pdb=" O GLN H 635 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR H 641 " --> pdb=" O ALA H 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 641 through 670 removed outlier: 3.941A pdb=" N GLN H 645 " --> pdb=" O THR H 641 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG H 670 " --> pdb=" O LEU H 666 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 21 removed outlier: 3.884A pdb=" N ARG I 11 " --> pdb=" O LYS I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 39 removed outlier: 3.690A pdb=" N GLU I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS I 29 " --> pdb=" O GLU I 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS I 30 " --> pdb=" O VAL I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 45 removed outlier: 3.598A pdb=" N TRP I 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU I 45 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 45' Processing helix chain 'I' and resid 70 through 83 removed outlier: 3.614A pdb=" N ASN I 83 " --> pdb=" O GLU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 114 removed outlier: 3.682A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 131 Processing helix chain 'I' and resid 162 through 165 Processing helix chain 'I' and resid 191 through 198 removed outlier: 3.596A pdb=" N GLU I 198 " --> pdb=" O LYS I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 261 removed outlier: 3.981A pdb=" N GLU I 260 " --> pdb=" O SER I 256 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP I 261 " --> pdb=" O ASP I 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 256 through 261' Processing helix chain 'I' and resid 328 through 330 No H-bonds generated for 'chain 'I' and resid 328 through 330' Processing helix chain 'I' and resid 331 through 352 removed outlier: 3.706A pdb=" N LEU I 340 " --> pdb=" O ARG I 336 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP I 347 " --> pdb=" O SER I 343 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR I 348 " --> pdb=" O MET I 344 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP I 352 " --> pdb=" O THR I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 365 removed outlier: 3.788A pdb=" N ILE I 364 " --> pdb=" O GLY I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 373 removed outlier: 3.739A pdb=" N TRP I 371 " --> pdb=" O LEU I 367 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA I 373 " --> pdb=" O LYS I 369 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 428 removed outlier: 3.649A pdb=" N ALA I 414 " --> pdb=" O ASN I 410 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 455 removed outlier: 3.845A pdb=" N MET I 455 " --> pdb=" O ASN I 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 451 through 455' Processing helix chain 'I' and resid 457 through 484 removed outlier: 3.594A pdb=" N ALA I 465 " --> pdb=" O LEU I 461 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS I 466 " --> pdb=" O ASP I 462 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG I 470 " --> pdb=" O LYS I 466 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG I 480 " --> pdb=" O LEU I 476 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU I 481 " --> pdb=" O SER I 477 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL I 482 " --> pdb=" O MET I 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 538 through 551 removed outlier: 3.606A pdb=" N ALA I 542 " --> pdb=" O ALA I 538 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 571 removed outlier: 3.917A pdb=" N ALA I 563 " --> pdb=" O PRO I 559 " (cutoff:3.500A) Processing helix chain 'I' and resid 577 through 591 removed outlier: 3.506A pdb=" N SER I 591 " --> pdb=" O GLN I 587 " (cutoff:3.500A) Processing helix chain 'I' and resid 604 through 615 Processing helix chain 'I' and resid 616 through 623 Processing helix chain 'I' and resid 628 through 641 removed outlier: 3.941A pdb=" N ASN I 639 " --> pdb=" O GLN I 635 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 670 removed outlier: 3.932A pdb=" N GLN I 645 " --> pdb=" O THR I 641 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG I 670 " --> pdb=" O LEU I 666 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 21 removed outlier: 3.907A pdb=" N ARG J 11 " --> pdb=" O LYS J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 39 removed outlier: 3.705A pdb=" N GLU J 28 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS J 29 " --> pdb=" O GLU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 45 removed outlier: 3.527A pdb=" N TRP J 44 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU J 45 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 45' Processing helix chain 'J' and resid 69 through 83 removed outlier: 4.387A pdb=" N LEU J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN J 83 " --> pdb=" O GLU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 114 removed outlier: 3.617A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 131 Processing helix chain 'J' and resid 162 through 165 Processing helix chain 'J' and resid 191 through 198 removed outlier: 3.699A pdb=" N GLU J 198 " --> pdb=" O LYS J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 removed outlier: 3.986A pdb=" N GLU J 260 " --> pdb=" O SER J 256 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASP J 261 " --> pdb=" O ASP J 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 256 through 261' Processing helix chain 'J' and resid 328 through 330 No H-bonds generated for 'chain 'J' and resid 328 through 330' Processing helix chain 'J' and resid 331 through 352 removed outlier: 3.797A pdb=" N LEU J 340 " --> pdb=" O ARG J 336 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP J 347 " --> pdb=" O SER J 343 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR J 348 " --> pdb=" O MET J 344 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ASP J 352 " --> pdb=" O THR J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 365 removed outlier: 3.747A pdb=" N ILE J 364 " --> pdb=" O GLY J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 373 removed outlier: 3.684A pdb=" N TRP J 371 " --> pdb=" O LEU J 367 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA J 373 " --> pdb=" O LYS J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 428 removed outlier: 3.607A pdb=" N ALA J 414 " --> pdb=" O ASN J 410 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN J 425 " --> pdb=" O SER J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 484 removed outlier: 3.678A pdb=" N ALA J 465 " --> pdb=" O LEU J 461 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS J 466 " --> pdb=" O ASP J 462 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG J 470 " --> pdb=" O LYS J 466 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG J 480 " --> pdb=" O LEU J 476 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU J 481 " --> pdb=" O SER J 477 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL J 482 " --> pdb=" O MET J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 551 removed outlier: 3.609A pdb=" N ALA J 542 " --> pdb=" O ALA J 538 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 571 removed outlier: 3.825A pdb=" N ALA J 563 " --> pdb=" O PRO J 559 " (cutoff:3.500A) Processing helix chain 'J' and resid 577 through 591 removed outlier: 3.520A pdb=" N SER J 591 " --> pdb=" O GLN J 587 " (cutoff:3.500A) Processing helix chain 'J' and resid 604 through 615 Processing helix chain 'J' and resid 615 through 623 removed outlier: 4.419A pdb=" N GLU J 619 " --> pdb=" O GLN J 615 " (cutoff:3.500A) Processing helix chain 'J' and resid 625 through 641 removed outlier: 4.047A pdb=" N ALA J 630 " --> pdb=" O GLN J 626 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN J 631 " --> pdb=" O MET J 627 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN J 639 " --> pdb=" O GLN J 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 641 through 669 removed outlier: 3.932A pdb=" N GLN J 645 " --> pdb=" O THR J 641 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 21 removed outlier: 3.780A pdb=" N ARG K 11 " --> pdb=" O LYS K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 39 removed outlier: 3.662A pdb=" N GLU K 28 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS K 29 " --> pdb=" O GLU K 25 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS K 30 " --> pdb=" O VAL K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 45 removed outlier: 3.536A pdb=" N TRP K 44 " --> pdb=" O GLY K 41 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU K 45 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 45' Processing helix chain 'K' and resid 70 through 83 removed outlier: 3.617A pdb=" N ASN K 83 " --> pdb=" O GLU K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 114 removed outlier: 3.628A pdb=" N ARG K 109 " --> pdb=" O ASN K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 116 through 131 Processing helix chain 'K' and resid 162 through 165 Processing helix chain 'K' and resid 191 through 198 removed outlier: 3.793A pdb=" N GLU K 198 " --> pdb=" O LYS K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 261 removed outlier: 3.853A pdb=" N GLU K 260 " --> pdb=" O SER K 256 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP K 261 " --> pdb=" O ASP K 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 256 through 261' Processing helix chain 'K' and resid 328 through 330 No H-bonds generated for 'chain 'K' and resid 328 through 330' Processing helix chain 'K' and resid 331 through 352 removed outlier: 3.721A pdb=" N LEU K 340 " --> pdb=" O ARG K 336 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP K 347 " --> pdb=" O SER K 343 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR K 348 " --> pdb=" O MET K 344 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP K 352 " --> pdb=" O THR K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 365 removed outlier: 3.686A pdb=" N ILE K 364 " --> pdb=" O GLY K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 373 removed outlier: 3.699A pdb=" N TRP K 371 " --> pdb=" O LEU K 367 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA K 373 " --> pdb=" O LYS K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 428 removed outlier: 3.714A pdb=" N ALA K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN K 425 " --> pdb=" O SER K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 455 removed outlier: 3.964A pdb=" N MET K 455 " --> pdb=" O ASN K 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 451 through 455' Processing helix chain 'K' and resid 457 through 484 removed outlier: 3.586A pdb=" N ALA K 465 " --> pdb=" O LEU K 461 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS K 466 " --> pdb=" O ASP K 462 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG K 470 " --> pdb=" O LYS K 466 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG K 480 " --> pdb=" O LEU K 476 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU K 481 " --> pdb=" O SER K 477 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL K 482 " --> pdb=" O MET K 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 538 through 551 removed outlier: 3.581A pdb=" N ALA K 542 " --> pdb=" O ALA K 538 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 571 removed outlier: 3.994A pdb=" N ALA K 563 " --> pdb=" O PRO K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 577 through 591 removed outlier: 3.606A pdb=" N SER K 591 " --> pdb=" O GLN K 587 " (cutoff:3.500A) Processing helix chain 'K' and resid 604 through 615 Processing helix chain 'K' and resid 615 through 623 removed outlier: 4.355A pdb=" N GLU K 619 " --> pdb=" O GLN K 615 " (cutoff:3.500A) Processing helix chain 'K' and resid 625 through 641 removed outlier: 4.059A pdb=" N ALA K 630 " --> pdb=" O GLN K 626 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN K 631 " --> pdb=" O MET K 627 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN K 639 " --> pdb=" O GLN K 635 " (cutoff:3.500A) Processing helix chain 'K' and resid 641 through 670 removed outlier: 3.944A pdb=" N GLN K 645 " --> pdb=" O THR K 641 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG K 670 " --> pdb=" O LEU K 666 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 18 removed outlier: 3.505A pdb=" N ILE N 10 " --> pdb=" O THR N 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 48 Processing helix chain 'N' and resid 75 through 77 No H-bonds generated for 'chain 'N' and resid 75 through 77' Processing helix chain 'N' and resid 78 through 91 removed outlier: 3.507A pdb=" N ARG N 89 " --> pdb=" O GLN N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 95 Processing helix chain 'N' and resid 99 through 116 removed outlier: 3.641A pdb=" N ASP N 116 " --> pdb=" O ALA N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 136 Processing helix chain 'O' and resid 8 through 17 Processing helix chain 'O' and resid 33 through 49 removed outlier: 3.957A pdb=" N GLY O 37 " --> pdb=" O SER O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 78 through 89 removed outlier: 3.595A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 95 Processing helix chain 'O' and resid 99 through 116 removed outlier: 3.526A pdb=" N ASP O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 136 Processing helix chain 'P' and resid 6 through 17 removed outlier: 3.602A pdb=" N ILE P 10 " --> pdb=" O THR P 6 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 49 removed outlier: 3.603A pdb=" N ILE P 34 " --> pdb=" O GLU P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 77 No H-bonds generated for 'chain 'P' and resid 75 through 77' Processing helix chain 'P' and resid 78 through 91 Processing helix chain 'P' and resid 92 through 95 Processing helix chain 'P' and resid 99 through 116 removed outlier: 3.563A pdb=" N ASP P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 132 through 136 removed outlier: 3.630A pdb=" N ASN P 135 " --> pdb=" O GLY P 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 20 Processing helix chain 'Q' and resid 31 through 49 Processing helix chain 'Q' and resid 75 through 77 No H-bonds generated for 'chain 'Q' and resid 75 through 77' Processing helix chain 'Q' and resid 78 through 91 Processing helix chain 'Q' and resid 92 through 95 Processing helix chain 'Q' and resid 99 through 116 removed outlier: 3.630A pdb=" N ASP Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 136 Processing helix chain 'R' and resid 8 through 18 removed outlier: 3.951A pdb=" N PHE R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 48 removed outlier: 3.754A pdb=" N ILE R 34 " --> pdb=" O GLU R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 77 No H-bonds generated for 'chain 'R' and resid 75 through 77' Processing helix chain 'R' and resid 78 through 91 Processing helix chain 'R' and resid 92 through 95 Processing helix chain 'R' and resid 99 through 116 removed outlier: 3.547A pdb=" N ASP R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 136 Processing helix chain 'S' and resid 6 through 18 removed outlier: 3.594A pdb=" N ILE S 10 " --> pdb=" O THR S 6 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL S 11 " --> pdb=" O LYS S 7 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 49 removed outlier: 3.639A pdb=" N ILE S 34 " --> pdb=" O GLU S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 78 through 91 Processing helix chain 'S' and resid 92 through 95 Processing helix chain 'S' and resid 99 through 116 removed outlier: 3.597A pdb=" N ASP S 116 " --> pdb=" O ALA S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 132 through 136 removed outlier: 3.613A pdb=" N ASN S 135 " --> pdb=" O GLY S 132 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 18 removed outlier: 3.613A pdb=" N ILE T 10 " --> pdb=" O THR T 6 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 48 removed outlier: 3.597A pdb=" N GLU T 35 " --> pdb=" O PRO T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 77 No H-bonds generated for 'chain 'T' and resid 75 through 77' Processing helix chain 'T' and resid 78 through 91 Processing helix chain 'T' and resid 92 through 95 Processing helix chain 'T' and resid 99 through 116 removed outlier: 3.587A pdb=" N ASP T 116 " --> pdb=" O ALA T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 132 through 136 removed outlier: 3.626A pdb=" N ASN T 135 " --> pdb=" O GLY T 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 18 removed outlier: 3.618A pdb=" N ILE U 10 " --> pdb=" O THR U 6 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL U 11 " --> pdb=" O LYS U 7 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE U 18 " --> pdb=" O ALA U 14 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 48 removed outlier: 3.647A pdb=" N ILE U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 77 No H-bonds generated for 'chain 'U' and resid 75 through 77' Processing helix chain 'U' and resid 78 through 91 removed outlier: 3.533A pdb=" N ARG U 89 " --> pdb=" O GLN U 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 95 Processing helix chain 'U' and resid 99 through 116 removed outlier: 3.620A pdb=" N ASP U 116 " --> pdb=" O ALA U 112 " (cutoff:3.500A) Processing helix chain 'U' and resid 132 through 136 Processing helix chain 'V' and resid 8 through 18 removed outlier: 3.894A pdb=" N PHE V 18 " --> pdb=" O ALA V 14 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 49 removed outlier: 3.506A pdb=" N ILE V 34 " --> pdb=" O GLU V 30 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU V 35 " --> pdb=" O PRO V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 77 No H-bonds generated for 'chain 'V' and resid 75 through 77' Processing helix chain 'V' and resid 78 through 91 Processing helix chain 'V' and resid 92 through 95 Processing helix chain 'V' and resid 99 through 116 removed outlier: 3.608A pdb=" N ASP V 116 " --> pdb=" O ALA V 112 " (cutoff:3.500A) Processing helix chain 'V' and resid 132 through 136 Processing helix chain 'W' and resid 6 through 16 removed outlier: 3.751A pdb=" N ILE W 10 " --> pdb=" O THR W 6 " (cutoff:3.500A) Processing helix chain 'W' and resid 32 through 48 Processing helix chain 'W' and resid 75 through 77 No H-bonds generated for 'chain 'W' and resid 75 through 77' Processing helix chain 'W' and resid 78 through 91 Processing helix chain 'W' and resid 92 through 95 Processing helix chain 'W' and resid 99 through 116 removed outlier: 3.540A pdb=" N ASP W 116 " --> pdb=" O ALA W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 136 Processing helix chain 'X' and resid 6 through 17 removed outlier: 3.599A pdb=" N ILE X 10 " --> pdb=" O THR X 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL X 11 " --> pdb=" O LYS X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 48 removed outlier: 3.922A pdb=" N ILE X 34 " --> pdb=" O GLU X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 77 No H-bonds generated for 'chain 'X' and resid 75 through 77' Processing helix chain 'X' and resid 78 through 91 Processing helix chain 'X' and resid 92 through 95 Processing helix chain 'X' and resid 99 through 116 removed outlier: 3.639A pdb=" N ASP X 116 " --> pdb=" O ALA X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 136 Processing helix chain 'L' and resid 6 through 18 removed outlier: 3.651A pdb=" N ILE L 10 " --> pdb=" O THR L 6 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL L 11 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 49 Processing helix chain 'L' and resid 75 through 77 No H-bonds generated for 'chain 'L' and resid 75 through 77' Processing helix chain 'L' and resid 78 through 91 Processing helix chain 'L' and resid 92 through 95 Processing helix chain 'L' and resid 99 through 116 removed outlier: 3.533A pdb=" N ASP L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 136 Processing sheet with id=AA1, first strand: chain 'M' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'M' and resid 154 through 159 Processing sheet with id=AA3, first strand: chain 'M' and resid 167 through 169 removed outlier: 4.898A pdb=" N VAL M 284 " --> pdb=" O ILE M 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL M 288 " --> pdb=" O LYS M 297 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS M 297 " --> pdb=" O VAL M 288 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 237 through 240 removed outlier: 3.826A pdb=" N ARG M 277 " --> pdb=" O VAL M 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 314 through 317 Processing sheet with id=AA6, first strand: chain 'M' and resid 402 through 403 removed outlier: 3.815A pdb=" N GLY M 402 " --> pdb=" O ILE M 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 382 through 383 removed outlier: 3.844A pdb=" N GLY A 402 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 387 through 388 removed outlier: 6.900A pdb=" N VAL M 387 " --> pdb=" O ILE M 395 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AB1, first strand: chain 'A' and resid 154 through 159 Processing sheet with id=AB2, first strand: chain 'A' and resid 167 through 169 removed outlier: 4.802A pdb=" N VAL A 284 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A 288 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS A 297 " --> pdb=" O VAL A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.813A pdb=" N ARG A 277 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 314 through 317 Processing sheet with id=AB5, first strand: chain 'A' and resid 382 through 383 removed outlier: 5.854A pdb=" N LEU A 382 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B 402 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.882A pdb=" N VAL A 387 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB8, first strand: chain 'B' and resid 156 through 159 Processing sheet with id=AB9, first strand: chain 'B' and resid 167 through 169 removed outlier: 4.914A pdb=" N VAL B 284 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL B 288 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS B 297 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 237 through 240 removed outlier: 3.766A pdb=" N ARG B 277 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 314 through 317 Processing sheet with id=AC3, first strand: chain 'B' and resid 382 through 383 removed outlier: 5.860A pdb=" N LEU B 382 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 402 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 387 through 388 removed outlier: 6.916A pdb=" N VAL B 387 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AC6, first strand: chain 'C' and resid 154 through 159 Processing sheet with id=AC7, first strand: chain 'C' and resid 167 through 169 removed outlier: 4.897A pdb=" N VAL C 284 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL C 288 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS C 297 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 237 through 240 removed outlier: 3.824A pdb=" N ARG C 277 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 314 through 317 Processing sheet with id=AD1, first strand: chain 'C' and resid 382 through 383 removed outlier: 3.839A pdb=" N GLY D 402 " --> pdb=" O ILE D 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.902A pdb=" N VAL C 387 " --> pdb=" O ILE C 395 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AD4, first strand: chain 'D' and resid 154 through 159 Processing sheet with id=AD5, first strand: chain 'D' and resid 167 through 169 removed outlier: 4.790A pdb=" N VAL D 284 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL D 288 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS D 297 " --> pdb=" O VAL D 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 237 through 240 removed outlier: 3.898A pdb=" N ARG D 277 " --> pdb=" O VAL D 240 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 314 through 317 Processing sheet with id=AD8, first strand: chain 'D' and resid 382 through 383 removed outlier: 5.865A pdb=" N LEU D 382 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY E 402 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 387 through 388 removed outlier: 6.885A pdb=" N VAL D 387 " --> pdb=" O ILE D 395 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE2, first strand: chain 'E' and resid 154 through 159 Processing sheet with id=AE3, first strand: chain 'E' and resid 167 through 169 removed outlier: 4.858A pdb=" N VAL E 284 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL E 288 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS E 297 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 237 through 240 removed outlier: 3.772A pdb=" N ARG E 277 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 314 through 317 Processing sheet with id=AE6, first strand: chain 'E' and resid 382 through 383 removed outlier: 5.897A pdb=" N LEU E 382 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY F 402 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 387 through 388 removed outlier: 6.921A pdb=" N VAL E 387 " --> pdb=" O ILE E 395 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AE9, first strand: chain 'F' and resid 154 through 159 Processing sheet with id=AF1, first strand: chain 'F' and resid 167 through 169 removed outlier: 4.899A pdb=" N VAL F 284 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL F 288 " --> pdb=" O LYS F 297 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS F 297 " --> pdb=" O VAL F 288 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 237 through 240 removed outlier: 3.825A pdb=" N ARG F 277 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 314 through 317 Processing sheet with id=AF4, first strand: chain 'F' and resid 382 through 383 removed outlier: 3.848A pdb=" N GLY G 402 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 387 through 388 removed outlier: 6.903A pdb=" N VAL F 387 " --> pdb=" O ILE F 395 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 86 through 87 Processing sheet with id=AF7, first strand: chain 'G' and resid 154 through 159 Processing sheet with id=AF8, first strand: chain 'G' and resid 167 through 169 removed outlier: 4.797A pdb=" N VAL G 284 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL G 288 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS G 297 " --> pdb=" O VAL G 288 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 237 through 240 removed outlier: 3.755A pdb=" N ARG G 277 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 314 through 317 Processing sheet with id=AG2, first strand: chain 'G' and resid 382 through 383 removed outlier: 5.861A pdb=" N LEU G 382 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY H 402 " --> pdb=" O ILE H 358 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 387 through 388 removed outlier: 6.884A pdb=" N VAL G 387 " --> pdb=" O ILE G 395 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 86 through 87 Processing sheet with id=AG5, first strand: chain 'H' and resid 156 through 159 Processing sheet with id=AG6, first strand: chain 'H' and resid 167 through 169 removed outlier: 4.924A pdb=" N VAL H 284 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL H 288 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS H 297 " --> pdb=" O VAL H 288 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 237 through 240 removed outlier: 3.775A pdb=" N ARG H 277 " --> pdb=" O VAL H 240 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 314 through 317 Processing sheet with id=AG9, first strand: chain 'H' and resid 382 through 383 removed outlier: 5.897A pdb=" N LEU H 382 " --> pdb=" O VAL I 359 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY I 402 " --> pdb=" O ILE I 358 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 387 through 388 removed outlier: 6.920A pdb=" N VAL H 387 " --> pdb=" O ILE H 395 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 86 through 87 Processing sheet with id=AH3, first strand: chain 'I' and resid 154 through 159 Processing sheet with id=AH4, first strand: chain 'I' and resid 167 through 169 removed outlier: 4.905A pdb=" N VAL I 284 " --> pdb=" O ILE I 301 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL I 288 " --> pdb=" O LYS I 297 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYS I 297 " --> pdb=" O VAL I 288 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 237 through 240 removed outlier: 3.861A pdb=" N ARG I 277 " --> pdb=" O VAL I 240 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 314 through 317 Processing sheet with id=AH7, first strand: chain 'I' and resid 382 through 383 removed outlier: 3.846A pdb=" N GLY J 402 " --> pdb=" O ILE J 358 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 387 through 388 removed outlier: 6.902A pdb=" N VAL I 387 " --> pdb=" O ILE I 395 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 86 through 87 Processing sheet with id=AI1, first strand: chain 'J' and resid 154 through 159 Processing sheet with id=AI2, first strand: chain 'J' and resid 167 through 169 removed outlier: 4.802A pdb=" N VAL J 284 " --> pdb=" O ILE J 301 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL J 288 " --> pdb=" O LYS J 297 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS J 297 " --> pdb=" O VAL J 288 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 237 through 240 removed outlier: 3.813A pdb=" N ARG J 277 " --> pdb=" O VAL J 240 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 314 through 317 Processing sheet with id=AI5, first strand: chain 'J' and resid 382 through 383 removed outlier: 5.858A pdb=" N LEU J 382 " --> pdb=" O VAL K 359 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY K 402 " --> pdb=" O ILE K 358 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 387 through 388 removed outlier: 6.885A pdb=" N VAL J 387 " --> pdb=" O ILE J 395 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 86 through 87 Processing sheet with id=AI8, first strand: chain 'K' and resid 156 through 159 Processing sheet with id=AI9, first strand: chain 'K' and resid 167 through 169 removed outlier: 4.858A pdb=" N VAL K 284 " --> pdb=" O ILE K 301 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL K 288 " --> pdb=" O LYS K 297 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS K 297 " --> pdb=" O VAL K 288 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 237 through 240 removed outlier: 3.763A pdb=" N ARG K 277 " --> pdb=" O VAL K 240 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 314 through 317 Processing sheet with id=AJ3, first strand: chain 'K' and resid 387 through 388 removed outlier: 6.920A pdb=" N VAL K 387 " --> pdb=" O ILE K 395 " (cutoff:3.500A) 3182 hydrogen bonds defined for protein. 9246 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: 25.23 Time building geometry restraints manager: 22.63 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: 23527 1.33 - 1.45: 10050 1.45 - 1.57: 40366 1.57 - 1.69: 0 1.69 - 1.81: 670 Bond restraints: 74613 Sorted by residual: bond pdb=" C VAL T 29 " pdb=" N GLU T 30 " ideal model delta sigma weight residual 1.331 1.439 -0.108 1.59e-02 3.96e+03 4.61e+01 bond pdb=" C GLU P 64 " pdb=" N GLN P 65 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.47e-02 4.63e+03 1.08e+01 bond pdb=" CB PHE Q 13 " pdb=" CG PHE Q 13 " ideal model delta sigma weight residual 1.502 1.427 0.075 2.30e-02 1.89e+03 1.06e+01 bond pdb=" CD2 PHE Q 13 " pdb=" CE2 PHE Q 13 " ideal model delta sigma weight residual 1.382 1.322 0.060 3.00e-02 1.11e+03 4.05e+00 bond pdb=" CG1 ILE B 328 " pdb=" CD1 ILE B 328 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.77e+00 ... (remaining 74608 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.50: 1688 105.50 - 112.64: 37502 112.64 - 119.78: 27135 119.78 - 126.93: 33807 126.93 - 134.07: 811 Bond angle restraints: 100943 Sorted by residual: angle pdb=" C GLU P 64 " pdb=" N GLN P 65 " pdb=" CA GLN P 65 " ideal model delta sigma weight residual 120.68 132.05 -11.37 1.52e+00 4.33e-01 5.60e+01 angle pdb=" C ALA N 2 " pdb=" CA ALA N 2 " pdb=" CB ALA N 2 " ideal model delta sigma weight residual 116.54 110.54 6.00 1.15e+00 7.56e-01 2.73e+01 angle pdb=" N PRO R 121 " pdb=" CA PRO R 121 " pdb=" C PRO R 121 " ideal model delta sigma weight residual 113.98 119.67 -5.69 1.29e+00 6.01e-01 1.95e+01 angle pdb=" N PRO L 121 " pdb=" CA PRO L 121 " pdb=" C PRO L 121 " ideal model delta sigma weight residual 113.98 119.64 -5.66 1.29e+00 6.01e-01 1.93e+01 angle pdb=" C LYS M 377 " pdb=" N ARG M 378 " pdb=" CA ARG M 378 " ideal model delta sigma weight residual 123.34 117.72 5.62 1.29e+00 6.01e-01 1.90e+01 ... (remaining 100938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 41593 17.92 - 35.84: 3435 35.84 - 53.76: 442 53.76 - 71.68: 118 71.68 - 89.60: 127 Dihedral angle restraints: 45715 sinusoidal: 18691 harmonic: 27024 Sorted by residual: dihedral pdb=" CA THR T 27 " pdb=" C THR T 27 " pdb=" N ASP T 28 " pdb=" CA ASP T 28 " ideal model delta harmonic sigma weight residual 180.00 147.53 32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA ASP W 143 " pdb=" C ASP W 143 " pdb=" N ARG W 144 " pdb=" CA ARG W 144 " ideal model delta harmonic sigma weight residual 180.00 152.34 27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ASP O 143 " pdb=" C ASP O 143 " pdb=" N ARG O 144 " pdb=" CA ARG O 144 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 45712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 8551 0.057 - 0.113: 2021 0.113 - 0.170: 322 0.170 - 0.226: 17 0.226 - 0.283: 3 Chirality restraints: 10914 Sorted by residual: chirality pdb=" CA SER W 22 " pdb=" N SER W 22 " pdb=" C SER W 22 " pdb=" CB SER W 22 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ASN W 51 " pdb=" N ASN W 51 " pdb=" C ASN W 51 " pdb=" CB ASN W 51 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA PRO U 66 " pdb=" N PRO U 66 " pdb=" C PRO U 66 " pdb=" CB PRO U 66 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 10911 not shown) Planarity restraints: 13412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 202 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO C 203 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 203 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 203 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS M 202 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO M 203 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO M 203 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 203 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 202 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO F 203 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO F 203 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 203 " 0.034 5.00e-02 4.00e+02 ... (remaining 13409 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 675 2.60 - 3.18: 64587 3.18 - 3.75: 107032 3.75 - 4.33: 149947 4.33 - 4.90: 252274 Nonbonded interactions: 574515 Sorted by model distance: nonbonded pdb=" O PRO J 204 " pdb=" OG1 THR J 205 " model vdw 2.029 2.440 nonbonded pdb=" O PRO E 204 " pdb=" OG1 THR E 205 " model vdw 2.031 2.440 nonbonded pdb=" O PRO B 204 " pdb=" OG1 THR B 205 " model vdw 2.031 2.440 nonbonded pdb=" O PRO G 204 " pdb=" OG1 THR G 205 " model vdw 2.034 2.440 nonbonded pdb=" O PRO A 204 " pdb=" OG1 THR A 205 " model vdw 2.034 2.440 ... (remaining 574510 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 'M' } ncs_group { reference = (chain 'L' and resid 5 through 150) selection = (chain 'N' and resid 5 through 150) selection = (chain 'O' and resid 5 through 150) selection = (chain 'P' and resid 5 through 150) selection = chain 'Q' selection = (chain 'R' and resid 5 through 150) selection = (chain 'S' and resid 5 through 150) selection = (chain 'T' and resid 5 through 150) selection = (chain 'U' and resid 5 through 150) selection = (chain 'V' and resid 5 through 150) selection = (chain 'W' and resid 5 through 150) selection = (chain 'X' and resid 5 through 150) } 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: 7.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 27.250 Check model and map are aligned: 0.790 Set scattering table: 0.510 Process input model: 138.360 Find NCS groups from input model: 3.900 Set up NCS constraints: 0.380 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 191.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.007 0.108 74613 Z= 0.443 Angle : 0.803 11.372 100943 Z= 0.451 Chirality : 0.049 0.283 10914 Planarity : 0.006 0.063 13412 Dihedral : 13.869 89.597 28299 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 1.14 % Allowed : 10.98 % Favored : 87.88 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.55 (0.09), residues: 9152 helix: 0.92 (0.09), residues: 3754 sheet: -1.10 (0.16), residues: 1032 loop : -2.93 (0.09), residues: 4366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 215 HIS 0.006 0.002 HIS M 245 PHE 0.029 0.002 PHE Q 18 TYR 0.032 0.002 TYR I 243 ARG 0.016 0.001 ARG Q 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 771 time to evaluate : 6.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8987 (mppt) cc_final: 0.8739 (mtmt) REVERT: M 243 TYR cc_start: 0.7890 (m-80) cc_final: 0.7653 (m-10) REVERT: A 7 LYS cc_start: 0.9080 (mppt) cc_final: 0.8791 (mtmt) REVERT: A 17 ASP cc_start: 0.8260 (m-30) cc_final: 0.8035 (m-30) REVERT: A 243 TYR cc_start: 0.8040 (m-80) cc_final: 0.7345 (m-80) REVERT: B 7 LYS cc_start: 0.9025 (mppt) cc_final: 0.8595 (mptp) REVERT: B 13 MET cc_start: 0.9031 (mmm) cc_final: 0.8814 (mmm) REVERT: B 196 GLU cc_start: 0.8369 (tp30) cc_final: 0.8103 (mm-30) REVERT: B 450 MET cc_start: 0.5974 (mtp) cc_final: 0.5720 (ttt) REVERT: C 7 LYS cc_start: 0.8988 (mppt) cc_final: 0.8742 (mtmt) REVERT: D 7 LYS cc_start: 0.9080 (mppt) cc_final: 0.8790 (mtmt) REVERT: D 243 TYR cc_start: 0.8045 (m-80) cc_final: 0.7349 (m-80) REVERT: E 7 LYS cc_start: 0.9021 (mppt) cc_final: 0.8595 (mptp) REVERT: E 13 MET cc_start: 0.9131 (mmm) cc_final: 0.8692 (mmm) REVERT: E 17 ASP cc_start: 0.8492 (m-30) cc_final: 0.8256 (m-30) REVERT: E 196 GLU cc_start: 0.8367 (tp30) cc_final: 0.8100 (mm-30) REVERT: E 450 MET cc_start: 0.5962 (mtp) cc_final: 0.5699 (ttt) REVERT: F 7 LYS cc_start: 0.8985 (mppt) cc_final: 0.8740 (mtmt) REVERT: F 17 ASP cc_start: 0.8372 (m-30) cc_final: 0.8119 (m-30) REVERT: F 243 TYR cc_start: 0.7888 (m-80) cc_final: 0.7506 (m-10) REVERT: G 7 LYS cc_start: 0.9044 (mppt) cc_final: 0.8696 (mtmt) REVERT: G 17 ASP cc_start: 0.8444 (m-30) cc_final: 0.8147 (m-30) REVERT: G 243 TYR cc_start: 0.8040 (m-80) cc_final: 0.7345 (m-80) REVERT: H 7 LYS cc_start: 0.9025 (mppt) cc_final: 0.8591 (mptp) REVERT: H 13 MET cc_start: 0.9032 (mmm) cc_final: 0.8812 (mmm) REVERT: I 7 LYS cc_start: 0.8992 (mppt) cc_final: 0.8760 (mtmt) REVERT: I 17 ASP cc_start: 0.8372 (m-30) cc_final: 0.8118 (m-30) REVERT: J 7 LYS cc_start: 0.9045 (mppt) cc_final: 0.8699 (mtmt) REVERT: J 10 GLU cc_start: 0.8162 (mp0) cc_final: 0.7960 (mp0) REVERT: J 17 ASP cc_start: 0.8446 (m-30) cc_final: 0.8152 (m-30) REVERT: J 243 TYR cc_start: 0.8028 (m-80) cc_final: 0.7306 (m-80) REVERT: K 7 LYS cc_start: 0.9029 (mppt) cc_final: 0.8594 (mptp) REVERT: K 13 MET cc_start: 0.9125 (mmm) cc_final: 0.8697 (mmm) REVERT: K 17 ASP cc_start: 0.8491 (m-30) cc_final: 0.8254 (m-30) REVERT: N 64 GLU cc_start: 0.7575 (pm20) cc_final: 0.7237 (pm20) REVERT: O 1 MET cc_start: 0.4527 (tmm) cc_final: 0.3629 (tpt) REVERT: P 61 THR cc_start: 0.8829 (t) cc_final: 0.8590 (p) REVERT: P 69 ASP cc_start: 0.8863 (m-30) cc_final: 0.8650 (m-30) REVERT: P 90 MET cc_start: 0.8794 (ptm) cc_final: 0.8566 (ptm) REVERT: R 108 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8402 (ttm-80) REVERT: S 23 ASN cc_start: 0.8213 (m110) cc_final: 0.7867 (m110) REVERT: S 30 GLU cc_start: 0.7781 (tt0) cc_final: 0.7491 (tt0) REVERT: S 64 GLU cc_start: 0.8435 (mp0) cc_final: 0.8100 (mp0) REVERT: T 1 MET cc_start: 0.4223 (pmm) cc_final: 0.3024 (ttt) REVERT: T 69 ASP cc_start: 0.8828 (m-30) cc_final: 0.8561 (m-30) REVERT: U 64 GLU cc_start: 0.6973 (mp0) cc_final: 0.6608 (mp0) REVERT: V 69 ASP cc_start: 0.8840 (m-30) cc_final: 0.8600 (m-30) REVERT: L 1 MET cc_start: 0.3739 (mmp) cc_final: 0.3161 (mmt) outliers start: 2 outliers final: 0 residues processed: 773 average time/residue: 1.7810 time to fit residues: 1748.4288 Evaluate side-chains 629 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 629 time to evaluate : 6.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 779 optimal weight: 0.0040 chunk 699 optimal weight: 1.9990 chunk 388 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 471 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 chunk 723 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 439 optimal weight: 5.9990 chunk 538 optimal weight: 4.9990 chunk 838 optimal weight: 0.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** B 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN ** D 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 613 GLN ** E 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 652 GLN ** F 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 652 GLN ** G 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 652 GLN ** I 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN ** J 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 613 GLN ** K 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 652 GLN P 23 ASN Q 23 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 74613 Z= 0.216 Angle : 0.661 7.912 100943 Z= 0.350 Chirality : 0.044 0.200 10914 Planarity : 0.006 0.062 13412 Dihedral : 4.948 31.147 10244 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.75 % Favored : 88.41 % Rotamer: Outliers : 0.79 % Allowed : 6.58 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -1.23 (0.09), residues: 9152 helix: 1.12 (0.09), residues: 3853 sheet: -0.69 (0.17), residues: 972 loop : -2.81 (0.09), residues: 4327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 215 HIS 0.010 0.001 HIS G 245 PHE 0.033 0.002 PHE Q 13 TYR 0.029 0.002 TYR J 243 ARG 0.006 0.000 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 708 time to evaluate : 6.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.9018 (mppt) cc_final: 0.8587 (mtmt) REVERT: A 17 ASP cc_start: 0.8080 (m-30) cc_final: 0.7863 (m-30) REVERT: A 243 TYR cc_start: 0.7987 (m-80) cc_final: 0.7262 (m-80) REVERT: B 7 LYS cc_start: 0.8949 (mppt) cc_final: 0.8313 (mptp) REVERT: B 609 GLN cc_start: 0.8641 (tp40) cc_final: 0.8324 (mt0) REVERT: C 255 ASP cc_start: 0.4327 (OUTLIER) cc_final: 0.3821 (t70) REVERT: D 7 LYS cc_start: 0.9062 (mppt) cc_final: 0.8684 (mtmt) REVERT: D 243 TYR cc_start: 0.7986 (m-80) cc_final: 0.7296 (m-80) REVERT: E 7 LYS cc_start: 0.8969 (mppt) cc_final: 0.8604 (mptp) REVERT: E 13 MET cc_start: 0.9055 (mmm) cc_final: 0.8632 (mmm) REVERT: E 17 ASP cc_start: 0.8315 (m-30) cc_final: 0.8044 (m-30) REVERT: E 609 GLN cc_start: 0.8644 (tp40) cc_final: 0.8327 (mt0) REVERT: F 17 ASP cc_start: 0.8291 (m-30) cc_final: 0.8017 (m-30) REVERT: F 609 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8530 (mt0) REVERT: G 7 LYS cc_start: 0.9016 (mppt) cc_final: 0.8552 (mtmt) REVERT: G 17 ASP cc_start: 0.8262 (m-30) cc_final: 0.7931 (m-30) REVERT: G 243 TYR cc_start: 0.7983 (m-80) cc_final: 0.7257 (m-80) REVERT: H 7 LYS cc_start: 0.8951 (mppt) cc_final: 0.8316 (mptp) REVERT: H 196 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8118 (tm-30) REVERT: H 627 MET cc_start: 0.8376 (pmm) cc_final: 0.8023 (ppp) REVERT: I 7 LYS cc_start: 0.8931 (mppt) cc_final: 0.8708 (mppt) REVERT: J 7 LYS cc_start: 0.9047 (mppt) cc_final: 0.8719 (mtmt) REVERT: J 10 GLU cc_start: 0.8098 (mp0) cc_final: 0.7858 (mp0) REVERT: J 17 ASP cc_start: 0.8303 (m-30) cc_final: 0.7973 (m-30) REVERT: J 207 LEU cc_start: 0.9154 (pt) cc_final: 0.8925 (pp) REVERT: J 243 TYR cc_start: 0.7972 (m-80) cc_final: 0.7265 (m-80) REVERT: K 7 LYS cc_start: 0.8955 (mppt) cc_final: 0.8319 (mptp) REVERT: K 13 MET cc_start: 0.9048 (mmm) cc_final: 0.8626 (mmm) REVERT: K 17 ASP cc_start: 0.8316 (m-30) cc_final: 0.8045 (m-30) REVERT: K 196 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8103 (tm-30) REVERT: K 609 GLN cc_start: 0.8652 (tp40) cc_final: 0.8364 (mt0) REVERT: O 108 ARG cc_start: 0.8651 (ttm-80) cc_final: 0.8290 (ttm-80) REVERT: P 69 ASP cc_start: 0.8834 (m-30) cc_final: 0.8579 (m-30) REVERT: P 90 MET cc_start: 0.8696 (ptm) cc_final: 0.8451 (ptm) REVERT: R 30 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: S 30 GLU cc_start: 0.7548 (tt0) cc_final: 0.7267 (tt0) REVERT: S 64 GLU cc_start: 0.8407 (mp0) cc_final: 0.8125 (mp0) REVERT: T 1 MET cc_start: 0.4419 (pmm) cc_final: 0.3195 (ttt) REVERT: T 64 GLU cc_start: 0.7686 (pm20) cc_final: 0.7461 (pm20) REVERT: T 69 ASP cc_start: 0.8807 (m-30) cc_final: 0.8502 (m-30) REVERT: V 69 ASP cc_start: 0.8785 (m-30) cc_final: 0.8495 (m-30) REVERT: L 1 MET cc_start: 0.3733 (mmp) cc_final: 0.3160 (mmt) REVERT: L 23 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6570 (m110) outliers start: 61 outliers final: 19 residues processed: 733 average time/residue: 1.6954 time to fit residues: 1597.6029 Evaluate side-chains 663 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 641 time to evaluate : 6.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 44 MET Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain R residue 30 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain L residue 23 ASN Chi-restraints excluded: chain L residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 465 optimal weight: 7.9990 chunk 260 optimal weight: 0.9990 chunk 697 optimal weight: 0.4980 chunk 570 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 839 optimal weight: 9.9990 chunk 907 optimal weight: 9.9990 chunk 747 optimal weight: 0.9980 chunk 832 optimal weight: 7.9990 chunk 286 optimal weight: 0.1980 chunk 673 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 652 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 631 GLN C 645 GLN C 652 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 645 GLN F 645 GLN F 652 GLN ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 451 ASN ** H 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 645 GLN ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 645 GLN I 652 GLN ** J 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 451 ASN ** K 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN W 32 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 74613 Z= 0.177 Angle : 0.619 8.185 100943 Z= 0.322 Chirality : 0.042 0.184 10914 Planarity : 0.005 0.062 13412 Dihedral : 4.630 30.318 10244 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.78 % Allowed : 10.73 % Favored : 88.49 % Rotamer: Outliers : 1.20 % Allowed : 8.75 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.09), residues: 9152 helix: 1.38 (0.09), residues: 3852 sheet: -0.66 (0.17), residues: 1008 loop : -2.71 (0.09), residues: 4292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 215 HIS 0.004 0.001 HIS C 245 PHE 0.028 0.001 PHE Q 18 TYR 0.027 0.001 TYR D 243 ARG 0.009 0.000 ARG E 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 695 time to evaluate : 6.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8950 (mppt) cc_final: 0.8580 (mptp) REVERT: M 255 ASP cc_start: 0.4469 (OUTLIER) cc_final: 0.3923 (t70) REVERT: A 7 LYS cc_start: 0.8800 (mppt) cc_final: 0.8529 (mppt) REVERT: A 17 ASP cc_start: 0.8031 (m-30) cc_final: 0.7800 (m-30) REVERT: A 243 TYR cc_start: 0.8017 (m-80) cc_final: 0.7298 (m-80) REVERT: B 7 LYS cc_start: 0.8676 (mppt) cc_final: 0.8311 (mptp) REVERT: B 17 ASP cc_start: 0.8088 (m-30) cc_final: 0.7828 (m-30) REVERT: B 196 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 609 GLN cc_start: 0.8710 (tp40) cc_final: 0.8469 (tp-100) REVERT: B 627 MET cc_start: 0.8438 (ppp) cc_final: 0.8073 (ppp) REVERT: C 7 LYS cc_start: 0.8707 (mppt) cc_final: 0.8448 (mppt) REVERT: C 243 TYR cc_start: 0.7745 (m-10) cc_final: 0.7469 (m-10) REVERT: C 627 MET cc_start: 0.8538 (pmm) cc_final: 0.7991 (pp-130) REVERT: D 7 LYS cc_start: 0.8815 (mppt) cc_final: 0.8539 (mppt) REVERT: D 243 TYR cc_start: 0.8041 (m-80) cc_final: 0.7402 (m-80) REVERT: E 7 LYS cc_start: 0.8864 (mppt) cc_final: 0.8471 (mptp) REVERT: E 13 MET cc_start: 0.9072 (mmm) cc_final: 0.8669 (mmm) REVERT: E 17 ASP cc_start: 0.8239 (m-30) cc_final: 0.7975 (m-30) REVERT: E 196 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8117 (mm-30) REVERT: E 609 GLN cc_start: 0.8713 (tp40) cc_final: 0.8471 (tp-100) REVERT: F 7 LYS cc_start: 0.8688 (mppt) cc_final: 0.8428 (mppt) REVERT: F 255 ASP cc_start: 0.4366 (OUTLIER) cc_final: 0.3828 (t70) REVERT: G 7 LYS cc_start: 0.8784 (mppt) cc_final: 0.8517 (mppt) REVERT: G 17 ASP cc_start: 0.8245 (m-30) cc_final: 0.7943 (m-30) REVERT: G 243 TYR cc_start: 0.8018 (m-80) cc_final: 0.7357 (m-80) REVERT: H 7 LYS cc_start: 0.8680 (mppt) cc_final: 0.8313 (mptp) REVERT: H 409 MET cc_start: 0.9017 (tmt) cc_final: 0.8675 (tpp) REVERT: H 609 GLN cc_start: 0.8724 (tp40) cc_final: 0.8407 (mt0) REVERT: I 7 LYS cc_start: 0.8679 (mppt) cc_final: 0.8343 (mtmm) REVERT: I 255 ASP cc_start: 0.4396 (OUTLIER) cc_final: 0.3786 (t70) REVERT: J 7 LYS cc_start: 0.9011 (mppt) cc_final: 0.8729 (mppt) REVERT: J 10 GLU cc_start: 0.8021 (mp0) cc_final: 0.7767 (mp0) REVERT: J 17 ASP cc_start: 0.8256 (m-30) cc_final: 0.7938 (m-30) REVERT: J 243 TYR cc_start: 0.8010 (m-80) cc_final: 0.7312 (m-80) REVERT: K 7 LYS cc_start: 0.8687 (mppt) cc_final: 0.8318 (mptp) REVERT: K 13 MET cc_start: 0.9065 (mmm) cc_final: 0.8657 (mmm) REVERT: K 17 ASP cc_start: 0.8251 (m-30) cc_final: 0.7964 (m-30) REVERT: K 609 GLN cc_start: 0.8716 (tp40) cc_final: 0.8421 (mt0) REVERT: K 627 MET cc_start: 0.8605 (ppp) cc_final: 0.8342 (ppp) REVERT: O 108 ARG cc_start: 0.8615 (ttm-80) cc_final: 0.8281 (ttm-80) REVERT: P 69 ASP cc_start: 0.8827 (m-30) cc_final: 0.8535 (m-30) REVERT: P 90 MET cc_start: 0.8643 (ptm) cc_final: 0.8376 (ptm) REVERT: R 30 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: S 1 MET cc_start: 0.5361 (OUTLIER) cc_final: 0.3145 (pmt) REVERT: S 30 GLU cc_start: 0.7382 (tt0) cc_final: 0.7164 (tt0) REVERT: S 61 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7630 (m) REVERT: S 64 GLU cc_start: 0.8375 (mp0) cc_final: 0.8069 (mp0) REVERT: T 1 MET cc_start: 0.3863 (pmm) cc_final: 0.2942 (ttt) REVERT: T 64 GLU cc_start: 0.7709 (pm20) cc_final: 0.7453 (pm20) REVERT: T 69 ASP cc_start: 0.8769 (m-30) cc_final: 0.8442 (m-30) REVERT: V 69 ASP cc_start: 0.8739 (m-30) cc_final: 0.8403 (m-30) REVERT: L 1 MET cc_start: 0.3729 (mmp) cc_final: 0.3169 (mmt) REVERT: L 23 ASN cc_start: 0.6822 (OUTLIER) cc_final: 0.6571 (m110) REVERT: L 108 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8271 (ttm-80) outliers start: 93 outliers final: 53 residues processed: 753 average time/residue: 1.6348 time to fit residues: 1593.4759 Evaluate side-chains 709 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 649 time to evaluate : 6.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 555 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 516 VAL Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 578 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain I residue 255 ASP Chi-restraints excluded: chain I residue 516 VAL Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 578 ASP Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 28 ASP Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 30 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain L residue 23 ASN Chi-restraints excluded: chain L residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 829 optimal weight: 2.9990 chunk 631 optimal weight: 8.9990 chunk 435 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 400 optimal weight: 9.9990 chunk 563 optimal weight: 9.9990 chunk 842 optimal weight: 5.9990 chunk 892 optimal weight: 8.9990 chunk 440 optimal weight: 7.9990 chunk 798 optimal weight: 8.9990 chunk 240 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 GLN ** K 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN Q 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 74613 Z= 0.315 Angle : 0.665 8.506 100943 Z= 0.347 Chirality : 0.045 0.324 10914 Planarity : 0.006 0.059 13412 Dihedral : 4.791 31.476 10244 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.32 % Favored : 87.86 % Rotamer: Outliers : 2.07 % Allowed : 10.52 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.09), residues: 9152 helix: 1.42 (0.09), residues: 3852 sheet: -0.80 (0.17), residues: 1032 loop : -2.74 (0.09), residues: 4268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 215 HIS 0.006 0.001 HIS V 80 PHE 0.031 0.002 PHE Q 18 TYR 0.025 0.002 TYR A 243 ARG 0.007 0.000 ARG E 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 663 time to evaluate : 6.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 243 TYR cc_start: 0.7904 (m-10) cc_final: 0.7675 (m-10) REVERT: M 255 ASP cc_start: 0.4719 (OUTLIER) cc_final: 0.4016 (t0) REVERT: M 510 ARG cc_start: 0.6773 (pmt-80) cc_final: 0.6387 (ppt170) REVERT: A 17 ASP cc_start: 0.8088 (m-30) cc_final: 0.7821 (m-30) REVERT: A 241 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7627 (pt) REVERT: A 243 TYR cc_start: 0.8114 (m-80) cc_final: 0.7335 (m-80) REVERT: B 7 LYS cc_start: 0.8696 (mppt) cc_final: 0.8323 (mptp) REVERT: B 17 ASP cc_start: 0.8120 (m-30) cc_final: 0.7839 (m-30) REVERT: B 241 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7732 (pt) REVERT: C 255 ASP cc_start: 0.4664 (OUTLIER) cc_final: 0.3918 (t70) REVERT: D 17 ASP cc_start: 0.8089 (m-30) cc_final: 0.7881 (m-30) REVERT: D 241 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7653 (pt) REVERT: D 243 TYR cc_start: 0.8109 (m-80) cc_final: 0.7463 (m-80) REVERT: E 7 LYS cc_start: 0.8931 (mppt) cc_final: 0.8232 (mptt) REVERT: E 13 MET cc_start: 0.9095 (mmm) cc_final: 0.8647 (mmm) REVERT: E 17 ASP cc_start: 0.8274 (m-30) cc_final: 0.7995 (m-30) REVERT: E 241 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7637 (pt) REVERT: F 243 TYR cc_start: 0.7919 (m-10) cc_final: 0.7512 (m-10) REVERT: F 255 ASP cc_start: 0.4830 (OUTLIER) cc_final: 0.4347 (t0) REVERT: F 613 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7664 (tm-30) REVERT: G 17 ASP cc_start: 0.8263 (m-30) cc_final: 0.7931 (m-30) REVERT: G 241 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7481 (pt) REVERT: G 243 TYR cc_start: 0.8110 (m-80) cc_final: 0.7455 (m-80) REVERT: H 7 LYS cc_start: 0.8707 (mppt) cc_final: 0.8483 (mtmm) REVERT: H 17 ASP cc_start: 0.8113 (m-30) cc_final: 0.7830 (m-30) REVERT: H 409 MET cc_start: 0.9043 (tmt) cc_final: 0.8678 (tpp) REVERT: H 609 GLN cc_start: 0.8742 (tp40) cc_final: 0.8528 (tp-100) REVERT: I 243 TYR cc_start: 0.7902 (m-80) cc_final: 0.7525 (m-10) REVERT: I 510 ARG cc_start: 0.6780 (pmt-80) cc_final: 0.6393 (ppt170) REVERT: J 7 LYS cc_start: 0.9045 (mppt) cc_final: 0.8755 (mptt) REVERT: J 17 ASP cc_start: 0.8278 (m-30) cc_final: 0.7934 (m-30) REVERT: J 241 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7621 (pt) REVERT: J 243 TYR cc_start: 0.8103 (m-80) cc_final: 0.7356 (m-80) REVERT: K 7 LYS cc_start: 0.8712 (mppt) cc_final: 0.8333 (mptp) REVERT: K 13 MET cc_start: 0.9126 (mmm) cc_final: 0.8776 (mmm) REVERT: K 17 ASP cc_start: 0.8265 (m-30) cc_final: 0.7983 (m-30) REVERT: K 241 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7728 (pt) REVERT: K 609 GLN cc_start: 0.8718 (tp40) cc_final: 0.8508 (tp-100) REVERT: P 1 MET cc_start: 0.4449 (OUTLIER) cc_final: 0.3962 (tpt) REVERT: P 69 ASP cc_start: 0.8847 (m-30) cc_final: 0.8560 (m-30) REVERT: P 90 MET cc_start: 0.8722 (ptm) cc_final: 0.8450 (ptm) REVERT: R 123 MET cc_start: 0.8581 (mtm) cc_final: 0.8092 (mtp) REVERT: S 1 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5648 (tmt) REVERT: S 30 GLU cc_start: 0.7646 (tt0) cc_final: 0.7430 (tt0) REVERT: S 64 GLU cc_start: 0.8476 (mp0) cc_final: 0.8150 (mp0) REVERT: T 1 MET cc_start: 0.4061 (pmm) cc_final: 0.2966 (ttt) REVERT: T 64 GLU cc_start: 0.7890 (pm20) cc_final: 0.7565 (pm20) REVERT: T 69 ASP cc_start: 0.8810 (m-30) cc_final: 0.8500 (m-30) REVERT: V 69 ASP cc_start: 0.8797 (m-30) cc_final: 0.8487 (m-30) REVERT: L 1 MET cc_start: 0.3769 (mmp) cc_final: 0.3196 (mmt) REVERT: L 23 ASN cc_start: 0.6813 (OUTLIER) cc_final: 0.6586 (m110) outliers start: 160 outliers final: 76 residues processed: 779 average time/residue: 1.5437 time to fit residues: 1572.5307 Evaluate side-chains 721 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 632 time to evaluate : 6.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 455 MET Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 555 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain F residue 516 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 578 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain H residue 555 LEU Chi-restraints excluded: chain I residue 255 ASP Chi-restraints excluded: chain I residue 455 MET Chi-restraints excluded: chain I residue 516 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 578 ASP Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 455 MET Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 555 LEU Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 28 ASP Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 138 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain L residue 23 ASN Chi-restraints excluded: chain L residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 743 optimal weight: 8.9990 chunk 506 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 664 optimal weight: 4.9990 chunk 368 optimal weight: 50.0000 chunk 761 optimal weight: 0.7980 chunk 616 optimal weight: 50.0000 chunk 1 optimal weight: 2.9990 chunk 455 optimal weight: 0.0870 chunk 800 optimal weight: 9.9990 chunk 225 optimal weight: 0.0670 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 645 GLN A 645 GLN B 258 GLN B 587 GLN D 258 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 587 GLN G 645 GLN H 587 GLN ** H 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 GLN J 645 GLN K 587 GLN ** K 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 645 GLN P 23 ASN V 135 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 74613 Z= 0.162 Angle : 0.613 12.154 100943 Z= 0.317 Chirality : 0.042 0.244 10914 Planarity : 0.005 0.059 13412 Dihedral : 4.468 30.302 10244 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.22 % Favored : 88.98 % Rotamer: Outliers : 1.96 % Allowed : 11.61 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.09), residues: 9152 helix: 1.57 (0.08), residues: 3852 sheet: -0.45 (0.17), residues: 1020 loop : -2.75 (0.09), residues: 4280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 215 HIS 0.004 0.001 HIS C 245 PHE 0.030 0.001 PHE Q 18 TYR 0.024 0.001 TYR J 243 ARG 0.007 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 673 time to evaluate : 6.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8847 (mppt) cc_final: 0.8197 (mtmm) REVERT: M 255 ASP cc_start: 0.4555 (OUTLIER) cc_final: 0.3775 (t70) REVERT: A 7 LYS cc_start: 0.8533 (mppt) cc_final: 0.8328 (mtmm) REVERT: A 241 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7309 (pt) REVERT: A 243 TYR cc_start: 0.8051 (m-80) cc_final: 0.7518 (m-80) REVERT: B 7 LYS cc_start: 0.8669 (mppt) cc_final: 0.8384 (mtmm) REVERT: B 17 ASP cc_start: 0.8046 (m-30) cc_final: 0.7804 (m-30) REVERT: B 255 ASP cc_start: 0.4299 (OUTLIER) cc_final: 0.3971 (t70) REVERT: B 609 GLN cc_start: 0.8653 (tp40) cc_final: 0.8283 (mt0) REVERT: B 620 MET cc_start: 0.7962 (tmm) cc_final: 0.7714 (mtp) REVERT: C 7 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8175 (mtmm) REVERT: C 243 TYR cc_start: 0.7678 (m-10) cc_final: 0.7439 (m-10) REVERT: C 255 ASP cc_start: 0.4632 (OUTLIER) cc_final: 0.3972 (t0) REVERT: D 7 LYS cc_start: 0.8534 (mppt) cc_final: 0.8330 (mtmm) REVERT: D 241 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7259 (pt) REVERT: D 243 TYR cc_start: 0.8054 (m-80) cc_final: 0.7578 (m-80) REVERT: E 7 LYS cc_start: 0.8576 (mppt) cc_final: 0.8302 (mtmm) REVERT: E 13 MET cc_start: 0.9109 (mmm) cc_final: 0.8657 (mmm) REVERT: E 17 ASP cc_start: 0.8227 (m-30) cc_final: 0.7950 (m-30) REVERT: E 609 GLN cc_start: 0.8650 (tp40) cc_final: 0.8288 (mt0) REVERT: F 241 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7511 (pt) REVERT: F 243 TYR cc_start: 0.7754 (m-10) cc_final: 0.7175 (m-10) REVERT: F 255 ASP cc_start: 0.4682 (OUTLIER) cc_final: 0.3690 (t0) REVERT: F 610 MET cc_start: 0.9060 (mmm) cc_final: 0.8565 (mmp) REVERT: G 7 LYS cc_start: 0.8524 (mppt) cc_final: 0.8314 (mtmm) REVERT: G 17 ASP cc_start: 0.8243 (m-30) cc_final: 0.7935 (m-30) REVERT: G 241 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7210 (pt) REVERT: G 243 TYR cc_start: 0.8052 (m-80) cc_final: 0.7492 (m-80) REVERT: H 7 LYS cc_start: 0.8676 (mppt) cc_final: 0.8272 (mptp) REVERT: H 17 ASP cc_start: 0.8040 (m-30) cc_final: 0.7797 (m-30) REVERT: H 241 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7445 (pt) REVERT: H 409 MET cc_start: 0.8955 (tmt) cc_final: 0.8732 (tpp) REVERT: H 609 GLN cc_start: 0.8757 (tp40) cc_final: 0.8535 (tp-100) REVERT: I 243 TYR cc_start: 0.7524 (m-10) cc_final: 0.7223 (m-10) REVERT: I 255 ASP cc_start: 0.4582 (OUTLIER) cc_final: 0.3896 (t0) REVERT: J 17 ASP cc_start: 0.8295 (m-30) cc_final: 0.7990 (m-30) REVERT: J 241 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7342 (pt) REVERT: J 243 TYR cc_start: 0.8037 (m-80) cc_final: 0.7404 (m-80) REVERT: K 7 LYS cc_start: 0.8712 (mppt) cc_final: 0.8441 (mtmm) REVERT: K 13 MET cc_start: 0.9132 (mmm) cc_final: 0.8679 (mmm) REVERT: K 17 ASP cc_start: 0.8226 (m-30) cc_final: 0.7947 (m-30) REVERT: K 255 ASP cc_start: 0.4314 (OUTLIER) cc_final: 0.3957 (t70) REVERT: K 609 GLN cc_start: 0.8737 (tp40) cc_final: 0.8517 (tp-100) REVERT: O 1 MET cc_start: 0.3235 (tmm) cc_final: 0.2045 (ppp) REVERT: O 108 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8250 (ttm-80) REVERT: P 1 MET cc_start: 0.4149 (OUTLIER) cc_final: 0.3735 (tpt) REVERT: P 30 GLU cc_start: 0.7516 (tt0) cc_final: 0.7098 (tm-30) REVERT: P 69 ASP cc_start: 0.8809 (m-30) cc_final: 0.8492 (m-30) REVERT: P 90 MET cc_start: 0.8646 (ptm) cc_final: 0.8386 (ptm) REVERT: Q 30 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6517 (tt0) REVERT: R 30 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6624 (mt-10) REVERT: S 1 MET cc_start: 0.5658 (OUTLIER) cc_final: 0.3684 (pmt) REVERT: S 30 GLU cc_start: 0.7479 (tt0) cc_final: 0.7240 (tt0) REVERT: S 64 GLU cc_start: 0.8351 (mp0) cc_final: 0.8036 (mp0) REVERT: T 1 MET cc_start: 0.4025 (pmm) cc_final: 0.2939 (ttt) REVERT: T 64 GLU cc_start: 0.7741 (pm20) cc_final: 0.7418 (pm20) REVERT: T 69 ASP cc_start: 0.8775 (m-30) cc_final: 0.8437 (m-30) REVERT: V 69 ASP cc_start: 0.8785 (m-30) cc_final: 0.8440 (m-30) REVERT: L 1 MET cc_start: 0.3750 (mmp) cc_final: 0.3163 (mmt) REVERT: L 108 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8243 (ttm-80) outliers start: 152 outliers final: 76 residues processed: 782 average time/residue: 1.5690 time to fit residues: 1603.7880 Evaluate side-chains 719 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 627 time to evaluate : 6.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 555 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 516 VAL Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 578 ASP Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain H residue 555 LEU Chi-restraints excluded: chain H residue 558 ASP Chi-restraints excluded: chain H residue 578 ASP Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 255 ASP Chi-restraints excluded: chain I residue 516 VAL Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 578 ASP Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 455 MET Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 555 LEU Chi-restraints excluded: chain K residue 558 ASP Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain Q residue 18 PHE Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 30 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 300 optimal weight: 0.0970 chunk 803 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 523 optimal weight: 7.9990 chunk 220 optimal weight: 0.0470 chunk 893 optimal weight: 10.0000 chunk 741 optimal weight: 30.0000 chunk 413 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 295 optimal weight: 9.9990 chunk 468 optimal weight: 4.9990 overall best weight: 3.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 GLN ** H 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 74613 Z= 0.252 Angle : 0.642 9.639 100943 Z= 0.332 Chirality : 0.043 0.215 10914 Planarity : 0.005 0.059 13412 Dihedral : 4.531 30.769 10244 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.85 % Allowed : 10.81 % Favored : 88.34 % Rotamer: Outliers : 2.03 % Allowed : 12.46 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.09), residues: 9152 helix: 1.60 (0.08), residues: 3864 sheet: -0.67 (0.17), residues: 1032 loop : -2.71 (0.09), residues: 4256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 215 HIS 0.004 0.001 HIS V 80 PHE 0.032 0.002 PHE Q 18 TYR 0.025 0.001 TYR A 243 ARG 0.007 0.000 ARG M 487 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 640 time to evaluate : 6.275 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: M 255 ASP cc_start: 0.4707 (OUTLIER) cc_final: 0.4039 (t0) REVERT: A 241 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7444 (pt) REVERT: A 243 TYR cc_start: 0.8070 (m-80) cc_final: 0.7578 (m-80) REVERT: B 7 LYS cc_start: 0.8704 (mppt) cc_final: 0.8409 (mptt) REVERT: B 17 ASP cc_start: 0.8112 (m-30) cc_final: 0.7815 (m-30) REVERT: B 241 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7497 (pt) REVERT: B 589 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8540 (pt) REVERT: B 601 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: B 609 GLN cc_start: 0.8672 (tp40) cc_final: 0.8281 (mt0) REVERT: B 620 MET cc_start: 0.8066 (tmm) cc_final: 0.7716 (mtp) REVERT: C 243 TYR cc_start: 0.7598 (m-10) cc_final: 0.7366 (m-10) REVERT: C 255 ASP cc_start: 0.4602 (OUTLIER) cc_final: 0.3901 (t70) REVERT: D 7 LYS cc_start: 0.8635 (mppt) cc_final: 0.8370 (mtmm) REVERT: D 241 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7596 (pt) REVERT: D 243 TYR cc_start: 0.8063 (m-80) cc_final: 0.7548 (m-80) REVERT: E 7 LYS cc_start: 0.8554 (mppt) cc_final: 0.8299 (mtmm) REVERT: E 13 MET cc_start: 0.9088 (mmm) cc_final: 0.8665 (mmm) REVERT: E 17 ASP cc_start: 0.8271 (m-30) cc_final: 0.7977 (m-30) REVERT: E 241 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7507 (pt) REVERT: E 589 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8571 (pt) REVERT: E 609 GLN cc_start: 0.8670 (tp40) cc_final: 0.8266 (mt0) REVERT: F 241 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7690 (pt) REVERT: F 243 TYR cc_start: 0.7559 (m-10) cc_final: 0.7327 (m-10) REVERT: F 255 ASP cc_start: 0.4764 (OUTLIER) cc_final: 0.3922 (t0) REVERT: F 409 MET cc_start: 0.8844 (tmm) cc_final: 0.8589 (tpt) REVERT: G 17 ASP cc_start: 0.8251 (m-30) cc_final: 0.7931 (m-30) REVERT: G 241 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7417 (pt) REVERT: G 243 TYR cc_start: 0.8065 (m-80) cc_final: 0.7567 (m-80) REVERT: H 7 LYS cc_start: 0.8691 (mppt) cc_final: 0.8389 (mptt) REVERT: H 17 ASP cc_start: 0.8110 (m-30) cc_final: 0.7836 (m-30) REVERT: H 241 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7543 (pt) REVERT: H 243 TYR cc_start: 0.7661 (m-10) cc_final: 0.7266 (m-10) REVERT: H 409 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8662 (tpp) REVERT: H 601 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: I 255 ASP cc_start: 0.4628 (OUTLIER) cc_final: 0.3745 (t70) REVERT: J 17 ASP cc_start: 0.8211 (m-30) cc_final: 0.7879 (m-30) REVERT: J 241 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7443 (pt) REVERT: J 243 TYR cc_start: 0.8057 (m-80) cc_final: 0.7545 (m-80) REVERT: K 7 LYS cc_start: 0.8698 (mppt) cc_final: 0.8396 (mptt) REVERT: K 13 MET cc_start: 0.9079 (mmm) cc_final: 0.8658 (mmm) REVERT: K 17 ASP cc_start: 0.8267 (m-30) cc_final: 0.7970 (m-30) REVERT: K 241 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7528 (pt) REVERT: K 601 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7354 (pm20) REVERT: K 609 GLN cc_start: 0.8770 (tp40) cc_final: 0.8557 (tp-100) REVERT: O 1 MET cc_start: 0.3090 (tmm) cc_final: 0.2063 (ppp) REVERT: P 1 MET cc_start: 0.4444 (OUTLIER) cc_final: 0.4016 (tpt) REVERT: P 30 GLU cc_start: 0.7631 (tt0) cc_final: 0.6570 (mt-10) REVERT: P 69 ASP cc_start: 0.8828 (m-30) cc_final: 0.8514 (m-30) REVERT: P 90 MET cc_start: 0.8675 (ptm) cc_final: 0.8396 (ptm) REVERT: Q 30 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6574 (tt0) REVERT: R 30 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: S 30 GLU cc_start: 0.7635 (tt0) cc_final: 0.7412 (tt0) REVERT: S 64 GLU cc_start: 0.8403 (mp0) cc_final: 0.8072 (mp0) REVERT: T 1 MET cc_start: 0.4285 (pmm) cc_final: 0.3078 (ttt) REVERT: T 64 GLU cc_start: 0.7864 (pm20) cc_final: 0.7527 (pm20) REVERT: T 69 ASP cc_start: 0.8783 (m-30) cc_final: 0.8465 (m-30) REVERT: V 69 ASP cc_start: 0.8766 (m-30) cc_final: 0.8416 (m-30) REVERT: L 23 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6597 (m110) outliers start: 157 outliers final: 94 residues processed: 757 average time/residue: 1.5624 time to fit residues: 1550.6652 Evaluate side-chains 743 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 627 time to evaluate : 6.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 273 GLU Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 455 MET Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 555 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 555 LEU Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain F residue 516 VAL Chi-restraints excluded: chain F residue 555 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 578 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain H residue 558 ASP Chi-restraints excluded: chain H residue 578 ASP Chi-restraints excluded: chain H residue 601 GLU Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 255 ASP Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 455 MET Chi-restraints excluded: chain I residue 516 VAL Chi-restraints excluded: chain I residue 555 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 578 ASP Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 455 MET Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 558 ASP Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain K residue 601 GLU Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 28 ASP Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 18 PHE Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 30 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain L residue 23 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 861 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 508 optimal weight: 10.0000 chunk 652 optimal weight: 0.6980 chunk 505 optimal weight: 3.9990 chunk 751 optimal weight: 3.9990 chunk 498 optimal weight: 10.0000 chunk 889 optimal weight: 1.9990 chunk 556 optimal weight: 50.0000 chunk 542 optimal weight: 0.2980 chunk 410 optimal weight: 4.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 645 GLN ** H 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 519 ASN ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 74613 Z= 0.164 Angle : 0.612 10.243 100943 Z= 0.315 Chirality : 0.042 0.196 10914 Planarity : 0.005 0.058 13412 Dihedral : 4.356 30.131 10244 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.79 % Allowed : 10.06 % Favored : 89.15 % Rotamer: Outliers : 2.04 % Allowed : 13.04 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.09), residues: 9152 helix: 1.65 (0.08), residues: 3864 sheet: -0.41 (0.17), residues: 1020 loop : -2.71 (0.09), residues: 4268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 215 HIS 0.003 0.001 HIS J 9 PHE 0.025 0.001 PHE Q 18 TYR 0.025 0.001 TYR I 243 ARG 0.007 0.000 ARG J 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 650 time to evaluate : 6.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 255 ASP cc_start: 0.4601 (OUTLIER) cc_final: 0.4055 (t0) REVERT: A 241 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7239 (pt) REVERT: A 243 TYR cc_start: 0.8060 (m-80) cc_final: 0.7647 (m-80) REVERT: B 7 LYS cc_start: 0.8653 (mppt) cc_final: 0.8359 (mtmm) REVERT: B 13 MET cc_start: 0.8811 (mmm) cc_final: 0.8562 (mmm) REVERT: B 17 ASP cc_start: 0.8026 (m-30) cc_final: 0.7733 (m-30) REVERT: B 196 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8035 (mm-30) REVERT: B 241 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7341 (pt) REVERT: B 243 TYR cc_start: 0.7281 (m-10) cc_final: 0.7022 (m-10) REVERT: B 601 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: B 620 MET cc_start: 0.7918 (tmm) cc_final: 0.7621 (mtp) REVERT: C 255 ASP cc_start: 0.4542 (OUTLIER) cc_final: 0.3810 (t70) REVERT: C 426 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7846 (tm-30) REVERT: C 582 GLU cc_start: 0.8325 (tt0) cc_final: 0.8079 (tm-30) REVERT: D 7 LYS cc_start: 0.8598 (mppt) cc_final: 0.8323 (mtmm) REVERT: D 241 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7223 (pt) REVERT: D 243 TYR cc_start: 0.8065 (m-80) cc_final: 0.7702 (m-80) REVERT: E 7 LYS cc_start: 0.8501 (mppt) cc_final: 0.8239 (mtmm) REVERT: E 13 MET cc_start: 0.9088 (mmm) cc_final: 0.8640 (mmm) REVERT: E 17 ASP cc_start: 0.8224 (m-30) cc_final: 0.7945 (m-30) REVERT: E 196 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8031 (mm-30) REVERT: E 241 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7338 (pt) REVERT: E 243 TYR cc_start: 0.7285 (m-10) cc_final: 0.7020 (m-10) REVERT: E 589 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8571 (pt) REVERT: E 609 GLN cc_start: 0.8655 (tp40) cc_final: 0.8307 (mt0) REVERT: F 241 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7486 (pt) REVERT: F 255 ASP cc_start: 0.4684 (OUTLIER) cc_final: 0.3660 (t70) REVERT: F 409 MET cc_start: 0.8822 (tmm) cc_final: 0.8620 (tpt) REVERT: G 17 ASP cc_start: 0.8218 (m-30) cc_final: 0.7881 (m-30) REVERT: G 241 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7215 (pt) REVERT: G 243 TYR cc_start: 0.8040 (m-80) cc_final: 0.7595 (m-80) REVERT: H 7 LYS cc_start: 0.8662 (mppt) cc_final: 0.8368 (mtmm) REVERT: H 17 ASP cc_start: 0.8020 (m-30) cc_final: 0.7751 (m-30) REVERT: H 241 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7246 (pt) REVERT: H 255 ASP cc_start: 0.4395 (OUTLIER) cc_final: 0.3765 (t70) REVERT: H 409 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8606 (tpp) REVERT: H 601 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: H 609 GLN cc_start: 0.8614 (tp40) cc_final: 0.8285 (mt0) REVERT: I 426 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7841 (tm-30) REVERT: J 17 ASP cc_start: 0.8257 (m-30) cc_final: 0.7920 (m-30) REVERT: J 241 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.7190 (pt) REVERT: J 243 TYR cc_start: 0.8155 (m-80) cc_final: 0.7726 (m-80) REVERT: K 7 LYS cc_start: 0.8648 (mppt) cc_final: 0.8350 (mtmm) REVERT: K 13 MET cc_start: 0.9091 (mmm) cc_final: 0.8642 (mmm) REVERT: K 17 ASP cc_start: 0.8239 (m-30) cc_final: 0.7948 (m-30) REVERT: K 241 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7268 (pt) REVERT: K 255 ASP cc_start: 0.4447 (OUTLIER) cc_final: 0.3817 (t70) REVERT: K 601 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7241 (pm20) REVERT: K 627 MET cc_start: 0.8394 (ppp) cc_final: 0.8192 (ppp) REVERT: O 1 MET cc_start: 0.2983 (tmm) cc_final: 0.2147 (ptt) REVERT: O 108 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8249 (ttm-80) REVERT: P 1 MET cc_start: 0.4187 (OUTLIER) cc_final: 0.3620 (tmt) REVERT: P 69 ASP cc_start: 0.8802 (m-30) cc_final: 0.8478 (m-30) REVERT: P 90 MET cc_start: 0.8645 (ptm) cc_final: 0.8396 (ptm) REVERT: Q 30 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6520 (tt0) REVERT: S 1 MET cc_start: 0.4844 (tmt) cc_final: 0.3863 (pmt) REVERT: S 30 GLU cc_start: 0.7551 (tt0) cc_final: 0.7315 (tt0) REVERT: S 64 GLU cc_start: 0.8284 (mp0) cc_final: 0.8067 (mp0) REVERT: T 1 MET cc_start: 0.4274 (pmm) cc_final: 0.3062 (ttt) REVERT: T 64 GLU cc_start: 0.7762 (pm20) cc_final: 0.7382 (pm20) REVERT: T 69 ASP cc_start: 0.8768 (m-30) cc_final: 0.8425 (m-30) REVERT: V 69 ASP cc_start: 0.8757 (m-30) cc_final: 0.8383 (m-30) REVERT: L 108 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8243 (ttm-80) outliers start: 158 outliers final: 92 residues processed: 770 average time/residue: 1.5792 time to fit residues: 1591.4344 Evaluate side-chains 747 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 635 time to evaluate : 6.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 638 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 589 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 516 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 578 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain H residue 196 GLU Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain H residue 558 ASP Chi-restraints excluded: chain H residue 578 ASP Chi-restraints excluded: chain H residue 601 GLU Chi-restraints excluded: chain H residue 638 THR Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 516 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 558 ASP Chi-restraints excluded: chain J residue 578 ASP Chi-restraints excluded: chain J residue 638 THR Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 455 MET Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 558 ASP Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain K residue 601 GLU Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 18 PHE Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 550 optimal weight: 0.6980 chunk 355 optimal weight: 6.9990 chunk 531 optimal weight: 0.0060 chunk 267 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 565 optimal weight: 4.9990 chunk 606 optimal weight: 7.9990 chunk 439 optimal weight: 6.9990 chunk 82 optimal weight: 20.0000 chunk 699 optimal weight: 10.0000 overall best weight: 3.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN E 587 GLN E 631 GLN H 258 GLN H 587 GLN ** H 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN K 587 GLN ** K 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 74613 Z= 0.291 Angle : 0.671 11.423 100943 Z= 0.345 Chirality : 0.044 0.194 10914 Planarity : 0.005 0.059 13412 Dihedral : 4.532 31.042 10244 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.92 % Allowed : 11.06 % Favored : 88.02 % Rotamer: Outliers : 2.09 % Allowed : 13.48 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.09), residues: 9152 helix: 1.52 (0.08), residues: 3930 sheet: -0.64 (0.17), residues: 1032 loop : -2.64 (0.09), residues: 4190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 215 HIS 0.005 0.001 HIS V 80 PHE 0.033 0.002 PHE Q 18 TYR 0.057 0.002 TYR H 195 ARG 0.007 0.000 ARG K 487 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 640 time to evaluate : 6.356 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: M 255 ASP cc_start: 0.4767 (OUTLIER) cc_final: 0.4180 (t0) REVERT: A 241 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7418 (pt) REVERT: A 243 TYR cc_start: 0.8182 (m-80) cc_final: 0.7789 (m-80) REVERT: B 7 LYS cc_start: 0.8661 (mppt) cc_final: 0.8367 (mptt) REVERT: B 17 ASP cc_start: 0.8137 (m-30) cc_final: 0.7825 (m-30) REVERT: B 241 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7526 (pt) REVERT: B 601 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: B 620 MET cc_start: 0.7798 (tmm) cc_final: 0.7491 (mtp) REVERT: C 255 ASP cc_start: 0.4727 (OUTLIER) cc_final: 0.4181 (t70) REVERT: C 426 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7882 (tm-30) REVERT: C 582 GLU cc_start: 0.8362 (tt0) cc_final: 0.8128 (tm-30) REVERT: C 620 MET cc_start: 0.8066 (tmm) cc_final: 0.7745 (mtp) REVERT: D 241 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7534 (pt) REVERT: D 243 TYR cc_start: 0.8191 (m-80) cc_final: 0.7849 (m-80) REVERT: E 7 LYS cc_start: 0.8566 (mppt) cc_final: 0.8293 (mptt) REVERT: E 13 MET cc_start: 0.9089 (mmm) cc_final: 0.8657 (mmm) REVERT: E 17 ASP cc_start: 0.8283 (m-30) cc_final: 0.7981 (m-30) REVERT: E 241 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7508 (pt) REVERT: E 243 TYR cc_start: 0.7264 (m-10) cc_final: 0.6993 (m-10) REVERT: E 609 GLN cc_start: 0.8745 (tp40) cc_final: 0.8404 (tp-100) REVERT: F 243 TYR cc_start: 0.7706 (m-10) cc_final: 0.7427 (m-80) REVERT: F 610 MET cc_start: 0.8682 (mmm) cc_final: 0.8009 (pp-130) REVERT: G 17 ASP cc_start: 0.8276 (m-30) cc_final: 0.7933 (m-30) REVERT: G 241 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7421 (pt) REVERT: G 243 TYR cc_start: 0.8172 (m-80) cc_final: 0.7756 (m-80) REVERT: H 7 LYS cc_start: 0.8668 (mppt) cc_final: 0.8372 (mptt) REVERT: H 17 ASP cc_start: 0.8129 (m-30) cc_final: 0.7840 (m-30) REVERT: H 409 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8723 (tpp) REVERT: H 601 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: H 609 GLN cc_start: 0.8672 (tp40) cc_final: 0.8338 (mt0) REVERT: I 426 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7876 (tm-30) REVERT: J 17 ASP cc_start: 0.8236 (m-30) cc_final: 0.7890 (m-30) REVERT: J 241 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7421 (pt) REVERT: J 243 TYR cc_start: 0.8132 (m-80) cc_final: 0.7738 (m-80) REVERT: K 7 LYS cc_start: 0.8676 (mppt) cc_final: 0.8380 (mptt) REVERT: K 13 MET cc_start: 0.9086 (mmm) cc_final: 0.8655 (mmm) REVERT: K 17 ASP cc_start: 0.8295 (m-30) cc_final: 0.7974 (m-30) REVERT: K 241 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7565 (pt) REVERT: K 271 PHE cc_start: 0.7651 (m-10) cc_final: 0.7321 (m-80) REVERT: K 601 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7369 (pm20) REVERT: K 609 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8243 (mt0) REVERT: O 1 MET cc_start: 0.2771 (tmm) cc_final: 0.2020 (ptt) REVERT: P 1 MET cc_start: 0.4594 (OUTLIER) cc_final: 0.4192 (tpt) REVERT: P 30 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7123 (tm-30) REVERT: P 69 ASP cc_start: 0.8835 (m-30) cc_final: 0.8527 (m-30) REVERT: P 90 MET cc_start: 0.8687 (ptm) cc_final: 0.8387 (ptm) REVERT: Q 30 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6517 (tt0) REVERT: R 30 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6567 (mt-10) REVERT: S 1 MET cc_start: 0.5257 (tmt) cc_final: 0.4292 (pmt) REVERT: S 30 GLU cc_start: 0.7682 (tt0) cc_final: 0.7436 (tt0) REVERT: S 64 GLU cc_start: 0.8390 (mp0) cc_final: 0.8046 (mp0) REVERT: T 1 MET cc_start: 0.4429 (pmm) cc_final: 0.3143 (ttt) REVERT: T 64 GLU cc_start: 0.7869 (pm20) cc_final: 0.7499 (pm20) REVERT: T 69 ASP cc_start: 0.8794 (m-30) cc_final: 0.8471 (m-30) REVERT: V 69 ASP cc_start: 0.8774 (m-30) cc_final: 0.8416 (m-30) outliers start: 162 outliers final: 103 residues processed: 761 average time/residue: 1.6149 time to fit residues: 1602.8016 Evaluate side-chains 738 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 620 time to evaluate : 6.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 279 VAL Chi-restraints excluded: chain M residue 455 MET Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 638 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 455 MET Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 455 MET Chi-restraints excluded: chain F residue 516 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 578 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 274 VAL Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain H residue 578 ASP Chi-restraints excluded: chain H residue 601 GLU Chi-restraints excluded: chain H residue 638 THR Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 455 MET Chi-restraints excluded: chain I residue 516 VAL Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 578 ASP Chi-restraints excluded: chain J residue 638 THR Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 274 VAL Chi-restraints excluded: chain K residue 455 MET Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain K residue 601 GLU Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 18 PHE Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 30 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 25 SER Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 809 optimal weight: 0.0170 chunk 852 optimal weight: 6.9990 chunk 777 optimal weight: 1.9990 chunk 829 optimal weight: 3.9990 chunk 498 optimal weight: 9.9990 chunk 361 optimal weight: 6.9990 chunk 650 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 749 optimal weight: 7.9990 chunk 784 optimal weight: 0.8980 chunk 826 optimal weight: 6.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN ** H 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 652 GLN K 613 GLN ** K 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 74613 Z= 0.167 Angle : 0.634 12.047 100943 Z= 0.324 Chirality : 0.042 0.189 10914 Planarity : 0.005 0.063 13412 Dihedral : 4.331 30.025 10244 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.86 % Favored : 89.29 % Rotamer: Outliers : 1.78 % Allowed : 14.23 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.09), residues: 9152 helix: 1.66 (0.08), residues: 3876 sheet: -0.38 (0.17), residues: 1020 loop : -2.72 (0.09), residues: 4256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 215 HIS 0.003 0.001 HIS K 245 PHE 0.023 0.001 PHE Q 18 TYR 0.030 0.001 TYR I 243 ARG 0.007 0.000 ARG J 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 648 time to evaluate : 6.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 255 ASP cc_start: 0.4733 (OUTLIER) cc_final: 0.4154 (t70) REVERT: A 241 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7211 (pt) REVERT: A 243 TYR cc_start: 0.8137 (m-80) cc_final: 0.7911 (m-80) REVERT: B 7 LYS cc_start: 0.8634 (mppt) cc_final: 0.8344 (mptt) REVERT: B 17 ASP cc_start: 0.8032 (m-30) cc_final: 0.7758 (m-30) REVERT: B 241 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7286 (pt) REVERT: B 243 TYR cc_start: 0.7187 (m-10) cc_final: 0.6983 (m-10) REVERT: B 601 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: B 620 MET cc_start: 0.7705 (tmm) cc_final: 0.7433 (mtp) REVERT: C 255 ASP cc_start: 0.4526 (OUTLIER) cc_final: 0.3999 (t70) REVERT: C 426 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 582 GLU cc_start: 0.8350 (tt0) cc_final: 0.8096 (tm-30) REVERT: C 620 MET cc_start: 0.7998 (tmm) cc_final: 0.7718 (mtp) REVERT: D 7 LYS cc_start: 0.8766 (mppt) cc_final: 0.8337 (mtmm) REVERT: D 241 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7254 (pt) REVERT: D 243 TYR cc_start: 0.8166 (m-80) cc_final: 0.7936 (m-80) REVERT: E 13 MET cc_start: 0.9063 (mmm) cc_final: 0.8563 (mmm) REVERT: E 17 ASP cc_start: 0.8228 (m-30) cc_final: 0.7944 (m-30) REVERT: E 241 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7246 (pt) REVERT: E 255 ASP cc_start: 0.4442 (OUTLIER) cc_final: 0.3825 (t70) REVERT: E 609 GLN cc_start: 0.8716 (tp40) cc_final: 0.8502 (tp-100) REVERT: F 243 TYR cc_start: 0.7507 (m-10) cc_final: 0.7234 (m-10) REVERT: F 255 ASP cc_start: 0.5353 (OUTLIER) cc_final: 0.4639 (t0) REVERT: F 409 MET cc_start: 0.8882 (tmm) cc_final: 0.8587 (tpt) REVERT: G 17 ASP cc_start: 0.8217 (m-30) cc_final: 0.7889 (m-30) REVERT: G 241 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7174 (pt) REVERT: G 243 TYR cc_start: 0.8163 (m-80) cc_final: 0.7955 (m-80) REVERT: H 7 LYS cc_start: 0.8643 (mppt) cc_final: 0.8350 (mptt) REVERT: H 17 ASP cc_start: 0.8020 (m-30) cc_final: 0.7744 (m-30) REVERT: H 255 ASP cc_start: 0.4853 (OUTLIER) cc_final: 0.4315 (t70) REVERT: H 409 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8577 (tpp) REVERT: H 601 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: H 609 GLN cc_start: 0.8660 (tp40) cc_final: 0.8362 (mt0) REVERT: H 627 MET cc_start: 0.8283 (ppp) cc_final: 0.8055 (ppp) REVERT: I 426 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7852 (tm-30) REVERT: I 582 GLU cc_start: 0.8355 (tt0) cc_final: 0.8099 (tm-30) REVERT: J 17 ASP cc_start: 0.8250 (m-30) cc_final: 0.7915 (m-30) REVERT: J 241 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.7208 (pt) REVERT: J 243 TYR cc_start: 0.8137 (m-80) cc_final: 0.7849 (m-80) REVERT: K 7 LYS cc_start: 0.8649 (mppt) cc_final: 0.8357 (mptt) REVERT: K 13 MET cc_start: 0.9080 (mmm) cc_final: 0.8617 (mmm) REVERT: K 17 ASP cc_start: 0.8227 (m-30) cc_final: 0.7939 (m-30) REVERT: K 241 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7311 (pt) REVERT: K 243 TYR cc_start: 0.7194 (m-10) cc_final: 0.6994 (m-10) REVERT: K 601 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: K 609 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8360 (mt0) REVERT: O 1 MET cc_start: 0.2822 (tmm) cc_final: 0.2154 (ptt) REVERT: O 64 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7979 (mt-10) REVERT: O 108 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8249 (ttm-80) REVERT: P 1 MET cc_start: 0.4146 (OUTLIER) cc_final: 0.3608 (tmt) REVERT: P 30 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7081 (tm-30) REVERT: P 69 ASP cc_start: 0.8805 (m-30) cc_final: 0.8477 (m-30) REVERT: P 90 MET cc_start: 0.8656 (ptm) cc_final: 0.8398 (ptm) REVERT: Q 30 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6524 (tt0) REVERT: R 1 MET cc_start: 0.5467 (OUTLIER) cc_final: 0.4857 (ppp) REVERT: R 30 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6498 (mt-10) REVERT: S 1 MET cc_start: 0.5319 (tmt) cc_final: 0.4596 (pp-130) REVERT: S 30 GLU cc_start: 0.7550 (tt0) cc_final: 0.7315 (tt0) REVERT: S 64 GLU cc_start: 0.8232 (mp0) cc_final: 0.8022 (mp0) REVERT: T 1 MET cc_start: 0.4398 (pmm) cc_final: 0.3075 (ttt) REVERT: T 64 GLU cc_start: 0.7688 (pm20) cc_final: 0.7477 (pm20) REVERT: T 69 ASP cc_start: 0.8765 (m-30) cc_final: 0.8438 (m-30) REVERT: V 69 ASP cc_start: 0.8751 (m-30) cc_final: 0.8386 (m-30) REVERT: L 108 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8270 (ttm-80) outliers start: 138 outliers final: 87 residues processed: 754 average time/residue: 1.6042 time to fit residues: 1580.8263 Evaluate side-chains 733 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 627 time to evaluate : 7.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 558 ASP Chi-restraints excluded: chain M residue 638 THR Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 558 ASP Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 516 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain H residue 558 ASP Chi-restraints excluded: chain H residue 578 ASP Chi-restraints excluded: chain H residue 601 GLU Chi-restraints excluded: chain H residue 638 THR Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 516 VAL Chi-restraints excluded: chain I residue 558 ASP Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 555 LEU Chi-restraints excluded: chain J residue 578 ASP Chi-restraints excluded: chain J residue 638 THR Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 455 MET Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 558 ASP Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain K residue 601 GLU Chi-restraints excluded: chain K residue 613 GLN Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 18 PHE Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 30 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 544 optimal weight: 8.9990 chunk 876 optimal weight: 0.9980 chunk 535 optimal weight: 9.9990 chunk 415 optimal weight: 1.9990 chunk 609 optimal weight: 4.9990 chunk 919 optimal weight: 8.9990 chunk 846 optimal weight: 6.9990 chunk 732 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 565 optimal weight: 3.9990 chunk 448 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 74613 Z= 0.254 Angle : 0.671 12.416 100943 Z= 0.344 Chirality : 0.043 0.185 10914 Planarity : 0.005 0.060 13412 Dihedral : 4.430 30.828 10244 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.91 % Allowed : 10.64 % Favored : 88.45 % Rotamer: Outliers : 1.53 % Allowed : 14.66 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.09), residues: 9152 helix: 1.52 (0.08), residues: 3954 sheet: -0.47 (0.17), residues: 1008 loop : -2.64 (0.09), residues: 4190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 215 HIS 0.004 0.001 HIS V 80 PHE 0.031 0.002 PHE Q 18 TYR 0.035 0.002 TYR I 243 ARG 0.007 0.000 ARG J 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18304 Ramachandran restraints generated. 9152 Oldfield, 0 Emsley, 9152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 628 time to evaluate : 6.378 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: M 255 ASP cc_start: 0.4674 (OUTLIER) cc_final: 0.4090 (t70) REVERT: A 241 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7550 (pt) REVERT: B 7 LYS cc_start: 0.8660 (mppt) cc_final: 0.8362 (mptt) REVERT: B 13 MET cc_start: 0.8820 (mmm) cc_final: 0.8586 (mmm) REVERT: B 17 ASP cc_start: 0.8097 (m-30) cc_final: 0.7813 (m-30) REVERT: B 241 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7431 (pt) REVERT: B 601 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: B 620 MET cc_start: 0.7734 (tmm) cc_final: 0.7445 (mpp) REVERT: C 255 ASP cc_start: 0.4683 (OUTLIER) cc_final: 0.4075 (t70) REVERT: C 426 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7887 (tm-30) REVERT: C 582 GLU cc_start: 0.8330 (tt0) cc_final: 0.8091 (tm-30) REVERT: C 620 MET cc_start: 0.8005 (tmm) cc_final: 0.7741 (mtp) REVERT: D 241 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7603 (pt) REVERT: E 13 MET cc_start: 0.9079 (mmm) cc_final: 0.8620 (mmm) REVERT: E 17 ASP cc_start: 0.8283 (m-30) cc_final: 0.7967 (m-30) REVERT: E 241 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7441 (pt) REVERT: F 243 TYR cc_start: 0.7359 (m-10) cc_final: 0.7090 (m-10) REVERT: F 255 ASP cc_start: 0.5508 (OUTLIER) cc_final: 0.4783 (t0) REVERT: F 409 MET cc_start: 0.8967 (tmm) cc_final: 0.8612 (tpt) REVERT: F 610 MET cc_start: 0.8700 (mmm) cc_final: 0.8120 (pp-130) REVERT: G 17 ASP cc_start: 0.8262 (m-30) cc_final: 0.7943 (m-30) REVERT: G 241 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7449 (pt) REVERT: H 7 LYS cc_start: 0.8669 (mppt) cc_final: 0.8367 (mptt) REVERT: H 17 ASP cc_start: 0.8087 (m-30) cc_final: 0.7797 (m-30) REVERT: H 255 ASP cc_start: 0.4658 (OUTLIER) cc_final: 0.4082 (t70) REVERT: H 409 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8666 (tpp) REVERT: H 601 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: H 609 GLN cc_start: 0.8645 (tp40) cc_final: 0.8423 (tp-100) REVERT: H 627 MET cc_start: 0.8304 (ppp) cc_final: 0.8081 (ppp) REVERT: I 426 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7879 (tm-30) REVERT: J 17 ASP cc_start: 0.8275 (m-30) cc_final: 0.7958 (m-30) REVERT: J 241 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7433 (pt) REVERT: J 243 TYR cc_start: 0.8200 (m-80) cc_final: 0.7994 (m-80) REVERT: K 7 LYS cc_start: 0.8674 (mppt) cc_final: 0.8374 (mptt) REVERT: K 13 MET cc_start: 0.9089 (mmm) cc_final: 0.8639 (mmm) REVERT: K 17 ASP cc_start: 0.8284 (m-30) cc_final: 0.7980 (m-30) REVERT: K 241 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7377 (pt) REVERT: K 243 TYR cc_start: 0.7190 (m-10) cc_final: 0.6972 (m-10) REVERT: K 601 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: K 609 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8399 (mt0) REVERT: O 1 MET cc_start: 0.2992 (tmm) cc_final: 0.2495 (ptt) REVERT: O 64 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8020 (mt-10) REVERT: P 1 MET cc_start: 0.4307 (OUTLIER) cc_final: 0.3944 (tpt) REVERT: P 30 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7111 (tm-30) REVERT: P 69 ASP cc_start: 0.8828 (m-30) cc_final: 0.8513 (m-30) REVERT: P 90 MET cc_start: 0.8668 (ptm) cc_final: 0.8368 (ptm) REVERT: Q 17 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8294 (mtpp) REVERT: Q 30 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6577 (tt0) REVERT: R 1 MET cc_start: 0.5522 (OUTLIER) cc_final: 0.4908 (ppp) REVERT: R 30 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: S 1 MET cc_start: 0.5447 (tmt) cc_final: 0.4722 (pp-130) REVERT: S 30 GLU cc_start: 0.7641 (tt0) cc_final: 0.7406 (tt0) REVERT: S 64 GLU cc_start: 0.8326 (mp0) cc_final: 0.8028 (mp0) REVERT: T 1 MET cc_start: 0.4411 (pmm) cc_final: 0.2999 (ttt) REVERT: T 64 GLU cc_start: 0.7761 (pm20) cc_final: 0.7383 (pm20) REVERT: T 69 ASP cc_start: 0.8774 (m-30) cc_final: 0.8450 (m-30) REVERT: V 69 ASP cc_start: 0.8802 (m-30) cc_final: 0.8453 (m-30) outliers start: 118 outliers final: 87 residues processed: 716 average time/residue: 1.6546 time to fit residues: 1558.3072 Evaluate side-chains 717 residues out of total 7749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 612 time to evaluate : 6.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain M residue 255 ASP Chi-restraints excluded: chain M residue 516 VAL Chi-restraints excluded: chain M residue 638 THR Chi-restraints excluded: chain A residue 215 TRP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 601 GLU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain D residue 213 THR Chi-restraints excluded: chain D residue 241 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 516 VAL Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 255 ASP Chi-restraints excluded: chain E residue 455 MET Chi-restraints excluded: chain E residue 516 VAL Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 255 ASP Chi-restraints excluded: chain F residue 516 VAL Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain G residue 215 TRP Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain G residue 578 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 409 MET Chi-restraints excluded: chain H residue 455 MET Chi-restraints excluded: chain H residue 516 VAL Chi-restraints excluded: chain H residue 558 ASP Chi-restraints excluded: chain H residue 578 ASP Chi-restraints excluded: chain H residue 601 GLU Chi-restraints excluded: chain H residue 621 VAL Chi-restraints excluded: chain H residue 638 THR Chi-restraints excluded: chain I residue 7 LYS Chi-restraints excluded: chain I residue 223 ASP Chi-restraints excluded: chain I residue 516 VAL Chi-restraints excluded: chain I residue 638 THR Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 516 VAL Chi-restraints excluded: chain J residue 578 ASP Chi-restraints excluded: chain J residue 638 THR Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 223 ASP Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 255 ASP Chi-restraints excluded: chain K residue 455 MET Chi-restraints excluded: chain K residue 516 VAL Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain K residue 601 GLU Chi-restraints excluded: chain K residue 638 THR Chi-restraints excluded: chain N residue 3 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain O residue 119 VAL Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 18 PHE Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 23 ASN Chi-restraints excluded: chain R residue 30 GLU Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 581 optimal weight: 6.9990 chunk 780 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 675 optimal weight: 0.0170 chunk 108 optimal weight: 0.0060 chunk 203 optimal weight: 5.9990 chunk 733 optimal weight: 3.9990 chunk 306 optimal weight: 10.0000 chunk 753 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 overall best weight: 2.4040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.067420 restraints weight = 145950.417| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 3.05 r_work: 0.2804 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 74613 Z= 0.213 Angle : 0.659 13.405 100943 Z= 0.337 Chirality : 0.043 0.188 10914 Planarity : 0.005 0.059 13412 Dihedral : 4.448 30.739 10244 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.89 % Allowed : 10.74 % Favored : 88.37 % Rotamer: Outliers : 1.67 % Allowed : 14.68 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.09), residues: 9152 helix: 1.51 (0.08), residues: 3954 sheet: -0.51 (0.17), residues: 1008 loop : -2.63 (0.09), residues: 4190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 215 HIS 0.003 0.001 HIS V 80 PHE 0.027 0.001 PHE Q 18 TYR 0.037 0.001 TYR I 243 ARG 0.008 0.000 ARG J 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23327.76 seconds wall clock time: 406 minutes 35.74 seconds (24395.74 seconds total)