Starting phenix.real_space_refine on Tue Feb 13 13:45:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2024/8hdw_34681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2024/8hdw_34681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2024/8hdw_34681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2024/8hdw_34681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2024/8hdw_34681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2024/8hdw_34681.pdb" } resolution = 3.0 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= 0.001 sd= 0.013 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 204 5.16 5 C 34452 2.51 5 N 9312 2.21 5 O 10584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 125": "NH1" <-> "NH2" Residue "2 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 125": "NH1" <-> "NH2" Residue "M ARG 16": "NH1" <-> "NH2" Residue "M PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 167": "NH1" <-> "NH2" Residue "M ARG 218": "NH1" <-> "NH2" Residue "M PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 283": "NH1" <-> "NH2" Residue "M TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 82": "NH1" <-> "NH2" Residue "N TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 167": "NH1" <-> "NH2" Residue "N ARG 218": "NH1" <-> "NH2" Residue "N PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 167": "NH1" <-> "NH2" Residue "O ARG 218": "NH1" <-> "NH2" Residue "O PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 283": "NH1" <-> "NH2" Residue "O TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 16": "NH1" <-> "NH2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 167": "NH1" <-> "NH2" Residue "P ARG 218": "NH1" <-> "NH2" Residue "P PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 283": "NH1" <-> "NH2" Residue "P TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 16": "NH1" <-> "NH2" Residue "Q PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "Q TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 167": "NH1" <-> "NH2" Residue "Q ARG 218": "NH1" <-> "NH2" Residue "Q PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 283": "NH1" <-> "NH2" Residue "Q TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 16": "NH1" <-> "NH2" Residue "R PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 82": "NH1" <-> "NH2" Residue "R TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 167": "NH1" <-> "NH2" Residue "R ARG 218": "NH1" <-> "NH2" Residue "R PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 16": "NH1" <-> "NH2" Residue "S PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "S TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 167": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "S PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 283": "NH1" <-> "NH2" Residue "S TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 16": "NH1" <-> "NH2" Residue "T PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 82": "NH1" <-> "NH2" Residue "T TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 167": "NH1" <-> "NH2" Residue "T ARG 218": "NH1" <-> "NH2" Residue "T PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 283": "NH1" <-> "NH2" Residue "T TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 16": "NH1" <-> "NH2" Residue "U PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 167": "NH1" <-> "NH2" Residue "U ARG 218": "NH1" <-> "NH2" Residue "U PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 283": "NH1" <-> "NH2" Residue "U TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 16": "NH1" <-> "NH2" Residue "V PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 82": "NH1" <-> "NH2" Residue "V TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 167": "NH1" <-> "NH2" Residue "V ARG 218": "NH1" <-> "NH2" Residue "V PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 283": "NH1" <-> "NH2" Residue "V TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 16": "NH1" <-> "NH2" Residue "W PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 82": "NH1" <-> "NH2" Residue "W TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 167": "NH1" <-> "NH2" Residue "W ARG 218": "NH1" <-> "NH2" Residue "W PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 283": "NH1" <-> "NH2" Residue "W TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 16": "NH1" <-> "NH2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 82": "NH1" <-> "NH2" Residue "X TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 167": "NH1" <-> "NH2" Residue "X ARG 218": "NH1" <-> "NH2" Residue "X PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 283": "NH1" <-> "NH2" Residue "X TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 125": "NH1" <-> "NH2" Residue "Z PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 125": "NH1" <-> "NH2" Residue "m PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 125": "NH1" <-> "NH2" Residue "n PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 125": "NH1" <-> "NH2" Residue "o PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 125": "NH1" <-> "NH2" Residue "p PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 125": "NH1" <-> "NH2" Residue "q PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 125": "NH1" <-> "NH2" Residue "r PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 125": "NH1" <-> "NH2" Residue "s PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 125": "NH1" <-> "NH2" Residue "t PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 125": "NH1" <-> "NH2" Residue "u PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 125": "NH1" <-> "NH2" Residue "v PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 125": "NH1" <-> "NH2" Residue "w PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 125": "NH1" <-> "NH2" Residue "x PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 125": "NH1" <-> "NH2" Residue "y PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 125": "NH1" <-> "NH2" Residue "z PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 125": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 54552 Number of models: 1 Model: "" Number of chains: 30 Chain: "1" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "2" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "M" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "N" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "O" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "P" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "Q" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "R" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "S" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "T" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "U" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "V" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "W" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "X" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2938 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain: "Y" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "Z" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "m" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "n" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "o" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "p" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "q" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "r" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "s" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "t" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "u" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "v" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "w" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "x" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "y" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "z" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1072 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Time building chain proxies: 21.22, per 1000 atoms: 0.39 Number of scatterers: 54552 At special positions: 0 Unit cell: (195.509, 197.535, 136.755, 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 204 16.00 O 10584 8.00 N 9312 7.00 C 34452 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: 16.23 Conformation dependent library (CDL) restraints added in 8.9 seconds 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13272 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 114 sheets defined 21.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain '1' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG 1 73 " --> pdb=" O SER 1 69 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG 2 73 " --> pdb=" O SER 2 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 8 Processing helix chain 'M' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 109 Processing helix chain 'M' and resid 129 through 131 No H-bonds generated for 'chain 'M' and resid 129 through 131' Processing helix chain 'M' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL M 136 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU M 140 " --> pdb=" O VAL M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER M 190 " --> pdb=" O TYR M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE M 274 " --> pdb=" O PHE M 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN M 294 " --> pdb=" O SER M 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN M 295 " --> pdb=" O LEU M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL M 311 " --> pdb=" O GLN M 307 " (cutoff:3.500A) Proline residue: M 312 - end of helix Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'N' and resid 5 through 8 Processing helix chain 'N' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER N 72 " --> pdb=" O LYS N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 109 Processing helix chain 'N' and resid 129 through 131 No H-bonds generated for 'chain 'N' and resid 129 through 131' Processing helix chain 'N' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL N 136 " --> pdb=" O LEU N 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU N 140 " --> pdb=" O VAL N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 168 Processing helix chain 'N' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER N 190 " --> pdb=" O TYR N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE N 274 " --> pdb=" O PHE N 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN N 294 " --> pdb=" O SER N 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN N 295 " --> pdb=" O LEU N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL N 311 " --> pdb=" O GLN N 307 " (cutoff:3.500A) Proline residue: N 312 - end of helix Processing helix chain 'N' and resid 351 through 356 Processing helix chain 'O' and resid 5 through 8 Processing helix chain 'O' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 109 Processing helix chain 'O' and resid 129 through 131 No H-bonds generated for 'chain 'O' and resid 129 through 131' Processing helix chain 'O' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL O 136 " --> pdb=" O LEU O 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU O 140 " --> pdb=" O VAL O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 163 through 168 Processing helix chain 'O' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER O 190 " --> pdb=" O TYR O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE O 274 " --> pdb=" O PHE O 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN O 294 " --> pdb=" O SER O 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN O 295 " --> pdb=" O LEU O 291 " (cutoff:3.500A) Processing helix chain 'O' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL O 311 " --> pdb=" O GLN O 307 " (cutoff:3.500A) Proline residue: O 312 - end of helix Processing helix chain 'O' and resid 351 through 356 Processing helix chain 'P' and resid 5 through 8 Processing helix chain 'P' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER P 72 " --> pdb=" O LYS P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 109 Processing helix chain 'P' and resid 129 through 131 No H-bonds generated for 'chain 'P' and resid 129 through 131' Processing helix chain 'P' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL P 136 " --> pdb=" O LEU P 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU P 140 " --> pdb=" O VAL P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 168 Processing helix chain 'P' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER P 190 " --> pdb=" O TYR P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE P 274 " --> pdb=" O PHE P 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN P 294 " --> pdb=" O SER P 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN P 295 " --> pdb=" O LEU P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL P 311 " --> pdb=" O GLN P 307 " (cutoff:3.500A) Proline residue: P 312 - end of helix Processing helix chain 'P' and resid 351 through 356 Processing helix chain 'Q' and resid 5 through 8 Processing helix chain 'Q' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER Q 72 " --> pdb=" O LYS Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 109 Processing helix chain 'Q' and resid 129 through 131 No H-bonds generated for 'chain 'Q' and resid 129 through 131' Processing helix chain 'Q' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL Q 136 " --> pdb=" O LEU Q 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU Q 140 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 168 Processing helix chain 'Q' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER Q 190 " --> pdb=" O TYR Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 295 removed outlier: 3.778A pdb=" N ILE Q 274 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN Q 294 " --> pdb=" O SER Q 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN Q 295 " --> pdb=" O LEU Q 291 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL Q 311 " --> pdb=" O GLN Q 307 " (cutoff:3.500A) Proline residue: Q 312 - end of helix Processing helix chain 'Q' and resid 351 through 356 Processing helix chain 'R' and resid 5 through 8 Processing helix chain 'R' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER R 72 " --> pdb=" O LYS R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 109 Processing helix chain 'R' and resid 129 through 131 No H-bonds generated for 'chain 'R' and resid 129 through 131' Processing helix chain 'R' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL R 136 " --> pdb=" O LEU R 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 168 Processing helix chain 'R' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER R 190 " --> pdb=" O TYR R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 295 removed outlier: 3.778A pdb=" N ILE R 274 " --> pdb=" O PHE R 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN R 294 " --> pdb=" O SER R 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN R 295 " --> pdb=" O LEU R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL R 311 " --> pdb=" O GLN R 307 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 351 through 356 Processing helix chain 'S' and resid 5 through 8 Processing helix chain 'S' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER S 72 " --> pdb=" O LYS S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 109 Processing helix chain 'S' and resid 129 through 131 No H-bonds generated for 'chain 'S' and resid 129 through 131' Processing helix chain 'S' and resid 132 through 140 removed outlier: 3.582A pdb=" N VAL S 136 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU S 140 " --> pdb=" O VAL S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 163 through 168 Processing helix chain 'S' and resid 186 through 191 removed outlier: 3.798A pdb=" N SER S 190 " --> pdb=" O TYR S 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE S 274 " --> pdb=" O PHE S 270 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN S 294 " --> pdb=" O SER S 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN S 295 " --> pdb=" O LEU S 291 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL S 311 " --> pdb=" O GLN S 307 " (cutoff:3.500A) Proline residue: S 312 - end of helix Processing helix chain 'S' and resid 351 through 356 Processing helix chain 'T' and resid 5 through 8 Processing helix chain 'T' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER T 72 " --> pdb=" O LYS T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 109 Processing helix chain 'T' and resid 129 through 131 No H-bonds generated for 'chain 'T' and resid 129 through 131' Processing helix chain 'T' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL T 136 " --> pdb=" O LEU T 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU T 140 " --> pdb=" O VAL T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 163 through 168 Processing helix chain 'T' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER T 190 " --> pdb=" O TYR T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE T 274 " --> pdb=" O PHE T 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN T 294 " --> pdb=" O SER T 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN T 295 " --> pdb=" O LEU T 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL T 311 " --> pdb=" O GLN T 307 " (cutoff:3.500A) Proline residue: T 312 - end of helix Processing helix chain 'T' and resid 351 through 356 Processing helix chain 'U' and resid 5 through 8 Processing helix chain 'U' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER U 72 " --> pdb=" O LYS U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 109 Processing helix chain 'U' and resid 129 through 131 No H-bonds generated for 'chain 'U' and resid 129 through 131' Processing helix chain 'U' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL U 136 " --> pdb=" O LEU U 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU U 140 " --> pdb=" O VAL U 136 " (cutoff:3.500A) Processing helix chain 'U' and resid 163 through 168 Processing helix chain 'U' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER U 190 " --> pdb=" O TYR U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE U 274 " --> pdb=" O PHE U 270 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN U 294 " --> pdb=" O SER U 290 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN U 295 " --> pdb=" O LEU U 291 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL U 311 " --> pdb=" O GLN U 307 " (cutoff:3.500A) Proline residue: U 312 - end of helix Processing helix chain 'U' and resid 351 through 356 Processing helix chain 'V' and resid 5 through 8 Processing helix chain 'V' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER V 72 " --> pdb=" O LYS V 68 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 109 Processing helix chain 'V' and resid 129 through 131 No H-bonds generated for 'chain 'V' and resid 129 through 131' Processing helix chain 'V' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU V 140 " --> pdb=" O VAL V 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 163 through 168 Processing helix chain 'V' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER V 190 " --> pdb=" O TYR V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE V 274 " --> pdb=" O PHE V 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN V 294 " --> pdb=" O SER V 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN V 295 " --> pdb=" O LEU V 291 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 323 removed outlier: 4.473A pdb=" N VAL V 311 " --> pdb=" O GLN V 307 " (cutoff:3.500A) Proline residue: V 312 - end of helix Processing helix chain 'V' and resid 351 through 356 Processing helix chain 'W' and resid 5 through 9 Processing helix chain 'W' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 109 Processing helix chain 'W' and resid 129 through 131 No H-bonds generated for 'chain 'W' and resid 129 through 131' Processing helix chain 'W' and resid 132 through 140 removed outlier: 3.581A pdb=" N VAL W 136 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU W 140 " --> pdb=" O VAL W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 168 Processing helix chain 'W' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER W 190 " --> pdb=" O TYR W 186 " (cutoff:3.500A) Processing helix chain 'W' and resid 270 through 295 removed outlier: 3.777A pdb=" N ILE W 274 " --> pdb=" O PHE W 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN W 294 " --> pdb=" O SER W 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN W 295 " --> pdb=" O LEU W 291 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL W 311 " --> pdb=" O GLN W 307 " (cutoff:3.500A) Proline residue: W 312 - end of helix Processing helix chain 'W' and resid 351 through 356 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 66 through 74 removed outlier: 4.024A pdb=" N SER X 72 " --> pdb=" O LYS X 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 109 Processing helix chain 'X' and resid 129 through 131 No H-bonds generated for 'chain 'X' and resid 129 through 131' Processing helix chain 'X' and resid 132 through 140 removed outlier: 3.580A pdb=" N VAL X 136 " --> pdb=" O LEU X 132 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU X 140 " --> pdb=" O VAL X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 168 Processing helix chain 'X' and resid 186 through 191 removed outlier: 3.797A pdb=" N SER X 190 " --> pdb=" O TYR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 295 removed outlier: 3.778A pdb=" N ILE X 274 " --> pdb=" O PHE X 270 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN X 294 " --> pdb=" O SER X 290 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN X 295 " --> pdb=" O LEU X 291 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 323 removed outlier: 4.474A pdb=" N VAL X 311 " --> pdb=" O GLN X 307 " (cutoff:3.500A) Proline residue: X 312 - end of helix Processing helix chain 'X' and resid 351 through 356 Processing helix chain 'Y' and resid 7 through 9 No H-bonds generated for 'chain 'Y' and resid 7 through 9' Processing helix chain 'Y' and resid 69 through 85 removed outlier: 3.589A pdb=" N ARG Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) Processing helix chain 'Z' and resid 7 through 9 No H-bonds generated for 'chain 'Z' and resid 7 through 9' Processing helix chain 'Z' and resid 69 through 85 removed outlier: 3.591A pdb=" N ARG Z 73 " --> pdb=" O SER Z 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 7 through 9 No H-bonds generated for 'chain 'm' and resid 7 through 9' Processing helix chain 'm' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG m 73 " --> pdb=" O SER m 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 9 No H-bonds generated for 'chain 'n' and resid 7 through 9' Processing helix chain 'n' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG n 73 " --> pdb=" O SER n 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 7 through 9 No H-bonds generated for 'chain 'o' and resid 7 through 9' Processing helix chain 'o' and resid 69 through 85 removed outlier: 3.591A pdb=" N ARG o 73 " --> pdb=" O SER o 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 7 through 9 No H-bonds generated for 'chain 'p' and resid 7 through 9' Processing helix chain 'p' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG p 73 " --> pdb=" O SER p 69 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG q 73 " --> pdb=" O SER q 69 " (cutoff:3.500A) Processing helix chain 'r' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG r 73 " --> pdb=" O SER r 69 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG s 73 " --> pdb=" O SER s 69 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG t 73 " --> pdb=" O SER t 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG u 73 " --> pdb=" O SER u 69 " (cutoff:3.500A) Processing helix chain 'v' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG v 73 " --> pdb=" O SER v 69 " (cutoff:3.500A) Processing helix chain 'w' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG w 73 " --> pdb=" O SER w 69 " (cutoff:3.500A) Processing helix chain 'x' and resid 69 through 85 removed outlier: 3.591A pdb=" N ARG x 73 " --> pdb=" O SER x 69 " (cutoff:3.500A) Processing helix chain 'y' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG y 73 " --> pdb=" O SER y 69 " (cutoff:3.500A) Processing helix chain 'z' and resid 69 through 85 removed outlier: 3.590A pdb=" N ARG z 73 " --> pdb=" O SER z 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain '1' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU 1 101 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY 1 102 " --> pdb=" O THR 1 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 108 through 112 removed outlier: 6.635A pdb=" N THR 1 128 " --> pdb=" O GLN 1 111 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA 1 59 " --> pdb=" O THR 1 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 39 through 43 Processing sheet with id=AA5, first strand: chain '1' and resid 116 through 117 removed outlier: 3.561A pdb=" N ALA 2 59 " --> pdb=" O THR 2 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR 2 128 " --> pdb=" O GLN 2 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 6 through 7 removed outlier: 6.881A pdb=" N TYR 2 6 " --> pdb=" O GLN r 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU 2 101 " --> pdb=" O ASP 2 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY 2 102 " --> pdb=" O THR 2 137 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 39 through 43 Processing sheet with id=AA9, first strand: chain '2' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA w 59 " --> pdb=" O THR w 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR w 128 " --> pdb=" O GLN w 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.184A pdb=" N ASN M 11 " --> pdb=" O ILE N 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 15 through 16 removed outlier: 6.316A pdb=" N THR M 15 " --> pdb=" O MET N 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 4.073A pdb=" N LEU M 122 " --> pdb=" O MET M 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 47 through 49 Processing sheet with id=AB5, first strand: chain 'M' and resid 251 through 252 Processing sheet with id=AB6, first strand: chain 'M' and resid 342 through 343 Processing sheet with id=AB7, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.859A pdb=" N TYR M 375 " --> pdb=" O ALA S 360 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ALA S 362 " --> pdb=" O TYR M 375 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL M 377 " --> pdb=" O ALA S 362 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN S 364 " --> pdb=" O VAL M 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 381 through 382 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.386A pdb=" N ASN N 11 " --> pdb=" O ILE Q 378 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR Q 375 " --> pdb=" O ALA W 360 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA W 362 " --> pdb=" O TYR Q 375 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL Q 377 " --> pdb=" O ALA W 362 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN W 364 " --> pdb=" O VAL Q 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU N 122 " --> pdb=" O MET N 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 47 through 49 Processing sheet with id=AC3, first strand: chain 'N' and resid 251 through 252 Processing sheet with id=AC4, first strand: chain 'N' and resid 342 through 343 Processing sheet with id=AC5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.705A pdb=" N ASN O 11 " --> pdb=" O ILE P 378 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR P 375 " --> pdb=" O ALA V 360 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA V 362 " --> pdb=" O TYR P 375 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL P 377 " --> pdb=" O ALA V 362 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN V 364 " --> pdb=" O VAL P 377 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU O 122 " --> pdb=" O MET O 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 47 through 49 Processing sheet with id=AC8, first strand: chain 'O' and resid 251 through 252 Processing sheet with id=AC9, first strand: chain 'O' and resid 342 through 343 Processing sheet with id=AD1, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.761A pdb=" N TYR O 375 " --> pdb=" O ALA U 360 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA U 362 " --> pdb=" O TYR O 375 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL O 377 " --> pdb=" O ALA U 362 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN U 364 " --> pdb=" O VAL O 377 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU P 122 " --> pdb=" O MET P 147 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 47 through 49 Processing sheet with id=AD4, first strand: chain 'P' and resid 251 through 252 Processing sheet with id=AD5, first strand: chain 'P' and resid 342 through 343 Processing sheet with id=AD6, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.578A pdb=" N ASN Q 11 " --> pdb=" O ILE R 378 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR R 375 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA X 362 " --> pdb=" O TYR R 375 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL R 377 " --> pdb=" O ALA X 362 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLN X 364 " --> pdb=" O VAL R 377 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU Q 122 " --> pdb=" O MET Q 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 47 through 49 Processing sheet with id=AD9, first strand: chain 'Q' and resid 251 through 252 Processing sheet with id=AE1, first strand: chain 'Q' and resid 342 through 343 Processing sheet with id=AE2, first strand: chain 'R' and resid 29 through 32 removed outlier: 4.073A pdb=" N LEU R 122 " --> pdb=" O MET R 147 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 47 through 49 Processing sheet with id=AE4, first strand: chain 'R' and resid 251 through 252 Processing sheet with id=AE5, first strand: chain 'R' and resid 342 through 343 Processing sheet with id=AE6, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.278A pdb=" N ASN S 11 " --> pdb=" O ILE T 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'S' and resid 15 through 16 removed outlier: 6.369A pdb=" N THR S 15 " --> pdb=" O MET T 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'S' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU S 122 " --> pdb=" O MET S 147 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 47 through 49 Processing sheet with id=AF1, first strand: chain 'S' and resid 251 through 252 Processing sheet with id=AF2, first strand: chain 'S' and resid 376 through 378 Processing sheet with id=AF3, first strand: chain 'S' and resid 381 through 382 Processing sheet with id=AF4, first strand: chain 'T' and resid 10 through 12 removed outlier: 6.414A pdb=" N ASN T 11 " --> pdb=" O ILE W 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'T' and resid 29 through 32 removed outlier: 4.073A pdb=" N LEU T 122 " --> pdb=" O MET T 147 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 47 through 49 Processing sheet with id=AF7, first strand: chain 'T' and resid 251 through 252 Processing sheet with id=AF8, first strand: chain 'T' and resid 342 through 343 Processing sheet with id=AF9, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.465A pdb=" N ASN U 11 " --> pdb=" O ILE V 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'U' and resid 15 through 16 removed outlier: 6.487A pdb=" N THR U 15 " --> pdb=" O MET V 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'U' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU U 122 " --> pdb=" O MET U 147 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 47 through 49 Processing sheet with id=AG4, first strand: chain 'U' and resid 251 through 252 Processing sheet with id=AG5, first strand: chain 'U' and resid 381 through 382 Processing sheet with id=AG6, first strand: chain 'V' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU V 122 " --> pdb=" O MET V 147 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 47 through 49 Processing sheet with id=AG8, first strand: chain 'V' and resid 251 through 252 Processing sheet with id=AG9, first strand: chain 'W' and resid 15 through 16 removed outlier: 6.195A pdb=" N THR W 15 " --> pdb=" O MET X 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'W' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU W 122 " --> pdb=" O MET W 147 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 47 through 49 Processing sheet with id=AH3, first strand: chain 'W' and resid 251 through 252 Processing sheet with id=AH4, first strand: chain 'X' and resid 29 through 32 removed outlier: 4.074A pdb=" N LEU X 122 " --> pdb=" O MET X 147 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'X' and resid 47 through 49 Processing sheet with id=AH6, first strand: chain 'X' and resid 251 through 252 Processing sheet with id=AH7, first strand: chain 'Y' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU Y 101 " --> pdb=" O ASP Y 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY Y 102 " --> pdb=" O THR Y 137 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Y' and resid 108 through 112 removed outlier: 6.635A pdb=" N THR Y 128 " --> pdb=" O GLN Y 111 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA Y 59 " --> pdb=" O THR Y 131 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 39 through 43 Processing sheet with id=AI1, first strand: chain 'Y' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA Z 59 " --> pdb=" O THR Z 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR Z 128 " --> pdb=" O GLN Z 111 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Z' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU Z 101 " --> pdb=" O ASP Z 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY Z 102 " --> pdb=" O THR Z 137 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Z' and resid 39 through 43 removed outlier: 7.957A pdb=" N TYR r 6 " --> pdb=" O TRP Z 49 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE Z 51 " --> pdb=" O TYR r 6 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Z' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA m 59 " --> pdb=" O THR m 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR m 128 " --> pdb=" O GLN m 111 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'm' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU m 101 " --> pdb=" O ASP m 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY m 102 " --> pdb=" O THR m 137 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'm' and resid 39 through 43 removed outlier: 7.967A pdb=" N TYR s 6 " --> pdb=" O TRP m 49 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE m 51 " --> pdb=" O TYR s 6 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'm' and resid 116 through 117 removed outlier: 3.561A pdb=" N ALA n 59 " --> pdb=" O THR n 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR n 128 " --> pdb=" O GLN n 111 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'n' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU n 101 " --> pdb=" O ASP n 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY n 102 " --> pdb=" O THR n 137 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'n' and resid 39 through 43 Processing sheet with id=AJ1, first strand: chain 'n' and resid 116 through 117 removed outlier: 3.561A pdb=" N ALA o 59 " --> pdb=" O THR o 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR o 128 " --> pdb=" O GLN o 111 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'o' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU o 101 " --> pdb=" O ASP o 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY o 102 " --> pdb=" O THR o 137 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'o' and resid 39 through 43 removed outlier: 8.113A pdb=" N TYR u 6 " --> pdb=" O TRP o 49 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE o 51 " --> pdb=" O TYR u 6 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'o' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA p 59 " --> pdb=" O THR p 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR p 128 " --> pdb=" O GLN p 111 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'p' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU p 101 " --> pdb=" O ASP p 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY p 102 " --> pdb=" O THR p 137 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'p' and resid 39 through 43 Processing sheet with id=AJ7, first strand: chain 'q' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU q 101 " --> pdb=" O ASP q 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY q 102 " --> pdb=" O THR q 137 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 108 through 112 removed outlier: 6.635A pdb=" N THR q 128 " --> pdb=" O GLN q 111 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA q 59 " --> pdb=" O THR q 131 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'q' and resid 116 through 117 removed outlier: 3.524A pdb=" N THR r 32 " --> pdb=" O ASP q 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA r 59 " --> pdb=" O THR r 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR r 128 " --> pdb=" O GLN r 111 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'r' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU r 101 " --> pdb=" O ASP r 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY r 102 " --> pdb=" O THR r 137 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'r' and resid 116 through 117 removed outlier: 3.561A pdb=" N ALA s 59 " --> pdb=" O THR s 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR s 128 " --> pdb=" O GLN s 111 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 's' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU s 101 " --> pdb=" O ASP s 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY s 102 " --> pdb=" O THR s 137 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 's' and resid 39 through 43 Processing sheet with id=AK5, first strand: chain 's' and resid 116 through 117 removed outlier: 3.563A pdb=" N ALA t 59 " --> pdb=" O THR t 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR t 128 " --> pdb=" O GLN t 111 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 't' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU t 101 " --> pdb=" O ASP t 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY t 102 " --> pdb=" O THR t 137 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 't' and resid 39 through 43 Processing sheet with id=AK8, first strand: chain 't' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA u 59 " --> pdb=" O THR u 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR u 128 " --> pdb=" O GLN u 111 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'u' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU u 101 " --> pdb=" O ASP u 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY u 102 " --> pdb=" O THR u 137 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'u' and resid 39 through 43 Processing sheet with id=AL2, first strand: chain 'u' and resid 116 through 117 removed outlier: 3.563A pdb=" N ALA v 59 " --> pdb=" O THR v 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR v 128 " --> pdb=" O GLN v 111 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'v' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU v 101 " --> pdb=" O ASP v 96 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY v 102 " --> pdb=" O THR v 137 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'v' and resid 39 through 43 Processing sheet with id=AL5, first strand: chain 'w' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU w 101 " --> pdb=" O ASP w 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY w 102 " --> pdb=" O THR w 137 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'w' and resid 39 through 43 Processing sheet with id=AL7, first strand: chain 'w' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA x 59 " --> pdb=" O THR x 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR x 128 " --> pdb=" O GLN x 111 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'x' and resid 18 through 19 removed outlier: 3.739A pdb=" N GLU x 101 " --> pdb=" O ASP x 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY x 102 " --> pdb=" O THR x 137 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'x' and resid 39 through 43 Processing sheet with id=AM1, first strand: chain 'x' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA y 59 " --> pdb=" O THR y 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR y 128 " --> pdb=" O GLN y 111 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'y' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU y 101 " --> pdb=" O ASP y 96 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY y 102 " --> pdb=" O THR y 137 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'y' and resid 39 through 43 Processing sheet with id=AM4, first strand: chain 'y' and resid 116 through 117 removed outlier: 3.562A pdb=" N ALA z 59 " --> pdb=" O THR z 131 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR z 128 " --> pdb=" O GLN z 111 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'z' and resid 18 through 19 removed outlier: 3.740A pdb=" N GLU z 101 " --> pdb=" O ASP z 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY z 102 " --> pdb=" O THR z 137 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'z' and resid 39 through 43 1646 hydrogen bonds defined for protein. 4545 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: 19.78 Time building geometry restraints manager: 17.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 18113 1.34 - 1.46: 9156 1.46 - 1.57: 28003 1.57 - 1.69: 0 1.69 - 1.81: 396 Bond restraints: 55668 Sorted by residual: bond pdb=" CB ARG O 297 " pdb=" CG ARG O 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.54e+00 bond pdb=" CB ARG P 297 " pdb=" CG ARG P 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" CB ARG W 297 " pdb=" CG ARG W 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.50e+00 bond pdb=" CB ARG X 297 " pdb=" CG ARG X 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.49e+00 bond pdb=" CB ARG T 297 " pdb=" CG ARG T 297 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.47e+00 ... (remaining 55663 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.79: 1752 106.79 - 113.60: 30977 113.60 - 120.40: 20699 120.40 - 127.21: 21789 127.21 - 134.02: 581 Bond angle restraints: 75798 Sorted by residual: angle pdb=" C PRO U 78 " pdb=" N ARG U 79 " pdb=" CA ARG U 79 " ideal model delta sigma weight residual 122.15 104.76 17.39 3.47e+00 8.31e-02 2.51e+01 angle pdb=" C PRO Q 78 " pdb=" N ARG Q 79 " pdb=" CA ARG Q 79 " ideal model delta sigma weight residual 122.15 104.77 17.38 3.47e+00 8.31e-02 2.51e+01 angle pdb=" C PRO M 78 " pdb=" N ARG M 79 " pdb=" CA ARG M 79 " ideal model delta sigma weight residual 122.15 104.78 17.37 3.47e+00 8.31e-02 2.51e+01 angle pdb=" C PRO N 78 " pdb=" N ARG N 79 " pdb=" CA ARG N 79 " ideal model delta sigma weight residual 122.15 104.78 17.37 3.47e+00 8.31e-02 2.51e+01 angle pdb=" C PRO R 78 " pdb=" N ARG R 79 " pdb=" CA ARG R 79 " ideal model delta sigma weight residual 122.15 104.79 17.36 3.47e+00 8.31e-02 2.50e+01 ... (remaining 75793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 29708 17.96 - 35.92: 2392 35.92 - 53.88: 804 53.88 - 71.84: 270 71.84 - 89.80: 24 Dihedral angle restraints: 33198 sinusoidal: 12594 harmonic: 20604 Sorted by residual: dihedral pdb=" CA TYR R 87 " pdb=" C TYR R 87 " pdb=" N ALA R 88 " pdb=" CA ALA R 88 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA TYR V 87 " pdb=" C TYR V 87 " pdb=" N ALA V 88 " pdb=" CA ALA V 88 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA TYR Q 87 " pdb=" C TYR Q 87 " pdb=" N ALA Q 88 " pdb=" CA ALA Q 88 " ideal model delta harmonic sigma weight residual -180.00 -150.79 -29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 33195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 5987 0.044 - 0.087: 1961 0.087 - 0.131: 720 0.131 - 0.174: 92 0.174 - 0.218: 18 Chirality restraints: 8778 Sorted by residual: chirality pdb=" CA PHE t 90 " pdb=" N PHE t 90 " pdb=" C PHE t 90 " pdb=" CB PHE t 90 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA PHE x 90 " pdb=" N PHE x 90 " pdb=" C PHE x 90 " pdb=" CB PHE x 90 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PHE v 90 " pdb=" N PHE v 90 " pdb=" C PHE v 90 " pdb=" CB PHE v 90 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 8775 not shown) Planarity restraints: 9822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE s 90 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C PHE s 90 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE s 90 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO s 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE u 90 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C PHE u 90 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE u 90 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO u 91 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE v 90 " -0.015 2.00e-02 2.50e+03 2.88e-02 8.29e+00 pdb=" C PHE v 90 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE v 90 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO v 91 " -0.017 2.00e-02 2.50e+03 ... (remaining 9819 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 444 2.53 - 3.12: 41154 3.12 - 3.72: 80812 3.72 - 4.31: 117204 4.31 - 4.90: 197051 Nonbonded interactions: 436665 Sorted by model distance: nonbonded pdb=" OG1 THR M 10 " pdb=" OE1 GLU T 285 " model vdw 1.939 2.440 nonbonded pdb=" OG1 THR P 10 " pdb=" OE1 GLU S 285 " model vdw 2.098 2.440 nonbonded pdb=" O THR R 197 " pdb=" OG1 THR R 197 " model vdw 2.136 2.440 nonbonded pdb=" O THR S 197 " pdb=" OG1 THR S 197 " model vdw 2.136 2.440 nonbonded pdb=" O THR Q 197 " pdb=" OG1 THR Q 197 " model vdw 2.136 2.440 ... (remaining 436660 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 '1' selection = chain '2' selection = chain 'Y' selection = chain 'Z' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.010 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 113.580 Find NCS groups from input model: 3.530 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 55668 Z= 0.387 Angle : 0.834 17.389 75798 Z= 0.478 Chirality : 0.050 0.218 8778 Planarity : 0.005 0.052 9822 Dihedral : 15.954 89.802 19926 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 11.19 % Allowed : 10.79 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.09), residues: 7080 helix: -0.78 (0.14), residues: 1476 sheet: -0.30 (0.13), residues: 1560 loop : -2.78 (0.08), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP p 127 HIS 0.004 0.001 HIS s 72 PHE 0.035 0.003 PHE m 90 TYR 0.015 0.002 TYR S 131 ARG 0.005 0.001 ARG N 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1914 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 645 poor density : 1269 time to evaluate : 4.794 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: 1 18 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7376 (mtt180) REVERT: 1 80 MET cc_start: 0.8338 (mmm) cc_final: 0.8060 (mmt) REVERT: 1 97 SER cc_start: 0.7983 (m) cc_final: 0.7461 (p) REVERT: 1 112 LYS cc_start: 0.8449 (mttp) cc_final: 0.8066 (mtpt) REVERT: 2 27 ASP cc_start: 0.7623 (m-30) cc_final: 0.7346 (m-30) REVERT: 2 97 SER cc_start: 0.8044 (m) cc_final: 0.7591 (p) REVERT: 2 100 ASN cc_start: 0.7891 (m-40) cc_final: 0.7681 (m-40) REVERT: 2 112 LYS cc_start: 0.8501 (mttp) cc_final: 0.8179 (mtpt) REVERT: 2 120 ASN cc_start: 0.8019 (t0) cc_final: 0.7681 (t0) REVERT: M 117 PHE cc_start: 0.5110 (p90) cc_final: 0.4758 (p90) REVERT: M 123 ASP cc_start: 0.3208 (OUTLIER) cc_final: 0.2954 (p0) REVERT: M 139 VAL cc_start: 0.7185 (OUTLIER) cc_final: 0.6845 (t) REVERT: M 318 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8605 (mt) REVERT: M 332 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6665 (mt) REVERT: M 341 THR cc_start: 0.8412 (p) cc_final: 0.8006 (t) REVERT: M 383 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7257 (t) REVERT: N 10 THR cc_start: 0.8711 (p) cc_final: 0.8381 (t) REVERT: N 29 GLN cc_start: 0.4280 (pt0) cc_final: 0.2688 (pm20) REVERT: N 48 LYS cc_start: 0.5890 (ttpt) cc_final: 0.4769 (tttm) REVERT: N 59 ASP cc_start: 0.0740 (OUTLIER) cc_final: 0.0413 (t0) REVERT: N 123 ASP cc_start: 0.3075 (OUTLIER) cc_final: 0.2564 (p0) REVERT: N 139 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6814 (t) REVERT: N 210 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6344 (tppp) REVERT: N 252 ASP cc_start: 0.6916 (p0) cc_final: 0.6662 (p0) REVERT: N 256 GLN cc_start: 0.6441 (mp10) cc_final: 0.6190 (mm-40) REVERT: N 287 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7133 (mm-30) REVERT: N 341 THR cc_start: 0.8360 (p) cc_final: 0.8030 (t) REVERT: N 364 GLN cc_start: 0.8119 (mt0) cc_final: 0.7689 (mm110) REVERT: O 29 GLN cc_start: 0.4259 (pt0) cc_final: 0.2574 (pm20) REVERT: O 81 ILE cc_start: 0.4263 (OUTLIER) cc_final: 0.3978 (mm) REVERT: O 123 ASP cc_start: 0.2871 (OUTLIER) cc_final: 0.2379 (p0) REVERT: O 139 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.6769 (m) REVERT: O 156 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5842 (mt-10) REVERT: O 169 LYS cc_start: 0.4840 (OUTLIER) cc_final: 0.4492 (ptmm) REVERT: O 287 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7109 (mm-30) REVERT: O 290 SER cc_start: 0.8295 (t) cc_final: 0.7758 (p) REVERT: O 318 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8562 (mt) REVERT: O 341 THR cc_start: 0.8340 (p) cc_final: 0.7944 (t) REVERT: O 364 GLN cc_start: 0.7871 (mt0) cc_final: 0.7635 (mm110) REVERT: P 55 GLU cc_start: 0.4288 (OUTLIER) cc_final: 0.3880 (mp0) REVERT: P 59 ASP cc_start: 0.0600 (OUTLIER) cc_final: 0.0191 (t0) REVERT: P 81 ILE cc_start: 0.4814 (OUTLIER) cc_final: 0.4436 (mm) REVERT: P 123 ASP cc_start: 0.2968 (OUTLIER) cc_final: 0.2521 (p0) REVERT: P 139 VAL cc_start: 0.6994 (OUTLIER) cc_final: 0.6645 (m) REVERT: P 169 LYS cc_start: 0.4745 (OUTLIER) cc_final: 0.4305 (ptmm) REVERT: P 202 ASP cc_start: 0.8012 (m-30) cc_final: 0.7752 (m-30) REVERT: P 252 ASP cc_start: 0.6837 (p0) cc_final: 0.6582 (p0) REVERT: P 290 SER cc_start: 0.7952 (t) cc_final: 0.7507 (p) REVERT: P 321 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7934 (tmm-80) REVERT: Q 48 LYS cc_start: 0.6210 (ttpt) cc_final: 0.5544 (ttpt) REVERT: Q 55 GLU cc_start: 0.4221 (OUTLIER) cc_final: 0.3747 (mp0) REVERT: Q 123 ASP cc_start: 0.2993 (OUTLIER) cc_final: 0.2723 (p0) REVERT: Q 139 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6801 (t) REVERT: Q 169 LYS cc_start: 0.4636 (OUTLIER) cc_final: 0.4193 (ptmm) REVERT: Q 210 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.6031 (tttp) REVERT: Q 290 SER cc_start: 0.8397 (t) cc_final: 0.8057 (p) REVERT: R 59 ASP cc_start: 0.1278 (OUTLIER) cc_final: 0.0853 (t0) REVERT: R 117 PHE cc_start: 0.4863 (p90) cc_final: 0.4557 (p90) REVERT: R 123 ASP cc_start: 0.2805 (OUTLIER) cc_final: 0.2429 (p0) REVERT: R 139 VAL cc_start: 0.7186 (OUTLIER) cc_final: 0.6778 (t) REVERT: R 332 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6786 (mt) REVERT: R 341 THR cc_start: 0.8356 (p) cc_final: 0.8060 (t) REVERT: S 32 LEU cc_start: 0.6792 (pp) cc_final: 0.6430 (tt) REVERT: S 55 GLU cc_start: 0.4555 (OUTLIER) cc_final: 0.4054 (mp0) REVERT: S 76 GLN cc_start: 0.6689 (tp40) cc_final: 0.5768 (mm110) REVERT: S 81 ILE cc_start: 0.4282 (OUTLIER) cc_final: 0.4041 (mt) REVERT: S 123 ASP cc_start: 0.2851 (OUTLIER) cc_final: 0.2449 (p0) REVERT: S 252 ASP cc_start: 0.7214 (p0) cc_final: 0.6978 (p0) REVERT: S 288 MET cc_start: 0.8069 (mmm) cc_final: 0.7795 (mmt) REVERT: S 290 SER cc_start: 0.8531 (t) cc_final: 0.8294 (p) REVERT: T 17 THR cc_start: 0.6591 (m) cc_final: 0.6183 (m) REVERT: T 23 ARG cc_start: 0.5329 (tpt170) cc_final: 0.3448 (mtm180) REVERT: T 29 GLN cc_start: 0.4113 (pt0) cc_final: 0.3741 (pt0) REVERT: T 32 LEU cc_start: 0.6618 (pp) cc_final: 0.6191 (tt) REVERT: T 48 LYS cc_start: 0.6109 (ttpt) cc_final: 0.5854 (ttpt) REVERT: T 123 ASP cc_start: 0.3466 (OUTLIER) cc_final: 0.3005 (p0) REVERT: T 169 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5503 (ptmm) REVERT: T 318 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7909 (mp) REVERT: U 29 GLN cc_start: 0.4084 (pt0) cc_final: 0.3708 (pt0) REVERT: U 32 LEU cc_start: 0.6565 (pp) cc_final: 0.6087 (tt) REVERT: U 55 GLU cc_start: 0.4590 (OUTLIER) cc_final: 0.4039 (mp0) REVERT: U 68 LYS cc_start: 0.5166 (mttt) cc_final: 0.4931 (tptp) REVERT: U 123 ASP cc_start: 0.2427 (OUTLIER) cc_final: 0.1946 (p0) REVERT: U 195 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7519 (ttp) REVERT: U 290 SER cc_start: 0.8602 (t) cc_final: 0.8362 (m) REVERT: U 382 MET cc_start: 0.7657 (ttp) cc_final: 0.7424 (ttm) REVERT: V 29 GLN cc_start: 0.4054 (pt0) cc_final: 0.3708 (pt0) REVERT: V 32 LEU cc_start: 0.6765 (pp) cc_final: 0.6323 (tt) REVERT: V 55 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4438 (mp0) REVERT: V 76 GLN cc_start: 0.6675 (tp40) cc_final: 0.6265 (tp-100) REVERT: V 123 ASP cc_start: 0.2660 (OUTLIER) cc_final: 0.2230 (p0) REVERT: V 252 ASP cc_start: 0.7019 (p0) cc_final: 0.6794 (p0) REVERT: V 367 PHE cc_start: 0.6208 (OUTLIER) cc_final: 0.5994 (t80) REVERT: W 29 GLN cc_start: 0.4050 (pt0) cc_final: 0.3719 (pt0) REVERT: W 32 LEU cc_start: 0.6666 (pp) cc_final: 0.6223 (tt) REVERT: W 55 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.4228 (mp0) REVERT: W 76 GLN cc_start: 0.6713 (tp40) cc_final: 0.6316 (tp-100) REVERT: W 81 ILE cc_start: 0.4027 (OUTLIER) cc_final: 0.3765 (mp) REVERT: W 123 ASP cc_start: 0.2712 (OUTLIER) cc_final: 0.2285 (p0) REVERT: W 204 ASN cc_start: 0.7957 (m-40) cc_final: 0.7660 (m110) REVERT: W 252 ASP cc_start: 0.6804 (p0) cc_final: 0.6526 (p0) REVERT: W 305 MET cc_start: 0.7870 (mmm) cc_final: 0.7594 (mmp) REVERT: W 343 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8388 (m) REVERT: W 367 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5887 (m-80) REVERT: X 55 GLU cc_start: 0.4874 (OUTLIER) cc_final: 0.4334 (mp0) REVERT: X 76 GLN cc_start: 0.6517 (tp40) cc_final: 0.5599 (mm110) REVERT: X 123 ASP cc_start: 0.3218 (OUTLIER) cc_final: 0.2902 (p0) REVERT: X 162 THR cc_start: 0.5076 (OUTLIER) cc_final: 0.4868 (m) REVERT: X 212 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6767 (mptt) REVERT: X 290 SER cc_start: 0.8525 (t) cc_final: 0.8233 (p) REVERT: Y 12 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8243 (t) REVERT: Y 16 ASP cc_start: 0.7654 (t0) cc_final: 0.7315 (t70) REVERT: Y 101 GLU cc_start: 0.8127 (tt0) cc_final: 0.7884 (tt0) REVERT: Y 112 LYS cc_start: 0.8477 (mttp) cc_final: 0.8166 (mtpt) REVERT: Y 120 ASN cc_start: 0.7945 (t0) cc_final: 0.7679 (t0) REVERT: Z 12 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8269 (t) REVERT: Z 16 ASP cc_start: 0.7722 (t0) cc_final: 0.7340 (t0) REVERT: Z 31 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8426 (p) REVERT: Z 54 THR cc_start: 0.8264 (p) cc_final: 0.8039 (t) REVERT: Z 112 LYS cc_start: 0.8489 (mttp) cc_final: 0.8203 (mtpt) REVERT: m 3 MET cc_start: 0.3706 (tmm) cc_final: 0.3460 (tmm) REVERT: m 16 ASP cc_start: 0.7805 (t0) cc_final: 0.7387 (t0) REVERT: m 31 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8293 (p) REVERT: m 73 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7925 (tmt90) REVERT: m 96 ASP cc_start: 0.8291 (t0) cc_final: 0.7892 (t0) REVERT: m 101 GLU cc_start: 0.8152 (tt0) cc_final: 0.7924 (tt0) REVERT: n 16 ASP cc_start: 0.7747 (t0) cc_final: 0.7486 (t70) REVERT: n 19 ARG cc_start: 0.7058 (mtp180) cc_final: 0.6769 (ttt-90) REVERT: n 86 ARG cc_start: 0.8148 (ttt90) cc_final: 0.7947 (ttt90) REVERT: n 96 ASP cc_start: 0.8145 (t0) cc_final: 0.7912 (t70) REVERT: n 112 LYS cc_start: 0.8509 (mttp) cc_final: 0.8193 (mtpt) REVERT: n 120 ASN cc_start: 0.7940 (t0) cc_final: 0.7717 (t0) REVERT: o 16 ASP cc_start: 0.7543 (t0) cc_final: 0.7247 (t70) REVERT: o 19 ARG cc_start: 0.7408 (mtp180) cc_final: 0.7184 (ttt-90) REVERT: o 41 MET cc_start: 0.8507 (tpp) cc_final: 0.8111 (tpp) REVERT: o 112 LYS cc_start: 0.8335 (mttp) cc_final: 0.8123 (mtpt) REVERT: p 3 MET cc_start: 0.3456 (tmm) cc_final: 0.3220 (tmm) REVERT: p 16 ASP cc_start: 0.7779 (t0) cc_final: 0.7362 (t0) REVERT: p 19 ARG cc_start: 0.7306 (mtp180) cc_final: 0.6984 (ttt-90) REVERT: p 93 ASP cc_start: 0.7922 (t70) cc_final: 0.7617 (t0) REVERT: p 96 ASP cc_start: 0.8154 (t0) cc_final: 0.7692 (t70) REVERT: p 133 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7789 (tp30) REVERT: q 33 SER cc_start: 0.8398 (p) cc_final: 0.8171 (t) REVERT: q 112 LYS cc_start: 0.8378 (mttp) cc_final: 0.8168 (mtpt) REVERT: q 133 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: r 76 THR cc_start: 0.8588 (t) cc_final: 0.8379 (m) REVERT: s 3 MET cc_start: 0.2483 (tmm) cc_final: 0.2227 (tmt) REVERT: s 8 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7709 (tpt) REVERT: s 90 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.6588 (p90) REVERT: t 33 SER cc_start: 0.8544 (p) cc_final: 0.8173 (t) REVERT: t 97 SER cc_start: 0.7975 (m) cc_final: 0.7536 (p) REVERT: u 24 MET cc_start: 0.8142 (mmm) cc_final: 0.7602 (tpt) REVERT: v 8 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7403 (tpt) REVERT: v 33 SER cc_start: 0.8550 (p) cc_final: 0.8207 (t) REVERT: v 90 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7169 (p90) REVERT: w 3 MET cc_start: 0.2671 (tmm) cc_final: 0.2226 (tmt) REVERT: w 12 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8123 (m) REVERT: w 31 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8098 (p) REVERT: w 32 THR cc_start: 0.8652 (p) cc_final: 0.8419 (t) REVERT: w 64 LYS cc_start: 0.8956 (mttt) cc_final: 0.8723 (mtmm) REVERT: w 133 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: x 16 ASP cc_start: 0.8101 (t0) cc_final: 0.7641 (t70) REVERT: x 80 MET cc_start: 0.8218 (mmm) cc_final: 0.8013 (mmt) REVERT: x 97 SER cc_start: 0.7875 (m) cc_final: 0.7359 (p) REVERT: x 112 LYS cc_start: 0.8658 (mttp) cc_final: 0.8252 (mtpt) REVERT: y 1 MET cc_start: 0.2217 (mtp) cc_final: 0.1943 (mpt) REVERT: y 12 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8489 (m) REVERT: y 97 SER cc_start: 0.8022 (m) cc_final: 0.7685 (p) REVERT: y 112 LYS cc_start: 0.8535 (mttp) cc_final: 0.8187 (mtpt) REVERT: y 120 ASN cc_start: 0.7960 (t0) cc_final: 0.7636 (t0) REVERT: y 133 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: z 1 MET cc_start: 0.2599 (mtp) cc_final: 0.2128 (mtt) REVERT: z 16 ASP cc_start: 0.8027 (t0) cc_final: 0.7688 (t70) REVERT: z 31 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8200 (m) REVERT: z 64 LYS cc_start: 0.8977 (mttt) cc_final: 0.8662 (mtmm) REVERT: z 97 SER cc_start: 0.8066 (m) cc_final: 0.7466 (p) REVERT: z 112 LYS cc_start: 0.8387 (mttp) cc_final: 0.8176 (mtpt) outliers start: 645 outliers final: 260 residues processed: 1728 average time/residue: 1.1613 time to fit residues: 2599.9685 Evaluate side-chains 1226 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 899 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 THR Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 61 VAL Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 94 PHE Chi-restraints excluded: chain 2 residue 133 GLU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 123 ASP Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 209 LEU Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 318 LEU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 348 PHE Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 209 LEU Chi-restraints excluded: chain N residue 210 LYS Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 348 PHE Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 85 VAL Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 169 LYS Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 208 THR Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 318 LEU Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 81 ILE Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 208 THR Chi-restraints excluded: chain P residue 209 LEU Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 343 THR Chi-restraints excluded: chain P residue 348 PHE Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 123 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 169 LYS Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 208 THR Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain Q residue 210 LYS Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 348 PHE Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 123 ASP Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 172 VAL Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 209 LEU Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 169 LYS Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 318 LEU Chi-restraints excluded: chain T residue 343 THR Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 13 THR Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 195 MET Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 343 THR Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 343 THR Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 367 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 55 GLU Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 343 THR Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 367 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 55 GLU Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 212 LYS Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 61 VAL Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 31 THR Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 95 ILE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 31 THR Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 61 VAL Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 31 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 61 VAL Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 31 THR Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 31 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 94 PHE Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 31 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 61 VAL Chi-restraints excluded: chain q residue 133 GLU Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 94 PHE Chi-restraints excluded: chain r residue 95 ILE Chi-restraints excluded: chain r residue 133 GLU Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 12 THR Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 31 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 61 VAL Chi-restraints excluded: chain s residue 90 PHE Chi-restraints excluded: chain s residue 133 GLU Chi-restraints excluded: chain t residue 12 THR Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 31 THR Chi-restraints excluded: chain t residue 56 ASP Chi-restraints excluded: chain t residue 61 VAL Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 31 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 61 VAL Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 94 PHE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 12 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 31 THR Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 61 VAL Chi-restraints excluded: chain v residue 90 PHE Chi-restraints excluded: chain v residue 133 GLU Chi-restraints excluded: chain w residue 12 THR Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 31 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 12 THR Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 31 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 61 VAL Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 12 THR Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 31 THR Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 133 GLU Chi-restraints excluded: chain z residue 12 THR Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 31 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 90 PHE Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 597 optimal weight: 6.9990 chunk 536 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 361 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 554 optimal weight: 20.0000 chunk 214 optimal weight: 0.0370 chunk 337 optimal weight: 2.9990 chunk 413 optimal weight: 0.9990 chunk 642 optimal weight: 9.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 100 ASN 1 121 ASN 2 121 ASN ** M 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 307 GLN O 307 GLN P 295 ASN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 GLN ** S 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 GLN ** T 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN U 317 GLN V 40 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN X 40 GLN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 GLN p 121 ASN q 121 ASN r 120 ASN u 120 ASN v 121 ASN x 121 ASN y 100 ASN y 121 ASN z 100 ASN z 121 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55668 Z= 0.187 Angle : 0.630 8.705 75798 Z= 0.339 Chirality : 0.045 0.161 8778 Planarity : 0.005 0.044 9822 Dihedral : 10.557 60.000 8204 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 9.61 % Allowed : 17.79 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.09), residues: 7080 helix: -0.02 (0.14), residues: 1476 sheet: -0.15 (0.13), residues: 1470 loop : -2.49 (0.08), residues: 4134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP z 127 HIS 0.004 0.001 HIS V 34 PHE 0.029 0.002 PHE v 90 TYR 0.018 0.002 TYR O 67 ARG 0.008 0.001 ARG R 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1583 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 554 poor density : 1029 time to evaluate : 4.906 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: 1 93 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7226 (t0) REVERT: 1 97 SER cc_start: 0.8221 (m) cc_final: 0.7663 (p) REVERT: 1 112 LYS cc_start: 0.8455 (mttp) cc_final: 0.8081 (mtpt) REVERT: 2 12 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8410 (m) REVERT: 2 27 ASP cc_start: 0.7514 (m-30) cc_final: 0.7224 (m-30) REVERT: 2 97 SER cc_start: 0.8256 (m) cc_final: 0.7761 (p) REVERT: 2 100 ASN cc_start: 0.7965 (m-40) cc_final: 0.7660 (m-40) REVERT: 2 112 LYS cc_start: 0.8392 (mttp) cc_final: 0.8138 (mtpt) REVERT: 2 120 ASN cc_start: 0.7708 (t0) cc_final: 0.7483 (t0) REVERT: 2 133 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: M 10 THR cc_start: 0.8578 (p) cc_final: 0.8031 (t) REVERT: M 40 GLN cc_start: 0.3623 (OUTLIER) cc_final: 0.2524 (mp10) REVERT: M 59 ASP cc_start: 0.1630 (OUTLIER) cc_final: 0.1367 (t0) REVERT: M 117 PHE cc_start: 0.5046 (p90) cc_final: 0.4746 (p90) REVERT: M 139 VAL cc_start: 0.6868 (p) cc_final: 0.6633 (t) REVERT: M 218 ARG cc_start: 0.2798 (OUTLIER) cc_final: 0.2522 (tpm170) REVERT: M 332 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6457 (mt) REVERT: N 10 THR cc_start: 0.8407 (p) cc_final: 0.8188 (t) REVERT: N 29 GLN cc_start: 0.4031 (pt0) cc_final: 0.3824 (pt0) REVERT: N 48 LYS cc_start: 0.5810 (ttpt) cc_final: 0.4712 (tttm) REVERT: N 123 ASP cc_start: 0.2462 (OUTLIER) cc_final: 0.2163 (p0) REVERT: N 139 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6850 (t) REVERT: N 147 MET cc_start: 0.2539 (tpp) cc_final: 0.2002 (tpp) REVERT: N 195 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7191 (mtp) REVERT: N 252 ASP cc_start: 0.6712 (p0) cc_final: 0.6462 (p0) REVERT: N 256 GLN cc_start: 0.6594 (mp10) cc_final: 0.6380 (pm20) REVERT: O 29 GLN cc_start: 0.3908 (pt0) cc_final: 0.2360 (pm20) REVERT: O 81 ILE cc_start: 0.4780 (OUTLIER) cc_final: 0.4440 (mp) REVERT: O 123 ASP cc_start: 0.2360 (OUTLIER) cc_final: 0.2130 (p0) REVERT: O 139 VAL cc_start: 0.7112 (OUTLIER) cc_final: 0.6851 (t) REVERT: O 305 MET cc_start: 0.8045 (mmp) cc_final: 0.7608 (mmm) REVERT: O 341 THR cc_start: 0.8291 (p) cc_final: 0.7987 (t) REVERT: P 3 LYS cc_start: 0.6523 (mppt) cc_final: 0.6308 (mppt) REVERT: P 59 ASP cc_start: 0.0752 (OUTLIER) cc_final: 0.0261 (t0) REVERT: P 290 SER cc_start: 0.8266 (t) cc_final: 0.7759 (p) REVERT: Q 48 LYS cc_start: 0.5739 (ttpt) cc_final: 0.5362 (ttpp) REVERT: Q 139 VAL cc_start: 0.6975 (p) cc_final: 0.6704 (t) REVERT: Q 147 MET cc_start: 0.2820 (tpp) cc_final: 0.1838 (tpp) REVERT: Q 164 ILE cc_start: 0.4557 (OUTLIER) cc_final: 0.4167 (tp) REVERT: Q 274 ILE cc_start: 0.7152 (mp) cc_final: 0.6910 (mt) REVERT: Q 290 SER cc_start: 0.8482 (t) cc_final: 0.8002 (p) REVERT: Q 343 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8492 (t) REVERT: R 10 THR cc_start: 0.8752 (p) cc_final: 0.8521 (p) REVERT: R 117 PHE cc_start: 0.4809 (p90) cc_final: 0.4490 (p90) REVERT: R 139 VAL cc_start: 0.6935 (p) cc_final: 0.6689 (t) REVERT: R 147 MET cc_start: 0.3120 (tpp) cc_final: 0.2648 (tpp) REVERT: R 332 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6600 (mt) REVERT: R 341 THR cc_start: 0.8245 (p) cc_final: 0.8031 (t) REVERT: S 76 GLN cc_start: 0.6354 (tp40) cc_final: 0.5854 (mm110) REVERT: S 81 ILE cc_start: 0.4154 (OUTLIER) cc_final: 0.3793 (mp) REVERT: S 84 LYS cc_start: 0.3840 (OUTLIER) cc_final: 0.3619 (tppt) REVERT: S 123 ASP cc_start: 0.1964 (OUTLIER) cc_final: 0.1729 (p0) REVERT: S 220 ILE cc_start: 0.6129 (OUTLIER) cc_final: 0.5692 (pt) REVERT: S 348 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.5070 (m-10) REVERT: T 23 ARG cc_start: 0.5607 (tpt170) cc_final: 0.3409 (mtm180) REVERT: T 29 GLN cc_start: 0.4038 (pt0) cc_final: 0.3804 (pt0) REVERT: T 59 ASP cc_start: 0.2082 (OUTLIER) cc_final: 0.1648 (t0) REVERT: T 81 ILE cc_start: 0.4416 (OUTLIER) cc_final: 0.4144 (mp) REVERT: T 123 ASP cc_start: 0.2582 (OUTLIER) cc_final: 0.2070 (p0) REVERT: T 169 LYS cc_start: 0.5847 (ttpm) cc_final: 0.5387 (ptmm) REVERT: T 220 ILE cc_start: 0.6414 (OUTLIER) cc_final: 0.5977 (pp) REVERT: T 290 SER cc_start: 0.8500 (t) cc_final: 0.8195 (m) REVERT: U 20 PHE cc_start: 0.6617 (m-80) cc_final: 0.6346 (m-80) REVERT: U 23 ARG cc_start: 0.5501 (tpt-90) cc_final: 0.3168 (mtm180) REVERT: U 29 GLN cc_start: 0.3966 (pt0) cc_final: 0.3547 (pt0) REVERT: U 68 LYS cc_start: 0.5282 (mttt) cc_final: 0.4990 (tptp) REVERT: U 123 ASP cc_start: 0.2105 (OUTLIER) cc_final: 0.1781 (p0) REVERT: U 164 ILE cc_start: 0.4336 (OUTLIER) cc_final: 0.4036 (mp) REVERT: U 290 SER cc_start: 0.8546 (t) cc_final: 0.8316 (m) REVERT: V 76 GLN cc_start: 0.6582 (tp40) cc_final: 0.5453 (mm110) REVERT: V 81 ILE cc_start: 0.4131 (OUTLIER) cc_final: 0.3837 (mt) REVERT: V 123 ASP cc_start: 0.2376 (OUTLIER) cc_final: 0.2141 (p0) REVERT: V 164 ILE cc_start: 0.4479 (OUTLIER) cc_final: 0.4005 (mp) REVERT: V 211 PHE cc_start: 0.6636 (t80) cc_final: 0.6330 (t80) REVERT: V 220 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6130 (pp) REVERT: W 76 GLN cc_start: 0.6631 (tp40) cc_final: 0.5467 (mm110) REVERT: W 81 ILE cc_start: 0.4249 (OUTLIER) cc_final: 0.3901 (mp) REVERT: W 164 ILE cc_start: 0.4913 (OUTLIER) cc_final: 0.4380 (mp) REVERT: W 201 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7519 (t70) REVERT: W 211 PHE cc_start: 0.6687 (t80) cc_final: 0.6386 (t80) REVERT: W 220 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.5959 (pp) REVERT: W 348 PHE cc_start: 0.5657 (OUTLIER) cc_final: 0.5123 (m-10) REVERT: X 23 ARG cc_start: 0.5545 (tmt-80) cc_final: 0.3118 (mtm180) REVERT: X 76 GLN cc_start: 0.6419 (tp40) cc_final: 0.5426 (mm110) REVERT: X 81 ILE cc_start: 0.4215 (OUTLIER) cc_final: 0.3793 (mp) REVERT: X 164 ILE cc_start: 0.4323 (OUTLIER) cc_final: 0.3967 (tp) REVERT: X 220 ILE cc_start: 0.6209 (OUTLIER) cc_final: 0.5775 (pt) REVERT: Y 19 ARG cc_start: 0.7059 (mtp180) cc_final: 0.6803 (ttt-90) REVERT: Y 66 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8503 (mtmp) REVERT: Y 100 ASN cc_start: 0.7758 (m-40) cc_final: 0.7502 (m-40) REVERT: Y 112 LYS cc_start: 0.8528 (mttp) cc_final: 0.8266 (mtpt) REVERT: Z 16 ASP cc_start: 0.7810 (t0) cc_final: 0.7413 (t0) REVERT: Z 19 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6859 (ttt-90) REVERT: Z 112 LYS cc_start: 0.8496 (mttp) cc_final: 0.8244 (mtpt) REVERT: m 96 ASP cc_start: 0.8212 (t0) cc_final: 0.7975 (t0) REVERT: n 16 ASP cc_start: 0.7629 (t0) cc_final: 0.7306 (t0) REVERT: n 19 ARG cc_start: 0.6891 (mtp180) cc_final: 0.6661 (ttt-90) REVERT: n 33 SER cc_start: 0.8186 (p) cc_final: 0.7978 (t) REVERT: n 112 LYS cc_start: 0.8502 (mttp) cc_final: 0.8236 (mtpt) REVERT: o 16 ASP cc_start: 0.7826 (t0) cc_final: 0.7519 (t0) REVERT: o 19 ARG cc_start: 0.7309 (mtp180) cc_final: 0.7086 (ttt-90) REVERT: o 112 LYS cc_start: 0.8479 (mttp) cc_final: 0.8213 (mtpt) REVERT: p 19 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6795 (ttt-90) REVERT: p 96 ASP cc_start: 0.8194 (t0) cc_final: 0.7826 (t0) REVERT: q 32 THR cc_start: 0.8846 (p) cc_final: 0.8589 (t) REVERT: q 97 SER cc_start: 0.7918 (m) cc_final: 0.7467 (p) REVERT: q 101 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: q 112 LYS cc_start: 0.8541 (mttp) cc_final: 0.8318 (mtpt) REVERT: r 90 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.6897 (p90) REVERT: r 96 ASP cc_start: 0.8532 (t0) cc_final: 0.8327 (t70) REVERT: s 3 MET cc_start: 0.2555 (tmm) cc_final: 0.2314 (tmt) REVERT: s 8 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7486 (tpt) REVERT: t 97 SER cc_start: 0.7978 (m) cc_final: 0.7437 (p) REVERT: t 101 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: t 107 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: u 12 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8065 (m) REVERT: u 90 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.6807 (p90) REVERT: v 8 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7699 (tpt) REVERT: v 52 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8187 (t) REVERT: w 3 MET cc_start: 0.2691 (tmm) cc_final: 0.2224 (tmt) REVERT: w 133 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: x 16 ASP cc_start: 0.8123 (t0) cc_final: 0.7651 (t70) REVERT: x 80 MET cc_start: 0.8432 (mmm) cc_final: 0.8191 (mmp) REVERT: x 97 SER cc_start: 0.8175 (m) cc_final: 0.7655 (p) REVERT: x 112 LYS cc_start: 0.8609 (mttp) cc_final: 0.8267 (mtpt) REVERT: y 1 MET cc_start: 0.2479 (mtp) cc_final: 0.2070 (mpt) REVERT: y 3 MET cc_start: 0.2889 (tmm) cc_final: 0.2331 (tmt) REVERT: y 16 ASP cc_start: 0.7815 (t0) cc_final: 0.7615 (t70) REVERT: y 97 SER cc_start: 0.8129 (m) cc_final: 0.7866 (p) REVERT: y 112 LYS cc_start: 0.8427 (mttp) cc_final: 0.8141 (mtpt) REVERT: y 115 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: y 133 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: z 1 MET cc_start: 0.2619 (mtp) cc_final: 0.2088 (mtt) REVERT: z 16 ASP cc_start: 0.7858 (t0) cc_final: 0.7564 (t70) REVERT: z 97 SER cc_start: 0.8364 (m) cc_final: 0.7853 (p) REVERT: z 100 ASN cc_start: 0.8177 (m-40) cc_final: 0.7802 (m-40) REVERT: z 112 LYS cc_start: 0.8532 (mttp) cc_final: 0.8253 (mtpt) REVERT: z 133 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7899 (mm-30) outliers start: 554 outliers final: 238 residues processed: 1407 average time/residue: 1.0819 time to fit residues: 2013.0259 Evaluate side-chains 1175 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 883 time to evaluate : 4.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 95 ILE Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 95 ILE Chi-restraints excluded: chain 2 residue 133 GLU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 218 ARG Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 348 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 195 MET Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 348 PHE Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 123 ASP Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 256 GLN Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 265 LEU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 195 MET Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 348 PHE Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 348 PHE Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 202 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 286 GLU Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 164 ILE Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 367 PHE Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 367 PHE Chi-restraints excluded: chain X residue 50 TYR Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 374 HIS Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 61 VAL Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 101 GLU Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 56 ASP Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 133 GLU Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 61 VAL Chi-restraints excluded: chain s residue 133 GLU Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 56 ASP Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 101 GLU Chi-restraints excluded: chain t residue 107 GLU Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 52 SER Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 133 GLU Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain y residue 133 GLU Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 95 ILE Chi-restraints excluded: chain z residue 104 THR Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 357 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 535 optimal weight: 0.8980 chunk 437 optimal weight: 10.0000 chunk 177 optimal weight: 0.0060 chunk 644 optimal weight: 8.9990 chunk 695 optimal weight: 10.0000 chunk 573 optimal weight: 5.9990 chunk 638 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 516 optimal weight: 20.0000 overall best weight: 4.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN M 119 GLN ** M 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 295 ASN N 307 GLN O 295 ASN O 307 GLN P 29 GLN P 119 GLN P 364 GLN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 GLN ** R 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 GLN V 119 GLN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN W 119 GLN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 374 HIS u 120 ASN v 121 ASN w 121 ASN x 121 ASN y 121 ASN z 121 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 55668 Z= 0.258 Angle : 0.675 8.261 75798 Z= 0.361 Chirality : 0.047 0.203 8778 Planarity : 0.005 0.043 9822 Dihedral : 9.553 59.599 7995 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 9.31 % Allowed : 19.39 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.09), residues: 7080 helix: 0.24 (0.14), residues: 1476 sheet: 0.30 (0.13), residues: 1266 loop : -2.47 (0.08), residues: 4338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP z 127 HIS 0.005 0.001 HIS V 34 PHE 0.040 0.002 PHE q 90 TYR 0.016 0.002 TYR P 67 ARG 0.005 0.001 ARG T 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 537 poor density : 939 time to evaluate : 4.699 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: 1 80 MET cc_start: 0.8436 (mmm) cc_final: 0.8234 (mmp) REVERT: 1 93 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7493 (t70) REVERT: 1 97 SER cc_start: 0.8256 (m) cc_final: 0.7742 (p) REVERT: 1 112 LYS cc_start: 0.8471 (mttp) cc_final: 0.8184 (mtpt) REVERT: 1 133 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: 2 12 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8480 (m) REVERT: 2 16 ASP cc_start: 0.7944 (t0) cc_final: 0.7702 (t70) REVERT: 2 27 ASP cc_start: 0.7699 (m-30) cc_final: 0.7410 (m-30) REVERT: 2 97 SER cc_start: 0.8220 (m) cc_final: 0.7901 (p) REVERT: 2 112 LYS cc_start: 0.8414 (mttp) cc_final: 0.8125 (mtpt) REVERT: 2 115 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: 2 133 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: M 10 THR cc_start: 0.8829 (p) cc_final: 0.8418 (t) REVERT: M 16 ARG cc_start: 0.6980 (mtt180) cc_final: 0.6749 (mtt90) REVERT: M 55 GLU cc_start: 0.4214 (OUTLIER) cc_final: 0.3532 (mp0) REVERT: M 117 PHE cc_start: 0.4988 (p90) cc_final: 0.4723 (p90) REVERT: M 139 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6652 (t) REVERT: M 218 ARG cc_start: 0.3097 (OUTLIER) cc_final: 0.1924 (mmm160) REVERT: M 332 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6788 (mt) REVERT: N 10 THR cc_start: 0.8529 (p) cc_final: 0.8214 (t) REVERT: N 29 GLN cc_start: 0.4393 (pt0) cc_final: 0.3998 (pt0) REVERT: N 48 LYS cc_start: 0.5788 (ttpt) cc_final: 0.4974 (ttmm) REVERT: N 139 VAL cc_start: 0.7132 (OUTLIER) cc_final: 0.6910 (t) REVERT: N 147 MET cc_start: 0.2893 (tpp) cc_final: 0.2421 (tpp) REVERT: N 164 ILE cc_start: 0.4167 (OUTLIER) cc_final: 0.3368 (tp) REVERT: N 256 GLN cc_start: 0.6738 (mp10) cc_final: 0.6465 (pm20) REVERT: N 274 ILE cc_start: 0.7472 (mp) cc_final: 0.7222 (mt) REVERT: N 321 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7123 (ttm170) REVERT: O 3 LYS cc_start: 0.6569 (mppt) cc_final: 0.6322 (mppt) REVERT: O 29 GLN cc_start: 0.3973 (pt0) cc_final: 0.3570 (pt0) REVERT: O 81 ILE cc_start: 0.4616 (OUTLIER) cc_final: 0.4165 (mp) REVERT: O 139 VAL cc_start: 0.7148 (OUTLIER) cc_final: 0.6913 (t) REVERT: O 164 ILE cc_start: 0.5046 (OUTLIER) cc_final: 0.4220 (tp) REVERT: O 220 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6145 (pt) REVERT: O 252 ASP cc_start: 0.7229 (p0) cc_final: 0.6671 (p0) REVERT: O 305 MET cc_start: 0.8022 (mmp) cc_final: 0.7593 (mmm) REVERT: O 321 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7039 (ttm170) REVERT: O 341 THR cc_start: 0.8333 (p) cc_final: 0.8051 (t) REVERT: P 59 ASP cc_start: 0.0646 (OUTLIER) cc_final: 0.0209 (t0) REVERT: P 123 ASP cc_start: 0.3110 (OUTLIER) cc_final: 0.2896 (p0) REVERT: P 164 ILE cc_start: 0.5013 (OUTLIER) cc_final: 0.4339 (tt) REVERT: P 290 SER cc_start: 0.8636 (t) cc_final: 0.8021 (p) REVERT: P 321 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7392 (ttp-170) REVERT: P 341 THR cc_start: 0.8313 (p) cc_final: 0.8108 (t) REVERT: Q 48 LYS cc_start: 0.5863 (ttpt) cc_final: 0.5110 (ttmm) REVERT: Q 139 VAL cc_start: 0.7066 (OUTLIER) cc_final: 0.6808 (t) REVERT: Q 147 MET cc_start: 0.2985 (tpp) cc_final: 0.2052 (tpp) REVERT: Q 164 ILE cc_start: 0.4664 (OUTLIER) cc_final: 0.4365 (tt) REVERT: Q 191 MET cc_start: 0.5342 (OUTLIER) cc_final: 0.4530 (ttm) REVERT: Q 274 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7056 (mt) REVERT: Q 290 SER cc_start: 0.8556 (t) cc_final: 0.8053 (p) REVERT: Q 296 ASP cc_start: 0.7247 (m-30) cc_final: 0.7032 (m-30) REVERT: Q 343 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8470 (t) REVERT: R 10 THR cc_start: 0.8752 (p) cc_final: 0.8509 (p) REVERT: R 48 LYS cc_start: 0.5490 (OUTLIER) cc_final: 0.4601 (tttm) REVERT: R 139 VAL cc_start: 0.7002 (OUTLIER) cc_final: 0.6734 (t) REVERT: R 147 MET cc_start: 0.3047 (tpp) cc_final: 0.2460 (tpp) REVERT: R 218 ARG cc_start: 0.3475 (OUTLIER) cc_final: 0.2979 (mmp80) REVERT: R 252 ASP cc_start: 0.7117 (p0) cc_final: 0.6776 (p0) REVERT: R 332 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6866 (mt) REVERT: R 341 THR cc_start: 0.8228 (p) cc_final: 0.7962 (t) REVERT: S 76 GLN cc_start: 0.6676 (tp40) cc_final: 0.5569 (mm110) REVERT: S 81 ILE cc_start: 0.4238 (OUTLIER) cc_final: 0.4026 (mt) REVERT: S 84 LYS cc_start: 0.4147 (OUTLIER) cc_final: 0.3917 (tppt) REVERT: S 123 ASP cc_start: 0.2333 (OUTLIER) cc_final: 0.1983 (p0) REVERT: S 220 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.5976 (pt) REVERT: S 294 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.7130 (t0) REVERT: S 348 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5406 (m-10) REVERT: T 23 ARG cc_start: 0.5474 (tpt170) cc_final: 0.3315 (mtm180) REVERT: T 59 ASP cc_start: 0.1644 (OUTLIER) cc_final: 0.0954 (t0) REVERT: T 76 GLN cc_start: 0.6336 (tp-100) cc_final: 0.5583 (mm110) REVERT: T 133 ASP cc_start: 0.5112 (t0) cc_final: 0.4775 (t70) REVERT: T 169 LYS cc_start: 0.5852 (ttpm) cc_final: 0.5331 (ptmm) REVERT: T 220 ILE cc_start: 0.6516 (OUTLIER) cc_final: 0.6104 (pp) REVERT: T 290 SER cc_start: 0.8559 (t) cc_final: 0.8267 (m) REVERT: U 23 ARG cc_start: 0.5402 (tpt-90) cc_final: 0.3077 (mtm180) REVERT: U 68 LYS cc_start: 0.5288 (mttt) cc_final: 0.4932 (tptp) REVERT: U 123 ASP cc_start: 0.2250 (OUTLIER) cc_final: 0.1924 (p0) REVERT: U 164 ILE cc_start: 0.4214 (OUTLIER) cc_final: 0.3900 (mp) REVERT: U 220 ILE cc_start: 0.6185 (OUTLIER) cc_final: 0.5766 (pt) REVERT: U 288 MET cc_start: 0.7973 (mmt) cc_final: 0.7551 (mmt) REVERT: U 290 SER cc_start: 0.8510 (t) cc_final: 0.8249 (m) REVERT: U 316 MET cc_start: 0.9009 (mmp) cc_final: 0.8781 (mmt) REVERT: U 348 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5506 (m-10) REVERT: V 76 GLN cc_start: 0.6741 (tp40) cc_final: 0.5835 (mm110) REVERT: V 119 GLN cc_start: 0.6583 (OUTLIER) cc_final: 0.6322 (pm20) REVERT: V 220 ILE cc_start: 0.6561 (OUTLIER) cc_final: 0.5926 (pt) REVERT: V 252 ASP cc_start: 0.6909 (p0) cc_final: 0.6703 (p0) REVERT: V 348 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5435 (m-10) REVERT: V 367 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5655 (m-80) REVERT: W 76 GLN cc_start: 0.6753 (tp40) cc_final: 0.5874 (mm110) REVERT: W 81 ILE cc_start: 0.4276 (OUTLIER) cc_final: 0.3923 (mt) REVERT: W 164 ILE cc_start: 0.4330 (OUTLIER) cc_final: 0.3794 (mp) REVERT: W 201 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7571 (t70) REVERT: W 208 THR cc_start: 0.3552 (OUTLIER) cc_final: 0.3343 (m) REVERT: W 220 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.5844 (pt) REVERT: W 294 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7212 (t0) REVERT: W 348 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5695 (m-10) REVERT: W 367 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.5740 (m-80) REVERT: X 76 GLN cc_start: 0.6414 (tp40) cc_final: 0.5378 (mm110) REVERT: X 164 ILE cc_start: 0.4446 (OUTLIER) cc_final: 0.3758 (tp) REVERT: X 220 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.5920 (pt) REVERT: X 348 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5485 (m-10) REVERT: Y 16 ASP cc_start: 0.7748 (t0) cc_final: 0.7410 (t0) REVERT: Y 66 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8499 (mtmp) REVERT: Y 100 ASN cc_start: 0.7894 (m-40) cc_final: 0.7653 (m-40) REVERT: Y 112 LYS cc_start: 0.8555 (mttp) cc_final: 0.8278 (mtpt) REVERT: Z 16 ASP cc_start: 0.7928 (t0) cc_final: 0.7523 (t0) REVERT: Z 112 LYS cc_start: 0.8450 (mttp) cc_final: 0.8213 (mtpt) REVERT: m 16 ASP cc_start: 0.7883 (t0) cc_final: 0.7502 (t70) REVERT: m 73 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8030 (ttm-80) REVERT: m 96 ASP cc_start: 0.8261 (t0) cc_final: 0.7921 (t0) REVERT: n 16 ASP cc_start: 0.7637 (t0) cc_final: 0.7297 (t0) REVERT: n 19 ARG cc_start: 0.7088 (mtp180) cc_final: 0.6856 (ttt-90) REVERT: n 33 SER cc_start: 0.8459 (p) cc_final: 0.8124 (p) REVERT: n 100 ASN cc_start: 0.7914 (m-40) cc_final: 0.7574 (m-40) REVERT: n 112 LYS cc_start: 0.8547 (mttp) cc_final: 0.8281 (mtpt) REVERT: o 16 ASP cc_start: 0.7900 (t0) cc_final: 0.7519 (t0) REVERT: o 19 ARG cc_start: 0.7247 (mtp180) cc_final: 0.7026 (ttt-90) REVERT: o 112 LYS cc_start: 0.8502 (mttp) cc_final: 0.8216 (mtpt) REVERT: p 16 ASP cc_start: 0.7912 (t0) cc_final: 0.7539 (t0) REVERT: p 19 ARG cc_start: 0.7305 (mtp180) cc_final: 0.7061 (ttt-90) REVERT: p 96 ASP cc_start: 0.8231 (t0) cc_final: 0.7923 (t0) REVERT: q 18 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6412 (mtt-85) REVERT: q 97 SER cc_start: 0.7962 (m) cc_final: 0.7359 (p) REVERT: q 101 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: q 111 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: q 112 LYS cc_start: 0.8512 (mttp) cc_final: 0.8261 (mtpt) REVERT: r 101 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: s 3 MET cc_start: 0.2689 (tmm) cc_final: 0.2310 (tmt) REVERT: s 8 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7514 (tpt) REVERT: t 18 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6331 (mtt-85) REVERT: t 97 SER cc_start: 0.7995 (m) cc_final: 0.7351 (p) REVERT: t 101 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: t 107 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: t 111 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: v 8 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7582 (tpt) REVERT: v 90 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7994 (p90) REVERT: v 133 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: w 3 MET cc_start: 0.2852 (tmm) cc_final: 0.2283 (tmt) REVERT: w 16 ASP cc_start: 0.7803 (t0) cc_final: 0.7546 (t70) REVERT: w 93 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7614 (t70) REVERT: w 133 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: x 16 ASP cc_start: 0.8089 (t0) cc_final: 0.7646 (t70) REVERT: x 97 SER cc_start: 0.8236 (m) cc_final: 0.7773 (p) REVERT: x 112 LYS cc_start: 0.8474 (mttp) cc_final: 0.8188 (mtpt) REVERT: x 133 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: y 3 MET cc_start: 0.2940 (tmm) cc_final: 0.2314 (tmt) REVERT: y 97 SER cc_start: 0.8144 (m) cc_final: 0.7849 (p) REVERT: y 107 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7800 (mt-10) REVERT: y 112 LYS cc_start: 0.8417 (mttp) cc_final: 0.8127 (mtpt) REVERT: y 115 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: y 120 ASN cc_start: 0.7770 (t0) cc_final: 0.7486 (t0) REVERT: y 133 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: z 1 MET cc_start: 0.3028 (mtp) cc_final: 0.2490 (mtt) REVERT: z 19 ARG cc_start: 0.7091 (mtp180) cc_final: 0.6770 (ttt-90) REVERT: z 93 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7557 (t70) REVERT: z 97 SER cc_start: 0.8342 (m) cc_final: 0.8017 (p) REVERT: z 112 LYS cc_start: 0.8458 (mttp) cc_final: 0.8213 (mtpt) REVERT: z 133 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7994 (tm-30) outliers start: 537 outliers final: 304 residues processed: 1300 average time/residue: 1.1014 time to fit residues: 1886.6556 Evaluate side-chains 1263 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 881 time to evaluate : 4.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 24 MET Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 104 THR Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain 2 residue 133 GLU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 218 ARG Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 348 PHE Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 348 PHE Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 209 LEU Chi-restraints excluded: chain O residue 220 ILE Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 123 ASP Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 321 ARG Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 348 PHE Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 191 MET Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 260 VAL Chi-restraints excluded: chain Q residue 264 THR Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 348 PHE Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 84 LYS Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 265 LEU Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 294 ASN Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 202 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 228 THR Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 59 ASP Chi-restraints excluded: chain U residue 81 ILE Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 164 ILE Chi-restraints excluded: chain U residue 169 LYS Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain V residue 4 LEU Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 119 GLN Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 367 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 164 ILE Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 201 ASP Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 367 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 61 VAL Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 95 ILE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 101 GLU Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 94 PHE Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 18 ARG Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 101 GLU Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 56 ASP Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 133 GLU Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 61 VAL Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 133 GLU Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 56 ASP Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 101 GLU Chi-restraints excluded: chain t residue 107 GLU Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 115 ASP Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 90 PHE Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 133 GLU Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 93 ASP Chi-restraints excluded: chain w residue 115 ASP Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 95 ILE Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 24 MET Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain y residue 133 GLU Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 93 ASP Chi-restraints excluded: chain z residue 133 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 10.0000 chunk 484 optimal weight: 0.0170 chunk 334 optimal weight: 10.0000 chunk 71 optimal weight: 0.0970 chunk 307 optimal weight: 0.0770 chunk 432 optimal weight: 20.0000 chunk 646 optimal weight: 7.9990 chunk 684 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 612 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 overall best weight: 1.7976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN M 119 GLN N 295 ASN O 119 GLN R 119 GLN ** S 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 119 GLN ** S 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 317 GLN V 119 GLN ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 121 ASN u 120 ASN v 121 ASN w 121 ASN x 121 ASN y 121 ASN z 121 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 55668 Z= 0.151 Angle : 0.580 7.289 75798 Z= 0.308 Chirality : 0.043 0.151 8778 Planarity : 0.004 0.046 9822 Dihedral : 8.678 59.946 7986 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.96 % Allowed : 21.23 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.09), residues: 7080 helix: 0.90 (0.14), residues: 1476 sheet: -0.00 (0.13), residues: 1410 loop : -2.37 (0.08), residues: 4194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP z 127 HIS 0.006 0.001 HIS W 34 PHE 0.025 0.002 PHE q 90 TYR 0.014 0.001 TYR R 67 ARG 0.004 0.000 ARG R 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 459 poor density : 939 time to evaluate : 4.731 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: 1 80 MET cc_start: 0.8506 (mmm) cc_final: 0.8209 (mmp) REVERT: 1 93 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7197 (t0) REVERT: 1 97 SER cc_start: 0.8272 (m) cc_final: 0.7771 (p) REVERT: 1 112 LYS cc_start: 0.8455 (mttp) cc_final: 0.8200 (mtpt) REVERT: 1 133 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: 2 1 MET cc_start: 0.3017 (mpt) cc_final: 0.2130 (mmm) REVERT: 2 27 ASP cc_start: 0.7709 (m-30) cc_final: 0.7450 (m-30) REVERT: 2 31 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8068 (m) REVERT: 2 97 SER cc_start: 0.8120 (m) cc_final: 0.7796 (p) REVERT: 2 112 LYS cc_start: 0.8461 (mttp) cc_final: 0.8139 (mtpt) REVERT: 2 115 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: M 10 THR cc_start: 0.8694 (p) cc_final: 0.8293 (t) REVERT: M 16 ARG cc_start: 0.6900 (mtt180) cc_final: 0.6693 (mtt90) REVERT: M 40 GLN cc_start: 0.3767 (OUTLIER) cc_final: 0.2398 (mp10) REVERT: M 117 PHE cc_start: 0.4962 (p90) cc_final: 0.4694 (p90) REVERT: M 164 ILE cc_start: 0.5052 (OUTLIER) cc_final: 0.3868 (tt) REVERT: M 252 ASP cc_start: 0.6733 (p0) cc_final: 0.6265 (p0) REVERT: M 332 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6577 (mt) REVERT: N 10 THR cc_start: 0.8395 (p) cc_final: 0.8153 (t) REVERT: N 29 GLN cc_start: 0.3974 (pt0) cc_final: 0.3689 (pt0) REVERT: N 48 LYS cc_start: 0.5679 (ttpt) cc_final: 0.4930 (ttmm) REVERT: N 147 MET cc_start: 0.3222 (tpp) cc_final: 0.2701 (tpp) REVERT: N 164 ILE cc_start: 0.4133 (OUTLIER) cc_final: 0.3550 (tp) REVERT: N 256 GLN cc_start: 0.6719 (mp10) cc_final: 0.6455 (pm20) REVERT: N 321 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7933 (tmm-80) REVERT: N 382 MET cc_start: 0.7383 (ttp) cc_final: 0.7155 (ttm) REVERT: O 81 ILE cc_start: 0.4402 (OUTLIER) cc_final: 0.4163 (mp) REVERT: O 139 VAL cc_start: 0.7117 (p) cc_final: 0.6895 (t) REVERT: O 164 ILE cc_start: 0.4818 (OUTLIER) cc_final: 0.4219 (tp) REVERT: O 235 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6298 (tp30) REVERT: O 252 ASP cc_start: 0.7140 (p0) cc_final: 0.6795 (p0) REVERT: O 305 MET cc_start: 0.7951 (mmp) cc_final: 0.7634 (mmm) REVERT: O 341 THR cc_start: 0.8202 (p) cc_final: 0.7999 (t) REVERT: P 59 ASP cc_start: 0.1041 (OUTLIER) cc_final: 0.0696 (m-30) REVERT: P 164 ILE cc_start: 0.4730 (OUTLIER) cc_final: 0.4272 (tt) REVERT: P 252 ASP cc_start: 0.6946 (p0) cc_final: 0.6650 (p0) REVERT: P 290 SER cc_start: 0.8665 (t) cc_final: 0.7988 (p) REVERT: P 321 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7306 (ttp-170) REVERT: Q 47 THR cc_start: 0.5050 (OUTLIER) cc_final: 0.4802 (p) REVERT: Q 139 VAL cc_start: 0.6855 (OUTLIER) cc_final: 0.6654 (t) REVERT: Q 252 ASP cc_start: 0.7112 (p0) cc_final: 0.6858 (p0) REVERT: Q 290 SER cc_start: 0.8690 (t) cc_final: 0.8027 (p) REVERT: Q 343 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8384 (t) REVERT: R 10 THR cc_start: 0.8655 (p) cc_final: 0.8439 (p) REVERT: R 48 LYS cc_start: 0.4961 (OUTLIER) cc_final: 0.4222 (ttmm) REVERT: R 164 ILE cc_start: 0.5340 (OUTLIER) cc_final: 0.4204 (tt) REVERT: R 252 ASP cc_start: 0.6792 (p0) cc_final: 0.6474 (p0) REVERT: R 332 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6649 (mt) REVERT: S 76 GLN cc_start: 0.6589 (tp40) cc_final: 0.5505 (mm110) REVERT: S 123 ASP cc_start: 0.2118 (OUTLIER) cc_final: 0.1758 (p0) REVERT: S 191 MET cc_start: 0.5112 (ttp) cc_final: 0.4206 (tpp) REVERT: S 202 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7399 (p0) REVERT: S 220 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5631 (pt) REVERT: S 348 PHE cc_start: 0.6078 (OUTLIER) cc_final: 0.5759 (m-10) REVERT: T 23 ARG cc_start: 0.5382 (tpt170) cc_final: 0.3119 (mtm180) REVERT: T 59 ASP cc_start: 0.1752 (OUTLIER) cc_final: 0.1127 (t0) REVERT: T 76 GLN cc_start: 0.6236 (tp-100) cc_final: 0.5443 (mm110) REVERT: T 133 ASP cc_start: 0.5187 (t0) cc_final: 0.4863 (t70) REVERT: T 139 VAL cc_start: 0.6225 (p) cc_final: 0.5629 (m) REVERT: T 169 LYS cc_start: 0.5909 (ttpm) cc_final: 0.5397 (ptmm) REVERT: T 218 ARG cc_start: 0.3527 (OUTLIER) cc_final: 0.1824 (mmt-90) REVERT: T 220 ILE cc_start: 0.6435 (OUTLIER) cc_final: 0.6155 (pp) REVERT: T 290 SER cc_start: 0.8598 (t) cc_final: 0.8225 (m) REVERT: U 23 ARG cc_start: 0.5466 (tpt-90) cc_final: 0.3147 (mtm180) REVERT: U 68 LYS cc_start: 0.5269 (mttt) cc_final: 0.4908 (tptp) REVERT: U 123 ASP cc_start: 0.2167 (OUTLIER) cc_final: 0.1588 (p0) REVERT: U 220 ILE cc_start: 0.5900 (OUTLIER) cc_final: 0.5484 (pt) REVERT: U 288 MET cc_start: 0.7972 (mmt) cc_final: 0.7495 (mmt) REVERT: U 290 SER cc_start: 0.8501 (t) cc_final: 0.8208 (m) REVERT: U 348 PHE cc_start: 0.6284 (OUTLIER) cc_final: 0.5977 (m-10) REVERT: V 3 LYS cc_start: 0.6860 (ttmm) cc_final: 0.5427 (tppt) REVERT: V 76 GLN cc_start: 0.6685 (tp40) cc_final: 0.5706 (mm110) REVERT: V 164 ILE cc_start: 0.4082 (OUTLIER) cc_final: 0.3704 (mp) REVERT: V 220 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5478 (pt) REVERT: V 252 ASP cc_start: 0.6788 (p0) cc_final: 0.6578 (OUTLIER) REVERT: V 294 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7229 (t0) REVERT: V 296 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7085 (t70) REVERT: V 348 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.5872 (m-10) REVERT: V 367 PHE cc_start: 0.6100 (OUTLIER) cc_final: 0.5556 (m-80) REVERT: W 76 GLN cc_start: 0.6652 (tp40) cc_final: 0.5713 (mm110) REVERT: W 81 ILE cc_start: 0.4252 (OUTLIER) cc_final: 0.3932 (mt) REVERT: W 139 VAL cc_start: 0.6086 (OUTLIER) cc_final: 0.5876 (t) REVERT: W 220 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5618 (pt) REVERT: W 294 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.7213 (t0) REVERT: W 348 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5775 (m-10) REVERT: W 367 PHE cc_start: 0.6123 (OUTLIER) cc_final: 0.5646 (m-80) REVERT: X 23 ARG cc_start: 0.5304 (tpt90) cc_final: 0.2937 (mtm180) REVERT: X 76 GLN cc_start: 0.6354 (tp40) cc_final: 0.5303 (mm110) REVERT: X 164 ILE cc_start: 0.4525 (OUTLIER) cc_final: 0.4132 (tp) REVERT: X 202 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7367 (p0) REVERT: X 220 ILE cc_start: 0.6161 (OUTLIER) cc_final: 0.5682 (pt) REVERT: X 296 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6833 (t0) REVERT: X 348 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5858 (m-10) REVERT: Y 16 ASP cc_start: 0.7754 (t0) cc_final: 0.7402 (t0) REVERT: Y 100 ASN cc_start: 0.7964 (m-40) cc_final: 0.7744 (m-40) REVERT: Y 112 LYS cc_start: 0.8494 (mttp) cc_final: 0.8217 (mtpt) REVERT: Z 16 ASP cc_start: 0.7868 (t0) cc_final: 0.7474 (t0) REVERT: Z 112 LYS cc_start: 0.8483 (mttp) cc_final: 0.8244 (mtpt) REVERT: m 16 ASP cc_start: 0.7843 (t0) cc_final: 0.7475 (t70) REVERT: m 33 SER cc_start: 0.8424 (p) cc_final: 0.8110 (t) REVERT: m 96 ASP cc_start: 0.8071 (t0) cc_final: 0.7815 (t70) REVERT: n 16 ASP cc_start: 0.7636 (t0) cc_final: 0.7296 (t0) REVERT: n 33 SER cc_start: 0.8419 (p) cc_final: 0.8066 (p) REVERT: n 100 ASN cc_start: 0.7913 (m-40) cc_final: 0.7622 (m-40) REVERT: n 112 LYS cc_start: 0.8501 (mttp) cc_final: 0.8211 (mtpt) REVERT: o 16 ASP cc_start: 0.7857 (t0) cc_final: 0.7488 (t0) REVERT: o 19 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6938 (ttt-90) REVERT: o 41 MET cc_start: 0.8482 (tpp) cc_final: 0.8255 (tpp) REVERT: o 112 LYS cc_start: 0.8547 (mttp) cc_final: 0.8295 (mtpt) REVERT: o 133 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8152 (tp30) REVERT: p 16 ASP cc_start: 0.7823 (t0) cc_final: 0.7445 (t70) REVERT: p 19 ARG cc_start: 0.7243 (mtp180) cc_final: 0.7027 (ttt-90) REVERT: p 96 ASP cc_start: 0.8036 (t0) cc_final: 0.7786 (t70) REVERT: q 97 SER cc_start: 0.7903 (m) cc_final: 0.7341 (p) REVERT: q 111 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: q 112 LYS cc_start: 0.8548 (mttp) cc_final: 0.8309 (mtpt) REVERT: r 90 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.6880 (p90) REVERT: r 101 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: s 3 MET cc_start: 0.2714 (tmm) cc_final: 0.2334 (tmt) REVERT: s 8 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7560 (tpt) REVERT: s 19 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6873 (ttt90) REVERT: s 101 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: s 111 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: t 18 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6511 (mtm-85) REVERT: t 97 SER cc_start: 0.7886 (m) cc_final: 0.7288 (p) REVERT: t 111 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: u 12 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8084 (m) REVERT: u 80 MET cc_start: 0.8581 (mmm) cc_final: 0.8293 (mmp) REVERT: u 90 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.6886 (p90) REVERT: u 101 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7738 (tt0) REVERT: v 8 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7601 (tpt) REVERT: v 111 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: w 3 MET cc_start: 0.2822 (tmm) cc_final: 0.2357 (tmt) REVERT: w 16 ASP cc_start: 0.7804 (t0) cc_final: 0.7518 (t70) REVERT: w 133 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: x 16 ASP cc_start: 0.8119 (t0) cc_final: 0.7679 (t70) REVERT: x 80 MET cc_start: 0.8487 (mmm) cc_final: 0.8280 (mmp) REVERT: x 93 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7229 (t0) REVERT: x 97 SER cc_start: 0.8281 (m) cc_final: 0.7776 (p) REVERT: x 112 LYS cc_start: 0.8448 (mttp) cc_final: 0.8174 (mtpt) REVERT: x 133 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: y 27 ASP cc_start: 0.7800 (m-30) cc_final: 0.7507 (m-30) REVERT: y 88 VAL cc_start: 0.7587 (OUTLIER) cc_final: 0.7381 (m) REVERT: y 97 SER cc_start: 0.8136 (m) cc_final: 0.7861 (p) REVERT: y 112 LYS cc_start: 0.8422 (mttp) cc_final: 0.8108 (mtpt) REVERT: y 115 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: z 1 MET cc_start: 0.2820 (mtp) cc_final: 0.2350 (mtt) REVERT: z 97 SER cc_start: 0.8329 (m) cc_final: 0.8020 (p) REVERT: z 112 LYS cc_start: 0.8483 (mttp) cc_final: 0.8220 (mtpt) outliers start: 459 outliers final: 248 residues processed: 1256 average time/residue: 1.1053 time to fit residues: 1826.4951 Evaluate side-chains 1186 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 872 time to evaluate : 4.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 104 THR Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 122 LEU Chi-restraints excluded: chain M residue 164 ILE Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 348 PHE Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 348 PHE Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 235 GLU Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 265 LEU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 321 ARG Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 348 PHE Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 343 THR Chi-restraints excluded: chain Q residue 348 PHE Chi-restraints excluded: chain Q residue 367 PHE Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 164 ILE Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 348 PHE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 202 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 218 ARG Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 209 LEU Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 367 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 367 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 202 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 265 LEU Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 296 ASP Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 101 GLU Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 37 ASP Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 12 THR Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 115 ASP Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 133 GLU Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 101 GLU Chi-restraints excluded: chain s residue 111 GLN Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 56 ASP Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 115 ASP Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 111 GLN Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 93 ASP Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 88 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 93 ASP Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 509 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 583 optimal weight: 9.9990 chunk 473 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 349 optimal weight: 20.0000 chunk 614 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN M 119 GLN N 119 GLN O 29 GLN O 180 HIS P 180 HIS Q 29 GLN Q 119 GLN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 239 GLN S 63 ASN ** S 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 GLN T 63 ASN T 119 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 29 GLN U 63 ASN V 29 GLN V 76 GLN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 GLN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 121 ASN w 121 ASN x 121 ASN y 121 ASN z 121 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 55668 Z= 0.437 Angle : 0.817 13.632 75798 Z= 0.436 Chirality : 0.053 0.260 8778 Planarity : 0.007 0.051 9822 Dihedral : 9.660 74.968 7943 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.72 % Favored : 88.05 % Rotamer: Outliers : 9.56 % Allowed : 21.71 % Favored : 68.73 % 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: -1.96 (0.09), residues: 7080 helix: 0.33 (0.14), residues: 1440 sheet: 0.05 (0.13), residues: 1368 loop : -2.51 (0.08), residues: 4272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP z 127 HIS 0.021 0.002 HIS O 180 PHE 0.055 0.003 PHE q 90 TYR 0.022 0.003 TYR S 67 ARG 0.007 0.001 ARG Q 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 551 poor density : 894 time to evaluate : 4.815 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: 1 97 SER cc_start: 0.8322 (m) cc_final: 0.7841 (p) REVERT: 1 112 LYS cc_start: 0.8518 (mttp) cc_final: 0.8132 (mtpt) REVERT: 1 133 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: 2 1 MET cc_start: 0.3459 (mpt) cc_final: 0.2382 (mtm) REVERT: 2 16 ASP cc_start: 0.7938 (t0) cc_final: 0.7608 (t70) REVERT: 2 97 SER cc_start: 0.8214 (m) cc_final: 0.7926 (p) REVERT: 2 112 LYS cc_start: 0.8428 (mttp) cc_final: 0.8131 (mtpt) REVERT: 2 115 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: M 10 THR cc_start: 0.8761 (p) cc_final: 0.8352 (t) REVERT: M 16 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6924 (mtt90) REVERT: M 40 GLN cc_start: 0.3612 (OUTLIER) cc_final: 0.2155 (mp10) REVERT: M 48 LYS cc_start: 0.5020 (OUTLIER) cc_final: 0.4668 (ttpm) REVERT: M 55 GLU cc_start: 0.4299 (OUTLIER) cc_final: 0.3928 (mp0) REVERT: M 59 ASP cc_start: 0.2213 (OUTLIER) cc_final: 0.1794 (t0) REVERT: M 84 LYS cc_start: 0.5024 (OUTLIER) cc_final: 0.4619 (ttpp) REVERT: M 117 PHE cc_start: 0.5097 (p90) cc_final: 0.4724 (p90) REVERT: M 294 ASN cc_start: 0.6606 (m-40) cc_final: 0.6380 (m-40) REVERT: M 321 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8036 (ttm170) REVERT: N 10 THR cc_start: 0.8633 (p) cc_final: 0.8295 (t) REVERT: N 29 GLN cc_start: 0.4442 (pt0) cc_final: 0.2242 (pm20) REVERT: N 48 LYS cc_start: 0.5991 (ttpt) cc_final: 0.5725 (ttpt) REVERT: N 132 LEU cc_start: 0.4025 (OUTLIER) cc_final: 0.3769 (mp) REVERT: N 164 ILE cc_start: 0.4070 (OUTLIER) cc_final: 0.3381 (tp) REVERT: N 191 MET cc_start: 0.5322 (ttm) cc_final: 0.5103 (ttp) REVERT: N 256 GLN cc_start: 0.6743 (mp10) cc_final: 0.6424 (pm20) REVERT: N 274 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7282 (mt) REVERT: N 297 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7644 (ptp-170) REVERT: N 321 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7290 (ttm170) REVERT: N 367 PHE cc_start: 0.5965 (OUTLIER) cc_final: 0.5418 (m-80) REVERT: O 10 THR cc_start: 0.8644 (p) cc_final: 0.8359 (t) REVERT: O 50 TYR cc_start: 0.3995 (t80) cc_final: 0.3683 (t80) REVERT: O 81 ILE cc_start: 0.4459 (OUTLIER) cc_final: 0.4168 (mp) REVERT: O 164 ILE cc_start: 0.4809 (OUTLIER) cc_final: 0.4241 (tp) REVERT: O 252 ASP cc_start: 0.7164 (p0) cc_final: 0.6829 (p0) REVERT: O 321 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7157 (ttm170) REVERT: O 341 THR cc_start: 0.8302 (p) cc_final: 0.7991 (t) REVERT: P 59 ASP cc_start: 0.0657 (OUTLIER) cc_final: 0.0446 (m-30) REVERT: P 139 VAL cc_start: 0.6882 (OUTLIER) cc_final: 0.6535 (t) REVERT: P 164 ILE cc_start: 0.4919 (OUTLIER) cc_final: 0.4416 (tt) REVERT: P 169 LYS cc_start: 0.4641 (OUTLIER) cc_final: 0.4177 (ptmm) REVERT: P 290 SER cc_start: 0.8736 (t) cc_final: 0.8008 (p) REVERT: P 321 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7431 (ttp-170) REVERT: P 341 THR cc_start: 0.8393 (p) cc_final: 0.8021 (t) REVERT: P 367 PHE cc_start: 0.6287 (OUTLIER) cc_final: 0.5324 (m-80) REVERT: Q 20 PHE cc_start: 0.5495 (m-80) cc_final: 0.5293 (m-80) REVERT: Q 48 LYS cc_start: 0.5528 (ttpt) cc_final: 0.4619 (tttm) REVERT: Q 139 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6874 (t) REVERT: Q 274 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7269 (mt) REVERT: Q 290 SER cc_start: 0.8774 (t) cc_final: 0.8059 (p) REVERT: Q 364 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7520 (mm-40) REVERT: R 10 THR cc_start: 0.8694 (p) cc_final: 0.8243 (t) REVERT: R 40 GLN cc_start: 0.3899 (mm-40) cc_final: 0.3534 (mm-40) REVERT: R 48 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.4726 (tttm) REVERT: R 117 PHE cc_start: 0.4725 (p90) cc_final: 0.4302 (p90) REVERT: R 294 ASN cc_start: 0.6628 (m-40) cc_final: 0.6396 (m-40) REVERT: S 76 GLN cc_start: 0.6593 (tp40) cc_final: 0.5431 (mm110) REVERT: S 123 ASP cc_start: 0.2759 (OUTLIER) cc_final: 0.2025 (p0) REVERT: S 212 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6852 (mptp) REVERT: S 220 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6248 (pt) REVERT: S 348 PHE cc_start: 0.6605 (OUTLIER) cc_final: 0.6225 (m-80) REVERT: S 364 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7948 (mm110) REVERT: T 23 ARG cc_start: 0.5431 (tpt170) cc_final: 0.3690 (mtm180) REVERT: T 59 ASP cc_start: 0.1988 (OUTLIER) cc_final: 0.1312 (t0) REVERT: T 63 ASN cc_start: 0.4414 (OUTLIER) cc_final: 0.4137 (p0) REVERT: T 76 GLN cc_start: 0.6328 (tp-100) cc_final: 0.5544 (mm110) REVERT: T 133 ASP cc_start: 0.5196 (t0) cc_final: 0.4875 (t70) REVERT: T 169 LYS cc_start: 0.5921 (ttpm) cc_final: 0.5533 (ptmt) REVERT: T 220 ILE cc_start: 0.6626 (OUTLIER) cc_final: 0.6219 (pt) REVERT: T 256 GLN cc_start: 0.6428 (mp10) cc_final: 0.6014 (mp10) REVERT: T 290 SER cc_start: 0.8656 (t) cc_final: 0.8352 (m) REVERT: T 382 MET cc_start: 0.7901 (ttm) cc_final: 0.7690 (ttm) REVERT: U 23 ARG cc_start: 0.5587 (tpt-90) cc_final: 0.3173 (mtm180) REVERT: U 68 LYS cc_start: 0.4997 (mttt) cc_final: 0.4717 (tptp) REVERT: U 123 ASP cc_start: 0.2561 (OUTLIER) cc_final: 0.1637 (p0) REVERT: U 210 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.5766 (tppt) REVERT: U 220 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6110 (pt) REVERT: U 288 MET cc_start: 0.8050 (mmt) cc_final: 0.7603 (mmt) REVERT: U 290 SER cc_start: 0.8599 (t) cc_final: 0.8302 (m) REVERT: U 348 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: V 76 GLN cc_start: 0.6692 (tp-100) cc_final: 0.5690 (mm110) REVERT: V 169 LYS cc_start: 0.5649 (OUTLIER) cc_final: 0.5419 (ptmt) REVERT: V 220 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6287 (pt) REVERT: V 294 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7299 (t0) REVERT: V 303 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7504 (mp10) REVERT: V 348 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: W 76 GLN cc_start: 0.6740 (tp-100) cc_final: 0.5702 (mm110) REVERT: W 81 ILE cc_start: 0.4550 (OUTLIER) cc_final: 0.4275 (mt) REVERT: W 169 LYS cc_start: 0.5713 (OUTLIER) cc_final: 0.5339 (ptmt) REVERT: W 220 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6202 (pt) REVERT: W 294 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7343 (t0) REVERT: W 303 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7530 (mp10) REVERT: W 348 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6313 (m-80) REVERT: X 220 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.6150 (pt) REVERT: X 348 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: X 364 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7992 (mm110) REVERT: Y 16 ASP cc_start: 0.7842 (t0) cc_final: 0.7469 (t0) REVERT: Y 66 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8530 (mtmp) REVERT: Y 112 LYS cc_start: 0.8578 (mttp) cc_final: 0.8264 (mtpt) REVERT: Z 16 ASP cc_start: 0.7933 (t0) cc_final: 0.7571 (t0) REVERT: Z 54 THR cc_start: 0.8366 (p) cc_final: 0.8097 (t) REVERT: Z 112 LYS cc_start: 0.8481 (mttp) cc_final: 0.8209 (mtpt) REVERT: m 16 ASP cc_start: 0.7978 (t0) cc_final: 0.7640 (t70) REVERT: m 73 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7962 (ttm-80) REVERT: m 96 ASP cc_start: 0.8263 (t0) cc_final: 0.7931 (t0) REVERT: n 16 ASP cc_start: 0.7760 (t0) cc_final: 0.7412 (t0) REVERT: n 21 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6960 (mt) REVERT: n 33 SER cc_start: 0.8523 (p) cc_final: 0.8148 (p) REVERT: n 100 ASN cc_start: 0.7858 (m-40) cc_final: 0.7527 (m-40) REVERT: n 112 LYS cc_start: 0.8579 (mttp) cc_final: 0.8268 (mtpt) REVERT: o 16 ASP cc_start: 0.7931 (t0) cc_final: 0.7572 (t0) REVERT: o 41 MET cc_start: 0.8539 (tpp) cc_final: 0.8211 (tpp) REVERT: o 112 LYS cc_start: 0.8532 (mttp) cc_final: 0.8242 (mtpt) REVERT: p 16 ASP cc_start: 0.7959 (t0) cc_final: 0.7642 (t70) REVERT: p 19 ARG cc_start: 0.7468 (mtp180) cc_final: 0.7205 (ttt-90) REVERT: p 86 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7762 (ttm-80) REVERT: p 96 ASP cc_start: 0.8307 (t0) cc_final: 0.7969 (t0) REVERT: q 18 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6510 (mtt-85) REVERT: q 90 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8056 (p90) REVERT: q 111 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: q 112 LYS cc_start: 0.8505 (mttp) cc_final: 0.8262 (mtpt) REVERT: r 101 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: s 8 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7557 (tpt) REVERT: s 90 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7792 (p90) REVERT: t 18 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6443 (mtt-85) REVERT: t 111 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: u 86 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: u 101 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: v 8 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7599 (tpt) REVERT: v 90 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7791 (p90) REVERT: w 19 ARG cc_start: 0.7095 (mtp180) cc_final: 0.6804 (ttt-90) REVERT: w 93 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7622 (t70) REVERT: w 133 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7211 (tm-30) REVERT: x 97 SER cc_start: 0.8323 (m) cc_final: 0.7840 (p) REVERT: x 112 LYS cc_start: 0.8497 (mttp) cc_final: 0.8130 (mtpt) REVERT: x 133 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: y 16 ASP cc_start: 0.7940 (t0) cc_final: 0.7601 (t70) REVERT: y 97 SER cc_start: 0.8271 (m) cc_final: 0.7958 (p) REVERT: y 112 LYS cc_start: 0.8470 (mttp) cc_final: 0.8175 (mtpt) REVERT: y 115 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: y 120 ASN cc_start: 0.7717 (t0) cc_final: 0.7510 (t0) REVERT: z 93 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7579 (t70) REVERT: z 97 SER cc_start: 0.8357 (m) cc_final: 0.8032 (p) REVERT: z 112 LYS cc_start: 0.8519 (mttp) cc_final: 0.8242 (mtpt) outliers start: 551 outliers final: 328 residues processed: 1269 average time/residue: 1.1204 time to fit residues: 1876.4851 Evaluate side-chains 1269 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 869 time to evaluate : 4.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 ILE Chi-restraints excluded: chain 1 residue 24 MET Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 32 THR Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 88 VAL Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 31 THR Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 104 THR Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 48 LYS Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 84 LYS Chi-restraints excluded: chain M residue 119 GLN Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 MET Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain M residue 228 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 321 ARG Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 132 LEU Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 212 LYS Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 266 THR Chi-restraints excluded: chain N residue 274 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 265 LEU Chi-restraints excluded: chain O residue 266 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 348 PHE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 191 MET Chi-restraints excluded: chain P residue 195 MET Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 265 LEU Chi-restraints excluded: chain P residue 321 ARG Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 202 ASP Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 257 GLU Chi-restraints excluded: chain Q residue 264 THR Chi-restraints excluded: chain Q residue 266 THR Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 332 LEU Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 364 GLN Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 383 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 257 GLU Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 202 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 212 LYS Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 348 PHE Chi-restraints excluded: chain S residue 364 GLN Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 50 TYR Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 63 ASN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 202 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 235 GLU Chi-restraints excluded: chain T residue 265 LEU Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 353 SER Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 59 ASP Chi-restraints excluded: chain U residue 85 VAL Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 210 LYS Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 348 PHE Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 81 ILE Chi-restraints excluded: chain V residue 85 VAL Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 164 ILE Chi-restraints excluded: chain V residue 169 LYS Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 341 THR Chi-restraints excluded: chain V residue 348 PHE Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 169 LYS Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 341 THR Chi-restraints excluded: chain W residue 348 PHE Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 202 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 246 CYS Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 348 PHE Chi-restraints excluded: chain X residue 364 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 95 ILE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 95 ILE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 33 SER Chi-restraints excluded: chain o residue 40 THR Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 95 ILE Chi-restraints excluded: chain o residue 101 GLU Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 86 ARG Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 95 ILE Chi-restraints excluded: chain p residue 115 ASP Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 18 ARG Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 95 ILE Chi-restraints excluded: chain q residue 110 ILE Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 24 MET Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 90 PHE Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 111 GLN Chi-restraints excluded: chain s residue 115 ASP Chi-restraints excluded: chain t residue 18 ARG Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 56 ASP Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain t residue 133 GLU Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 86 ARG Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 90 PHE Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 110 ILE Chi-restraints excluded: chain v residue 111 GLN Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 40 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 93 ASP Chi-restraints excluded: chain w residue 133 GLU Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 88 VAL Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain x residue 133 GLU Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 24 MET Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 88 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 40 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 93 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 230 optimal weight: 0.0670 chunk 616 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 401 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 685 optimal weight: 10.0000 chunk 568 optimal weight: 10.0000 chunk 317 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 359 optimal weight: 1.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 119 GLN P 256 GLN P 294 ASN Q 119 GLN Q 294 ASN S 29 GLN ** S 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 317 GLN T 29 GLN T 119 GLN ** T 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 317 GLN ** U 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN V 168 HIS ** V 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 GLN ** W 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 HIS ** W 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 GLN w 121 ASN z 121 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 55668 Z= 0.136 Angle : 0.576 8.741 75798 Z= 0.305 Chirality : 0.043 0.181 8778 Planarity : 0.004 0.051 9822 Dihedral : 7.927 59.857 7915 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 6.23 % Allowed : 25.48 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.10), residues: 7080 helix: 1.10 (0.14), residues: 1464 sheet: 0.12 (0.13), residues: 1338 loop : -2.25 (0.08), residues: 4278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 279 HIS 0.006 0.001 HIS V 34 PHE 0.020 0.001 PHE q 90 TYR 0.021 0.001 TYR R 113 ARG 0.007 0.000 ARG o 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 359 poor density : 909 time to evaluate : 4.716 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: 1 97 SER cc_start: 0.8279 (m) cc_final: 0.7806 (p) REVERT: 1 112 LYS cc_start: 0.8468 (mttp) cc_final: 0.8243 (mtpt) REVERT: 2 1 MET cc_start: 0.3142 (mpt) cc_final: 0.2213 (mmm) REVERT: 2 16 ASP cc_start: 0.7997 (t0) cc_final: 0.7712 (t70) REVERT: 2 24 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7656 (mmt) REVERT: 2 27 ASP cc_start: 0.7941 (m-30) cc_final: 0.7687 (m-30) REVERT: 2 97 SER cc_start: 0.8192 (m) cc_final: 0.7939 (p) REVERT: 2 112 LYS cc_start: 0.8444 (mttp) cc_final: 0.8148 (mtpt) REVERT: 2 115 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: M 10 THR cc_start: 0.8639 (p) cc_final: 0.8291 (t) REVERT: M 40 GLN cc_start: 0.3389 (OUTLIER) cc_final: 0.2082 (mp10) REVERT: M 48 LYS cc_start: 0.3935 (OUTLIER) cc_final: 0.3448 (mtmt) REVERT: N 10 THR cc_start: 0.8362 (p) cc_final: 0.8147 (t) REVERT: N 29 GLN cc_start: 0.4390 (pt0) cc_final: 0.3999 (pt0) REVERT: N 139 VAL cc_start: 0.6779 (OUTLIER) cc_final: 0.6474 (t) REVERT: N 256 GLN cc_start: 0.6731 (mp10) cc_final: 0.6472 (pm20) REVERT: N 321 ARG cc_start: 0.8255 (tmm160) cc_final: 0.7740 (ttm170) REVERT: O 10 THR cc_start: 0.8523 (p) cc_final: 0.8318 (t) REVERT: O 81 ILE cc_start: 0.4338 (OUTLIER) cc_final: 0.3929 (mp) REVERT: O 305 MET cc_start: 0.7912 (mmp) cc_final: 0.7514 (mmm) REVERT: P 59 ASP cc_start: 0.0648 (OUTLIER) cc_final: 0.0438 (m-30) REVERT: P 68 LYS cc_start: 0.5252 (OUTLIER) cc_final: 0.4086 (mmtt) REVERT: P 139 VAL cc_start: 0.6927 (OUTLIER) cc_final: 0.6529 (t) REVERT: P 212 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7079 (mmtm) REVERT: P 341 THR cc_start: 0.8320 (p) cc_final: 0.8115 (t) REVERT: P 367 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: Q 47 THR cc_start: 0.5230 (OUTLIER) cc_final: 0.5014 (p) REVERT: Q 139 VAL cc_start: 0.6708 (OUTLIER) cc_final: 0.6508 (t) REVERT: Q 252 ASP cc_start: 0.7020 (p0) cc_final: 0.6732 (p0) REVERT: Q 274 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6932 (mt) REVERT: Q 290 SER cc_start: 0.8621 (t) cc_final: 0.7939 (p) REVERT: R 10 THR cc_start: 0.8721 (p) cc_final: 0.8302 (t) REVERT: R 32 LEU cc_start: 0.5290 (OUTLIER) cc_final: 0.5009 (tp) REVERT: S 23 ARG cc_start: 0.5186 (tpt90) cc_final: 0.2928 (mtm180) REVERT: S 76 GLN cc_start: 0.6418 (tp40) cc_final: 0.5240 (mm110) REVERT: S 123 ASP cc_start: 0.2136 (OUTLIER) cc_final: 0.1927 (p0) REVERT: S 133 ASP cc_start: 0.5449 (t70) cc_final: 0.5196 (m-30) REVERT: S 191 MET cc_start: 0.4897 (ttp) cc_final: 0.4377 (tpp) REVERT: S 202 ASP cc_start: 0.7645 (m-30) cc_final: 0.7402 (m-30) REVERT: S 212 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6467 (mptt) REVERT: S 220 ILE cc_start: 0.6065 (OUTLIER) cc_final: 0.5677 (pt) REVERT: S 303 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.6795 (mm-40) REVERT: T 23 ARG cc_start: 0.5129 (tpt170) cc_final: 0.3246 (mtm180) REVERT: T 59 ASP cc_start: 0.1680 (OUTLIER) cc_final: 0.1436 (m-30) REVERT: T 123 ASP cc_start: 0.2162 (OUTLIER) cc_final: 0.1883 (p0) REVERT: T 133 ASP cc_start: 0.5397 (t0) cc_final: 0.5120 (t70) REVERT: T 139 VAL cc_start: 0.6162 (p) cc_final: 0.5579 (m) REVERT: T 169 LYS cc_start: 0.5777 (ttpm) cc_final: 0.5308 (ptmm) REVERT: T 220 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5628 (pt) REVERT: T 256 GLN cc_start: 0.6159 (mp10) cc_final: 0.5799 (mp10) REVERT: T 290 SER cc_start: 0.8702 (t) cc_final: 0.8268 (m) REVERT: U 23 ARG cc_start: 0.5316 (tpt-90) cc_final: 0.2980 (mtm180) REVERT: U 68 LYS cc_start: 0.5303 (mttt) cc_final: 0.4829 (tptp) REVERT: U 123 ASP cc_start: 0.2498 (OUTLIER) cc_final: 0.2160 (p0) REVERT: U 139 VAL cc_start: 0.6026 (p) cc_final: 0.5413 (m) REVERT: U 220 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5366 (pt) REVERT: U 286 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6933 (tt0) REVERT: U 288 MET cc_start: 0.7988 (mmt) cc_final: 0.7499 (mmt) REVERT: U 290 SER cc_start: 0.8543 (t) cc_final: 0.8240 (m) REVERT: V 76 GLN cc_start: 0.6350 (tp40) cc_final: 0.5344 (mm110) REVERT: V 139 VAL cc_start: 0.5982 (OUTLIER) cc_final: 0.5770 (t) REVERT: V 220 ILE cc_start: 0.6194 (OUTLIER) cc_final: 0.5501 (pt) REVERT: V 252 ASP cc_start: 0.6750 (p0) cc_final: 0.6502 (OUTLIER) REVERT: W 76 GLN cc_start: 0.6342 (tp40) cc_final: 0.5338 (mm110) REVERT: W 81 ILE cc_start: 0.4217 (OUTLIER) cc_final: 0.3993 (mt) REVERT: W 208 THR cc_start: 0.2942 (OUTLIER) cc_final: 0.2668 (m) REVERT: W 220 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5661 (pt) REVERT: X 23 ARG cc_start: 0.5251 (tpt90) cc_final: 0.2878 (mtm180) REVERT: X 148 ILE cc_start: 0.5122 (mp) cc_final: 0.4896 (mt) REVERT: X 220 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5547 (pt) REVERT: Y 3 MET cc_start: 0.3237 (tmt) cc_final: 0.2866 (tmt) REVERT: Y 16 ASP cc_start: 0.7744 (t0) cc_final: 0.7342 (t0) REVERT: Y 112 LYS cc_start: 0.8510 (mttp) cc_final: 0.8242 (mtpt) REVERT: Z 16 ASP cc_start: 0.7869 (t0) cc_final: 0.7469 (t0) REVERT: Z 112 LYS cc_start: 0.8532 (mttp) cc_final: 0.8268 (mtpt) REVERT: m 16 ASP cc_start: 0.7843 (t0) cc_final: 0.7446 (t70) REVERT: m 19 ARG cc_start: 0.7381 (ttt-90) cc_final: 0.7084 (ttt180) REVERT: m 33 SER cc_start: 0.8410 (p) cc_final: 0.8134 (t) REVERT: m 73 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7894 (ttm-80) REVERT: m 96 ASP cc_start: 0.8282 (t0) cc_final: 0.8054 (t70) REVERT: n 12 THR cc_start: 0.8501 (m) cc_final: 0.8195 (m) REVERT: n 16 ASP cc_start: 0.7691 (t0) cc_final: 0.7318 (t0) REVERT: n 33 SER cc_start: 0.8374 (p) cc_final: 0.8028 (t) REVERT: n 100 ASN cc_start: 0.7902 (m-40) cc_final: 0.7631 (m-40) REVERT: n 112 LYS cc_start: 0.8509 (mttp) cc_final: 0.8228 (mtpt) REVERT: o 16 ASP cc_start: 0.7868 (t0) cc_final: 0.7483 (t0) REVERT: o 41 MET cc_start: 0.8522 (tpp) cc_final: 0.8194 (tpp) REVERT: o 112 LYS cc_start: 0.8561 (mttp) cc_final: 0.8300 (mtpt) REVERT: p 16 ASP cc_start: 0.7828 (t0) cc_final: 0.7447 (t70) REVERT: p 96 ASP cc_start: 0.8343 (t0) cc_final: 0.8054 (t70) REVERT: q 97 SER cc_start: 0.8062 (m) cc_final: 0.7366 (p) REVERT: q 111 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: q 112 LYS cc_start: 0.8573 (mttp) cc_final: 0.8320 (mtpt) REVERT: r 90 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.6966 (p90) REVERT: s 3 MET cc_start: 0.2619 (tmm) cc_final: 0.2103 (tmt) REVERT: s 8 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7630 (tpt) REVERT: t 97 SER cc_start: 0.8083 (m) cc_final: 0.7380 (p) REVERT: u 90 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.6989 (p90) REVERT: v 8 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7566 (tpt) REVERT: w 3 MET cc_start: 0.3111 (tmm) cc_final: 0.2710 (tmt) REVERT: w 88 VAL cc_start: 0.7468 (t) cc_final: 0.7257 (m) REVERT: w 101 GLU cc_start: 0.7998 (tt0) cc_final: 0.7706 (tt0) REVERT: x 97 SER cc_start: 0.8293 (m) cc_final: 0.7815 (p) REVERT: x 112 LYS cc_start: 0.8470 (mttp) cc_final: 0.8240 (mtpt) REVERT: y 16 ASP cc_start: 0.7940 (t0) cc_final: 0.7661 (t70) REVERT: y 27 ASP cc_start: 0.7664 (m-30) cc_final: 0.7346 (m-30) REVERT: y 97 SER cc_start: 0.8248 (m) cc_final: 0.7953 (p) REVERT: y 112 LYS cc_start: 0.8483 (mttp) cc_final: 0.8170 (mtpt) REVERT: y 115 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: z 3 MET cc_start: 0.3106 (tmm) cc_final: 0.2448 (tmt) REVERT: z 97 SER cc_start: 0.8137 (m) cc_final: 0.7868 (p) REVERT: z 112 LYS cc_start: 0.8499 (mttp) cc_final: 0.8266 (mtpt) outliers start: 359 outliers final: 206 residues processed: 1160 average time/residue: 1.1378 time to fit residues: 1730.3303 Evaluate side-chains 1096 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 854 time to evaluate : 4.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 24 MET Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 104 THR Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 48 LYS Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 81 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 365 VAL Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain P residue 367 PHE Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 212 LYS Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 252 ASP Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 296 ASP Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 246 CYS Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 115 ASP Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 14 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 104 THR Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 660 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 390 optimal weight: 9.9990 chunk 500 optimal weight: 20.0000 chunk 387 optimal weight: 0.6980 chunk 576 optimal weight: 9.9990 chunk 382 optimal weight: 0.0470 chunk 682 optimal weight: 20.0000 chunk 427 optimal weight: 10.0000 chunk 416 optimal weight: 40.0000 chunk 315 optimal weight: 8.9990 overall best weight: 5.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN M 119 GLN P 29 GLN P 294 ASN Q 239 GLN Q 294 ASN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** U 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 GLN Y 100 ASN o 121 ASN w 121 ASN x 121 ASN y 121 ASN z 121 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55668 Z= 0.286 Angle : 0.689 8.312 75798 Z= 0.367 Chirality : 0.047 0.216 8778 Planarity : 0.006 0.049 9822 Dihedral : 8.284 62.205 7864 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.68 % Favored : 89.21 % Rotamer: Outliers : 7.35 % Allowed : 24.63 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.10), residues: 7080 helix: 0.64 (0.14), residues: 1500 sheet: 0.08 (0.13), residues: 1440 loop : -2.34 (0.09), residues: 4140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP n 134 HIS 0.005 0.001 HIS V 34 PHE 0.039 0.003 PHE v 90 TYR 0.020 0.002 TYR S 67 ARG 0.007 0.001 ARG p 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 424 poor density : 856 time to evaluate : 4.720 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: 1 97 SER cc_start: 0.8261 (m) cc_final: 0.7788 (p) REVERT: 1 112 LYS cc_start: 0.8478 (mttp) cc_final: 0.8195 (mtpt) REVERT: 2 1 MET cc_start: 0.3328 (mpt) cc_final: 0.2448 (mmm) REVERT: 2 16 ASP cc_start: 0.7917 (t0) cc_final: 0.7616 (t70) REVERT: 2 97 SER cc_start: 0.8198 (m) cc_final: 0.7922 (p) REVERT: 2 112 LYS cc_start: 0.8459 (mttp) cc_final: 0.8130 (mtpt) REVERT: 2 115 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: M 10 THR cc_start: 0.8746 (p) cc_final: 0.8427 (t) REVERT: M 40 GLN cc_start: 0.3608 (OUTLIER) cc_final: 0.2096 (mp10) REVERT: M 59 ASP cc_start: 0.1907 (OUTLIER) cc_final: 0.1530 (t0) REVERT: M 212 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7335 (mmtm) REVERT: N 10 THR cc_start: 0.8522 (p) cc_final: 0.8203 (t) REVERT: N 29 GLN cc_start: 0.4200 (pt0) cc_final: 0.2414 (pm20) REVERT: N 139 VAL cc_start: 0.6856 (OUTLIER) cc_final: 0.6581 (t) REVERT: N 164 ILE cc_start: 0.3751 (OUTLIER) cc_final: 0.3308 (tp) REVERT: N 235 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6358 (tp30) REVERT: N 256 GLN cc_start: 0.6834 (mp10) cc_final: 0.6541 (pm20) REVERT: N 274 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7285 (mt) REVERT: N 321 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7900 (tmm-80) REVERT: N 367 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.5267 (m-80) REVERT: O 10 THR cc_start: 0.8684 (p) cc_final: 0.8390 (t) REVERT: O 139 VAL cc_start: 0.6914 (OUTLIER) cc_final: 0.6630 (t) REVERT: O 164 ILE cc_start: 0.4542 (OUTLIER) cc_final: 0.4206 (tp) REVERT: O 235 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6511 (tp30) REVERT: O 321 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7070 (ttm170) REVERT: O 367 PHE cc_start: 0.5870 (OUTLIER) cc_final: 0.5343 (m-80) REVERT: P 139 VAL cc_start: 0.6734 (OUTLIER) cc_final: 0.6360 (t) REVERT: P 164 ILE cc_start: 0.4624 (OUTLIER) cc_final: 0.4378 (tt) REVERT: P 290 SER cc_start: 0.8751 (OUTLIER) cc_final: 0.8016 (p) REVERT: P 321 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7397 (ttp-170) REVERT: P 341 THR cc_start: 0.8326 (p) cc_final: 0.8042 (t) REVERT: Q 48 LYS cc_start: 0.5724 (ttpt) cc_final: 0.5159 (ttpp) REVERT: Q 139 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6743 (t) REVERT: Q 252 ASP cc_start: 0.7139 (p0) cc_final: 0.6938 (p0) REVERT: Q 274 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7115 (mt) REVERT: Q 290 SER cc_start: 0.8676 (t) cc_final: 0.7966 (p) REVERT: Q 341 THR cc_start: 0.8318 (p) cc_final: 0.8042 (t) REVERT: R 10 THR cc_start: 0.8651 (p) cc_final: 0.8248 (t) REVERT: R 32 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5454 (tt) REVERT: R 297 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7013 (ptm160) REVERT: S 123 ASP cc_start: 0.2148 (OUTLIER) cc_final: 0.1914 (p0) REVERT: S 133 ASP cc_start: 0.5214 (t70) cc_final: 0.4961 (m-30) REVERT: S 212 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6901 (mptp) REVERT: S 220 ILE cc_start: 0.6433 (OUTLIER) cc_final: 0.5940 (pt) REVERT: T 59 ASP cc_start: 0.1701 (OUTLIER) cc_final: 0.1272 (t0) REVERT: T 133 ASP cc_start: 0.5217 (t0) cc_final: 0.4935 (t70) REVERT: T 169 LYS cc_start: 0.5830 (ttpm) cc_final: 0.5499 (ptmt) REVERT: T 220 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5918 (pt) REVERT: T 256 GLN cc_start: 0.6314 (mp10) cc_final: 0.6050 (mp10) REVERT: T 290 SER cc_start: 0.8700 (t) cc_final: 0.8307 (m) REVERT: U 23 ARG cc_start: 0.5520 (tpt-90) cc_final: 0.3251 (mtm180) REVERT: U 68 LYS cc_start: 0.5319 (mttt) cc_final: 0.5107 (tptp) REVERT: U 123 ASP cc_start: 0.2620 (OUTLIER) cc_final: 0.1827 (p0) REVERT: U 210 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.5263 (tppt) REVERT: U 220 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5824 (pt) REVERT: U 286 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6943 (tt0) REVERT: U 288 MET cc_start: 0.8029 (mmt) cc_final: 0.7593 (mmt) REVERT: U 290 SER cc_start: 0.8580 (t) cc_final: 0.8277 (m) REVERT: V 139 VAL cc_start: 0.6249 (OUTLIER) cc_final: 0.5707 (m) REVERT: V 169 LYS cc_start: 0.5731 (OUTLIER) cc_final: 0.5515 (ptmt) REVERT: V 220 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.5975 (pt) REVERT: V 294 ASN cc_start: 0.7640 (OUTLIER) cc_final: 0.7308 (t0) REVERT: V 303 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7447 (mp10) REVERT: W 81 ILE cc_start: 0.4430 (OUTLIER) cc_final: 0.4217 (mt) REVERT: W 208 THR cc_start: 0.3326 (OUTLIER) cc_final: 0.3047 (m) REVERT: W 220 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.5951 (pt) REVERT: W 294 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7321 (t0) REVERT: W 303 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7480 (mp10) REVERT: X 220 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.5977 (pt) REVERT: X 364 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7855 (mm110) REVERT: Y 16 ASP cc_start: 0.7816 (t0) cc_final: 0.7413 (t0) REVERT: Y 66 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8532 (mtmp) REVERT: Y 112 LYS cc_start: 0.8571 (mttp) cc_final: 0.8255 (mtpt) REVERT: Z 16 ASP cc_start: 0.7931 (t0) cc_final: 0.7556 (t0) REVERT: Z 112 LYS cc_start: 0.8452 (mttp) cc_final: 0.8238 (mtpt) REVERT: m 16 ASP cc_start: 0.7931 (t0) cc_final: 0.7557 (t70) REVERT: m 73 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7939 (ttm-80) REVERT: m 96 ASP cc_start: 0.8274 (t0) cc_final: 0.7926 (t0) REVERT: n 16 ASP cc_start: 0.7836 (t0) cc_final: 0.7461 (t0) REVERT: n 100 ASN cc_start: 0.7916 (m-40) cc_final: 0.7582 (m-40) REVERT: n 112 LYS cc_start: 0.8567 (mttp) cc_final: 0.8256 (mtpt) REVERT: o 16 ASP cc_start: 0.7965 (t0) cc_final: 0.7571 (t0) REVERT: o 41 MET cc_start: 0.8534 (tpp) cc_final: 0.8170 (tpp) REVERT: o 112 LYS cc_start: 0.8523 (mttp) cc_final: 0.8283 (mtpt) REVERT: p 16 ASP cc_start: 0.7926 (t0) cc_final: 0.7560 (t70) REVERT: p 96 ASP cc_start: 0.8333 (t0) cc_final: 0.7975 (t0) REVERT: q 93 ASP cc_start: 0.7722 (OUTLIER) cc_final: 0.7486 (t0) REVERT: q 101 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: q 111 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: q 112 LYS cc_start: 0.8526 (mttp) cc_final: 0.8264 (mtpt) REVERT: r 101 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: s 8 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7556 (tpt) REVERT: t 111 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: u 101 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: v 8 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7460 (tpt) REVERT: w 3 MET cc_start: 0.2911 (tmm) cc_final: 0.2390 (tmt) REVERT: x 97 SER cc_start: 0.8321 (m) cc_final: 0.7839 (p) REVERT: x 112 LYS cc_start: 0.8485 (mttp) cc_final: 0.8208 (mtpt) REVERT: y 16 ASP cc_start: 0.7903 (t0) cc_final: 0.7597 (t70) REVERT: y 97 SER cc_start: 0.8250 (m) cc_final: 0.7947 (p) REVERT: y 112 LYS cc_start: 0.8441 (mttp) cc_final: 0.8118 (mtpt) REVERT: y 115 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: y 120 ASN cc_start: 0.7699 (t0) cc_final: 0.7408 (t0) REVERT: z 3 MET cc_start: 0.3036 (tmm) cc_final: 0.2455 (tmt) REVERT: z 97 SER cc_start: 0.8288 (m) cc_final: 0.8032 (p) REVERT: z 112 LYS cc_start: 0.8502 (mttp) cc_final: 0.8221 (mtpt) outliers start: 424 outliers final: 279 residues processed: 1146 average time/residue: 1.1542 time to fit residues: 1731.7178 Evaluate side-chains 1180 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 849 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 104 THR Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 212 LYS Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 235 GLU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 274 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 235 GLU Chi-restraints excluded: chain O residue 252 ASP Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 321 ARG Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain P residue 383 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 235 GLU Chi-restraints excluded: chain Q residue 264 THR Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 212 LYS Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 235 GLU Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 169 LYS Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 210 LYS Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 235 GLU Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 169 LYS Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 4 LEU Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 364 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 40 THR Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 101 GLU Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 115 ASP Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 93 ASP Chi-restraints excluded: chain q residue 101 GLU Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 115 ASP Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 115 ASP Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 93 ASP Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 111 GLN Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 104 THR Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 111 GLN Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 422 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 407 optimal weight: 9.9990 chunk 205 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 433 optimal weight: 8.9990 chunk 464 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 536 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN M 119 GLN P 294 ASN Q 294 ASN T 29 GLN T 76 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** U 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 100 ASN r 120 ASN w 121 ASN x 121 ASN y 121 ASN z 121 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 55668 Z= 0.298 Angle : 0.710 10.556 75798 Z= 0.378 Chirality : 0.048 0.218 8778 Planarity : 0.006 0.057 9822 Dihedral : 8.404 65.483 7858 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.87 % Favored : 90.11 % Rotamer: Outliers : 7.47 % Allowed : 24.99 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.09), residues: 7080 helix: 0.51 (0.14), residues: 1500 sheet: -0.14 (0.13), residues: 1488 loop : -2.40 (0.09), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP z 127 HIS 0.005 0.001 HIS V 34 PHE 0.043 0.003 PHE q 90 TYR 0.024 0.002 TYR S 67 ARG 0.006 0.001 ARG p 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 431 poor density : 850 time to evaluate : 4.961 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: 1 97 SER cc_start: 0.8301 (m) cc_final: 0.7831 (p) REVERT: 1 112 LYS cc_start: 0.8507 (mttp) cc_final: 0.8223 (mtpt) REVERT: 2 1 MET cc_start: 0.3492 (mpt) cc_final: 0.2437 (mmm) REVERT: 2 16 ASP cc_start: 0.7964 (t0) cc_final: 0.7630 (t70) REVERT: 2 97 SER cc_start: 0.8191 (m) cc_final: 0.7935 (p) REVERT: 2 112 LYS cc_start: 0.8452 (mttp) cc_final: 0.8120 (mtpt) REVERT: 2 115 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7763 (m-30) REVERT: M 10 THR cc_start: 0.8760 (p) cc_final: 0.8426 (t) REVERT: M 20 PHE cc_start: 0.5555 (m-80) cc_final: 0.5307 (m-80) REVERT: M 40 GLN cc_start: 0.3470 (OUTLIER) cc_final: 0.2391 (mp10) REVERT: M 48 LYS cc_start: 0.5419 (ttpt) cc_final: 0.5152 (ttpt) REVERT: M 59 ASP cc_start: 0.1905 (OUTLIER) cc_final: 0.1531 (t0) REVERT: M 68 LYS cc_start: 0.5486 (OUTLIER) cc_final: 0.5273 (tptp) REVERT: M 212 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7328 (mmtm) REVERT: N 10 THR cc_start: 0.8565 (p) cc_final: 0.8263 (t) REVERT: N 29 GLN cc_start: 0.4169 (pt0) cc_final: 0.2344 (pm20) REVERT: N 50 TYR cc_start: 0.3447 (t80) cc_final: 0.3173 (t80) REVERT: N 84 LYS cc_start: 0.4536 (ttpp) cc_final: 0.4181 (mtmm) REVERT: N 139 VAL cc_start: 0.6837 (OUTLIER) cc_final: 0.6565 (t) REVERT: N 164 ILE cc_start: 0.3758 (OUTLIER) cc_final: 0.3308 (tp) REVERT: N 191 MET cc_start: 0.4286 (ttp) cc_final: 0.4073 (tpp) REVERT: N 235 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6347 (tp30) REVERT: N 256 GLN cc_start: 0.6813 (mp10) cc_final: 0.6503 (pm20) REVERT: N 274 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7286 (mt) REVERT: N 297 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7713 (ptp-170) REVERT: N 321 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7911 (tmm-80) REVERT: N 367 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5387 (m-80) REVERT: O 10 THR cc_start: 0.8633 (p) cc_final: 0.8324 (t) REVERT: O 139 VAL cc_start: 0.6881 (OUTLIER) cc_final: 0.6604 (t) REVERT: O 164 ILE cc_start: 0.4537 (OUTLIER) cc_final: 0.4206 (tp) REVERT: O 252 ASP cc_start: 0.7150 (p0) cc_final: 0.6784 (p0) REVERT: O 321 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7013 (ttm170) REVERT: O 367 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.5347 (m-80) REVERT: P 59 ASP cc_start: 0.0881 (OUTLIER) cc_final: 0.0504 (m-30) REVERT: P 68 LYS cc_start: 0.5210 (OUTLIER) cc_final: 0.4048 (mmtt) REVERT: P 139 VAL cc_start: 0.6673 (OUTLIER) cc_final: 0.6283 (t) REVERT: P 169 LYS cc_start: 0.4786 (OUTLIER) cc_final: 0.4287 (ptmm) REVERT: P 290 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.7989 (p) REVERT: P 321 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7408 (ttp-170) REVERT: P 341 THR cc_start: 0.8315 (p) cc_final: 0.8001 (t) REVERT: Q 139 VAL cc_start: 0.7046 (OUTLIER) cc_final: 0.6777 (t) REVERT: Q 252 ASP cc_start: 0.7167 (p0) cc_final: 0.6928 (p0) REVERT: Q 274 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7268 (mt) REVERT: Q 290 SER cc_start: 0.8675 (t) cc_final: 0.7968 (p) REVERT: Q 341 THR cc_start: 0.8310 (p) cc_final: 0.8009 (t) REVERT: R 10 THR cc_start: 0.8653 (p) cc_final: 0.8264 (t) REVERT: R 32 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5489 (tt) REVERT: R 297 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7053 (ptm160) REVERT: R 332 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6661 (mt) REVERT: S 123 ASP cc_start: 0.2180 (OUTLIER) cc_final: 0.1911 (p0) REVERT: S 212 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6855 (mptp) REVERT: S 220 ILE cc_start: 0.6365 (OUTLIER) cc_final: 0.6012 (pt) REVERT: S 364 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7789 (mm110) REVERT: T 59 ASP cc_start: 0.2076 (OUTLIER) cc_final: 0.1344 (t0) REVERT: T 123 ASP cc_start: 0.2437 (OUTLIER) cc_final: 0.1668 (p0) REVERT: T 133 ASP cc_start: 0.5314 (t0) cc_final: 0.5021 (t70) REVERT: T 169 LYS cc_start: 0.5857 (ttpm) cc_final: 0.5241 (ptmt) REVERT: T 220 ILE cc_start: 0.6288 (OUTLIER) cc_final: 0.5896 (pt) REVERT: T 290 SER cc_start: 0.8706 (t) cc_final: 0.8333 (m) REVERT: U 23 ARG cc_start: 0.5495 (tpt-90) cc_final: 0.3130 (mtm180) REVERT: U 68 LYS cc_start: 0.5207 (mttt) cc_final: 0.4881 (tptp) REVERT: U 123 ASP cc_start: 0.2536 (OUTLIER) cc_final: 0.1875 (p0) REVERT: U 161 THR cc_start: 0.5029 (p) cc_final: 0.4611 (m) REVERT: U 286 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6918 (tt0) REVERT: U 288 MET cc_start: 0.8009 (mmt) cc_final: 0.7570 (mmt) REVERT: U 290 SER cc_start: 0.8595 (t) cc_final: 0.8283 (m) REVERT: V 169 LYS cc_start: 0.5753 (OUTLIER) cc_final: 0.5499 (ptmt) REVERT: V 220 ILE cc_start: 0.6611 (OUTLIER) cc_final: 0.5961 (pt) REVERT: V 294 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7316 (t0) REVERT: V 303 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7460 (mp10) REVERT: W 81 ILE cc_start: 0.4513 (OUTLIER) cc_final: 0.4208 (mt) REVERT: W 220 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6030 (pt) REVERT: W 274 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6858 (mt) REVERT: W 288 MET cc_start: 0.8256 (mmt) cc_final: 0.7769 (mmt) REVERT: W 294 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7378 (t0) REVERT: W 303 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7464 (mp10) REVERT: X 164 ILE cc_start: 0.4412 (OUTLIER) cc_final: 0.3610 (tp) REVERT: X 220 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.6074 (pt) REVERT: X 364 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7851 (mm110) REVERT: Y 16 ASP cc_start: 0.7734 (t0) cc_final: 0.7386 (t0) REVERT: Y 28 ASP cc_start: 0.6986 (p0) cc_final: 0.6766 (p0) REVERT: Y 66 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8564 (mtmp) REVERT: Y 112 LYS cc_start: 0.8585 (mttp) cc_final: 0.8263 (mtpt) REVERT: Z 16 ASP cc_start: 0.7968 (t0) cc_final: 0.7587 (t0) REVERT: Z 86 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7711 (ttm-80) REVERT: Z 112 LYS cc_start: 0.8483 (mttp) cc_final: 0.8262 (mtpt) REVERT: m 16 ASP cc_start: 0.7924 (t0) cc_final: 0.7554 (t70) REVERT: m 73 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.8016 (ttm-80) REVERT: m 96 ASP cc_start: 0.8308 (t0) cc_final: 0.7971 (t0) REVERT: n 16 ASP cc_start: 0.7741 (t0) cc_final: 0.7393 (t0) REVERT: n 28 ASP cc_start: 0.6995 (p0) cc_final: 0.6650 (p0) REVERT: n 100 ASN cc_start: 0.7950 (m-40) cc_final: 0.7589 (m-40) REVERT: n 112 LYS cc_start: 0.8577 (mttp) cc_final: 0.8264 (mtpt) REVERT: o 16 ASP cc_start: 0.7985 (t0) cc_final: 0.7586 (t0) REVERT: o 41 MET cc_start: 0.8547 (tpp) cc_final: 0.8191 (tpp) REVERT: o 86 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7731 (ttm-80) REVERT: o 112 LYS cc_start: 0.8487 (mttp) cc_final: 0.8216 (mtpt) REVERT: p 16 ASP cc_start: 0.7928 (t0) cc_final: 0.7560 (t70) REVERT: p 96 ASP cc_start: 0.8356 (t0) cc_final: 0.8013 (t0) REVERT: q 111 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: q 112 LYS cc_start: 0.8488 (mttp) cc_final: 0.8218 (mtpt) REVERT: r 90 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.6897 (p90) REVERT: r 101 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: s 8 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7565 (tpt) REVERT: t 46 ASP cc_start: 0.7276 (p0) cc_final: 0.7069 (p0) REVERT: t 93 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7373 (t0) REVERT: t 111 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: u 90 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.6889 (p90) REVERT: u 101 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: v 8 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7459 (tpt) REVERT: w 3 MET cc_start: 0.2966 (tmm) cc_final: 0.2407 (tmt) REVERT: w 93 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7557 (t70) REVERT: x 97 SER cc_start: 0.8316 (m) cc_final: 0.7848 (p) REVERT: x 112 LYS cc_start: 0.8496 (mttp) cc_final: 0.8219 (mtpt) REVERT: y 16 ASP cc_start: 0.7935 (t0) cc_final: 0.7625 (t70) REVERT: y 93 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7480 (t0) REVERT: y 97 SER cc_start: 0.8250 (m) cc_final: 0.7952 (p) REVERT: y 112 LYS cc_start: 0.8443 (mttp) cc_final: 0.8110 (mtpt) REVERT: y 115 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7797 (m-30) REVERT: y 120 ASN cc_start: 0.7682 (t0) cc_final: 0.7406 (t0) REVERT: z 3 MET cc_start: 0.3006 (tmm) cc_final: 0.2413 (tmt) REVERT: z 93 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7528 (t70) REVERT: z 97 SER cc_start: 0.8294 (m) cc_final: 0.8038 (p) REVERT: z 112 LYS cc_start: 0.8500 (mttp) cc_final: 0.8237 (mtpt) outliers start: 431 outliers final: 294 residues processed: 1156 average time/residue: 1.1356 time to fit residues: 1722.3437 Evaluate side-chains 1194 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 838 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 MET Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 104 THR Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 68 LYS Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 212 LYS Chi-restraints excluded: chain M residue 235 GLU Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 235 GLU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 274 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain N residue 367 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 352 GLU Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 68 LYS Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 169 LYS Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 202 ASP Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 321 ARG Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain P residue 383 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 59 ASP Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 235 GLU Chi-restraints excluded: chain Q residue 264 THR Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 383 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 169 LYS Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 212 LYS Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 364 GLN Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 202 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 265 LEU Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 169 LYS Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 169 LYS Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 59 ASP Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 274 ILE Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 332 LEU Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 121 THR Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 364 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 86 ARG Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 93 ASP Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 40 THR Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 86 ARG Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 115 ASP Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 115 ASP Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 115 ASP Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 93 ASP Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 93 ASP Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 111 GLN Chi-restraints excluded: chain u residue 115 ASP Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain w residue 93 ASP Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 104 THR Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 93 ASP Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 111 GLN Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 93 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 620 optimal weight: 4.9990 chunk 653 optimal weight: 9.9990 chunk 596 optimal weight: 10.0000 chunk 635 optimal weight: 9.9990 chunk 382 optimal weight: 10.0000 chunk 277 optimal weight: 0.0170 chunk 499 optimal weight: 10.0000 chunk 195 optimal weight: 30.0000 chunk 574 optimal weight: 10.0000 chunk 601 optimal weight: 8.9990 chunk 633 optimal weight: 1.9990 overall best weight: 5.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 ASN Q 294 ASN S 168 HIS ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** U 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 40 GLN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 GLN Y 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 55668 Z= 0.291 Angle : 0.711 9.513 75798 Z= 0.377 Chirality : 0.048 0.213 8778 Planarity : 0.006 0.059 9822 Dihedral : 8.376 64.775 7858 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.19 % Favored : 88.79 % Rotamer: Outliers : 7.18 % Allowed : 25.60 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.10), residues: 7080 helix: 0.50 (0.14), residues: 1500 sheet: -0.17 (0.13), residues: 1488 loop : -2.40 (0.09), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP x 127 HIS 0.005 0.001 HIS V 34 PHE 0.042 0.003 PHE q 90 TYR 0.024 0.002 TYR S 67 ARG 0.008 0.001 ARG v 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 857 time to evaluate : 4.931 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: 1 93 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7665 (t70) REVERT: 1 97 SER cc_start: 0.8296 (m) cc_final: 0.7819 (p) REVERT: 1 112 LYS cc_start: 0.8515 (mttp) cc_final: 0.8228 (mtpt) REVERT: 2 1 MET cc_start: 0.3411 (mpt) cc_final: 0.2708 (mmm) REVERT: 2 16 ASP cc_start: 0.7946 (t0) cc_final: 0.7629 (t70) REVERT: 2 97 SER cc_start: 0.8189 (m) cc_final: 0.7939 (p) REVERT: 2 112 LYS cc_start: 0.8450 (mttp) cc_final: 0.8119 (mtpt) REVERT: 2 115 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7757 (m-30) REVERT: M 10 THR cc_start: 0.8757 (p) cc_final: 0.8427 (t) REVERT: M 20 PHE cc_start: 0.5971 (m-80) cc_final: 0.5715 (m-80) REVERT: M 40 GLN cc_start: 0.3719 (OUTLIER) cc_final: 0.2592 (mp10) REVERT: M 48 LYS cc_start: 0.5132 (ttpt) cc_final: 0.4926 (ttpt) REVERT: M 59 ASP cc_start: 0.1950 (OUTLIER) cc_final: 0.1590 (t0) REVERT: M 212 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7311 (mmtm) REVERT: M 332 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6739 (mt) REVERT: N 10 THR cc_start: 0.8536 (p) cc_final: 0.8235 (t) REVERT: N 29 GLN cc_start: 0.3972 (pt0) cc_final: 0.2178 (pm20) REVERT: N 139 VAL cc_start: 0.6801 (OUTLIER) cc_final: 0.6550 (t) REVERT: N 235 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6315 (tp30) REVERT: N 256 GLN cc_start: 0.6816 (mp10) cc_final: 0.6508 (pm20) REVERT: N 274 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7296 (mt) REVERT: N 297 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7732 (ptp-170) REVERT: N 321 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7924 (tmm-80) REVERT: O 10 THR cc_start: 0.8627 (p) cc_final: 0.8316 (t) REVERT: O 139 VAL cc_start: 0.6779 (OUTLIER) cc_final: 0.6504 (t) REVERT: O 164 ILE cc_start: 0.4547 (OUTLIER) cc_final: 0.4237 (tp) REVERT: O 226 VAL cc_start: 0.6448 (OUTLIER) cc_final: 0.6143 (m) REVERT: O 321 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7019 (ttm170) REVERT: O 367 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: P 59 ASP cc_start: 0.0855 (OUTLIER) cc_final: 0.0463 (m-30) REVERT: P 139 VAL cc_start: 0.6657 (OUTLIER) cc_final: 0.6286 (t) REVERT: P 290 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.7994 (p) REVERT: P 321 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7418 (ttp-170) REVERT: P 341 THR cc_start: 0.8307 (p) cc_final: 0.7996 (t) REVERT: Q 48 LYS cc_start: 0.5833 (ttpt) cc_final: 0.5567 (ttpm) REVERT: Q 139 VAL cc_start: 0.7028 (OUTLIER) cc_final: 0.6764 (t) REVERT: Q 274 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7253 (mt) REVERT: Q 290 SER cc_start: 0.8672 (t) cc_final: 0.7937 (p) REVERT: Q 341 THR cc_start: 0.8297 (p) cc_final: 0.8003 (t) REVERT: R 10 THR cc_start: 0.8694 (p) cc_final: 0.8308 (t) REVERT: R 20 PHE cc_start: 0.6021 (m-80) cc_final: 0.5686 (m-80) REVERT: R 32 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5488 (tt) REVERT: R 48 LYS cc_start: 0.5479 (ttpm) cc_final: 0.4670 (tttm) REVERT: R 297 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7113 (ptm160) REVERT: R 332 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6702 (mt) REVERT: S 123 ASP cc_start: 0.2446 (OUTLIER) cc_final: 0.1474 (p0) REVERT: S 212 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6883 (mptp) REVERT: S 220 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.5994 (pt) REVERT: S 364 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7861 (mm110) REVERT: T 59 ASP cc_start: 0.2167 (OUTLIER) cc_final: 0.1262 (t0) REVERT: T 64 THR cc_start: 0.2965 (OUTLIER) cc_final: 0.2752 (p) REVERT: T 123 ASP cc_start: 0.2601 (OUTLIER) cc_final: 0.1733 (p0) REVERT: T 133 ASP cc_start: 0.5484 (t0) cc_final: 0.5212 (t70) REVERT: T 169 LYS cc_start: 0.5860 (ttpm) cc_final: 0.5411 (ptmt) REVERT: T 220 ILE cc_start: 0.6317 (OUTLIER) cc_final: 0.5886 (pt) REVERT: T 290 SER cc_start: 0.8727 (t) cc_final: 0.8332 (m) REVERT: U 23 ARG cc_start: 0.5456 (tpt-90) cc_final: 0.3026 (mtm180) REVERT: U 68 LYS cc_start: 0.5181 (mttt) cc_final: 0.4868 (tptp) REVERT: U 123 ASP cc_start: 0.2717 (OUTLIER) cc_final: 0.2037 (p0) REVERT: U 201 ASP cc_start: 0.7288 (m-30) cc_final: 0.7045 (m-30) REVERT: U 286 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6923 (tt0) REVERT: U 288 MET cc_start: 0.7999 (mmt) cc_final: 0.7563 (mmt) REVERT: U 290 SER cc_start: 0.8588 (t) cc_final: 0.8277 (m) REVERT: V 220 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.5970 (pt) REVERT: V 294 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7314 (t0) REVERT: V 303 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7453 (mp10) REVERT: W 81 ILE cc_start: 0.4494 (OUTLIER) cc_final: 0.4210 (mt) REVERT: W 208 THR cc_start: 0.3320 (OUTLIER) cc_final: 0.3044 (m) REVERT: W 220 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6007 (pt) REVERT: W 245 HIS cc_start: 0.5997 (OUTLIER) cc_final: 0.5349 (m-70) REVERT: W 288 MET cc_start: 0.8263 (mmt) cc_final: 0.7771 (mmt) REVERT: W 294 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7386 (t0) REVERT: W 303 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7470 (mp10) REVERT: X 164 ILE cc_start: 0.4406 (OUTLIER) cc_final: 0.3601 (tp) REVERT: X 191 MET cc_start: 0.6358 (ttp) cc_final: 0.5785 (ttm) REVERT: X 220 ILE cc_start: 0.6503 (OUTLIER) cc_final: 0.6025 (pt) REVERT: X 364 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7847 (mm110) REVERT: Y 3 MET cc_start: 0.3166 (tmt) cc_final: 0.2340 (tmm) REVERT: Y 16 ASP cc_start: 0.7840 (t0) cc_final: 0.7449 (t0) REVERT: Y 66 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8555 (mtmp) REVERT: Y 112 LYS cc_start: 0.8585 (mttp) cc_final: 0.8268 (mtpt) REVERT: Z 16 ASP cc_start: 0.7981 (t0) cc_final: 0.7563 (t0) REVERT: Z 86 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7652 (ttm-80) REVERT: Z 112 LYS cc_start: 0.8485 (mttp) cc_final: 0.8261 (mtpt) REVERT: m 16 ASP cc_start: 0.7929 (t0) cc_final: 0.7560 (t70) REVERT: m 73 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8014 (ttm-80) REVERT: m 96 ASP cc_start: 0.8288 (t0) cc_final: 0.7951 (t0) REVERT: n 16 ASP cc_start: 0.7762 (t0) cc_final: 0.7405 (t0) REVERT: n 28 ASP cc_start: 0.6954 (p0) cc_final: 0.6749 (p0) REVERT: n 33 SER cc_start: 0.8634 (p) cc_final: 0.8231 (p) REVERT: n 100 ASN cc_start: 0.7919 (m-40) cc_final: 0.7562 (m-40) REVERT: n 112 LYS cc_start: 0.8559 (mttp) cc_final: 0.8261 (mtpt) REVERT: o 16 ASP cc_start: 0.7965 (t0) cc_final: 0.7551 (t0) REVERT: o 41 MET cc_start: 0.8547 (tpp) cc_final: 0.8239 (tpp) REVERT: o 112 LYS cc_start: 0.8467 (mttp) cc_final: 0.8208 (mtpt) REVERT: p 16 ASP cc_start: 0.7933 (t0) cc_final: 0.7560 (t70) REVERT: p 96 ASP cc_start: 0.8343 (t0) cc_final: 0.7999 (t0) REVERT: q 93 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7312 (t0) REVERT: q 111 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: q 112 LYS cc_start: 0.8533 (mttp) cc_final: 0.8275 (mtpt) REVERT: r 101 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: s 8 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7430 (tpt) REVERT: t 93 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7375 (t0) REVERT: t 111 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: u 86 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7897 (ttp80) REVERT: u 101 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: v 8 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7461 (tpt) REVERT: w 3 MET cc_start: 0.3109 (tmm) cc_final: 0.2583 (tmt) REVERT: x 93 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7668 (t70) REVERT: x 97 SER cc_start: 0.8306 (m) cc_final: 0.7822 (p) REVERT: x 112 LYS cc_start: 0.8507 (mttp) cc_final: 0.8222 (mtpt) REVERT: y 16 ASP cc_start: 0.7933 (t0) cc_final: 0.7640 (t70) REVERT: y 93 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7492 (t0) REVERT: y 97 SER cc_start: 0.8242 (m) cc_final: 0.7949 (p) REVERT: y 112 LYS cc_start: 0.8468 (mttp) cc_final: 0.8141 (mtpt) REVERT: y 115 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: z 3 MET cc_start: 0.2991 (tmm) cc_final: 0.2418 (tmt) REVERT: z 93 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7542 (t70) REVERT: z 97 SER cc_start: 0.8278 (m) cc_final: 0.8036 (p) REVERT: z 112 LYS cc_start: 0.8502 (mttp) cc_final: 0.8239 (mtpt) outliers start: 414 outliers final: 302 residues processed: 1145 average time/residue: 1.1293 time to fit residues: 1694.8567 Evaluate side-chains 1207 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 845 time to evaluate : 4.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 MET Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 1 residue 115 ASP Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 104 THR Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 71 LEU Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 212 LYS Chi-restraints excluded: chain M residue 235 GLU Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain M residue 383 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 235 GLU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 274 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 290 SER Chi-restraints excluded: chain N residue 297 ARG Chi-restraints excluded: chain N residue 321 ARG Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 190 SER Chi-restraints excluded: chain O residue 202 ASP Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 321 ARG Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 139 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 202 ASP Chi-restraints excluded: chain P residue 212 LYS Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 321 ARG Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain P residue 383 THR Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 164 ILE Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 202 ASP Chi-restraints excluded: chain Q residue 209 LEU Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 235 GLU Chi-restraints excluded: chain Q residue 264 THR Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain Q residue 383 THR Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 235 GLU Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 332 LEU Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 212 LYS Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 265 LEU Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 364 GLN Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 121 THR Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 172 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 169 LYS Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 220 ILE Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 353 SER Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 13 THR Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 245 HIS Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 332 LEU Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 85 VAL Chi-restraints excluded: chain X residue 121 THR Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 228 THR Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 364 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 66 LYS Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 86 ARG Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 93 ASP Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 40 THR Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 115 ASP Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 93 ASP Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 111 GLN Chi-restraints excluded: chain r residue 115 ASP Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 97 SER Chi-restraints excluded: chain s residue 115 ASP Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 93 ASP Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 86 ARG Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 93 ASP Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 111 GLN Chi-restraints excluded: chain u residue 115 ASP Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 95 ILE Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 21 ILE Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 32 THR Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 93 ASP Chi-restraints excluded: chain x residue 104 THR Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 3 MET Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 93 ASP Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 111 GLN Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Chi-restraints excluded: chain z residue 93 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 417 optimal weight: 40.0000 chunk 672 optimal weight: 1.9990 chunk 410 optimal weight: 6.9990 chunk 318 optimal weight: 8.9990 chunk 467 optimal weight: 0.0980 chunk 705 optimal weight: 2.9990 chunk 649 optimal weight: 8.9990 chunk 561 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 433 optimal weight: 20.0000 chunk 344 optimal weight: 0.4980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN P 294 ASN Q 294 ASN S 239 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 239 GLN U 63 ASN X 239 GLN Y 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 55668 Z= 0.184 Angle : 0.628 10.595 75798 Z= 0.331 Chirality : 0.044 0.164 8778 Planarity : 0.005 0.056 9822 Dihedral : 7.757 59.881 7856 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 6.00 % Allowed : 27.04 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.10), residues: 7080 helix: 0.86 (0.14), residues: 1500 sheet: -0.00 (0.13), residues: 1488 loop : -2.32 (0.09), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 127 HIS 0.005 0.001 HIS V 34 PHE 0.028 0.002 PHE q 90 TYR 0.018 0.002 TYR S 67 ARG 0.008 0.000 ARG v 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14160 Ramachandran restraints generated. 7080 Oldfield, 0 Emsley, 7080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 858 time to evaluate : 4.755 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: 1 93 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7371 (t70) REVERT: 1 97 SER cc_start: 0.8256 (m) cc_final: 0.7787 (p) REVERT: 1 112 LYS cc_start: 0.8463 (mttp) cc_final: 0.8207 (mtpt) REVERT: 2 1 MET cc_start: 0.3345 (mpt) cc_final: 0.2650 (mmm) REVERT: 2 16 ASP cc_start: 0.7993 (t0) cc_final: 0.7685 (t70) REVERT: 2 97 SER cc_start: 0.8180 (m) cc_final: 0.7939 (p) REVERT: 2 112 LYS cc_start: 0.8464 (mttp) cc_final: 0.8178 (mtpt) REVERT: 2 115 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7757 (m-30) REVERT: M 10 THR cc_start: 0.8823 (p) cc_final: 0.8418 (t) REVERT: M 40 GLN cc_start: 0.3545 (OUTLIER) cc_final: 0.2622 (mp10) REVERT: M 48 LYS cc_start: 0.5215 (ttpt) cc_final: 0.4885 (ttpt) REVERT: M 59 ASP cc_start: 0.1754 (OUTLIER) cc_final: 0.1469 (t0) REVERT: N 10 THR cc_start: 0.8455 (p) cc_final: 0.8208 (t) REVERT: N 29 GLN cc_start: 0.4027 (pt0) cc_final: 0.2271 (pm20) REVERT: N 84 LYS cc_start: 0.4245 (ttpp) cc_final: 0.3975 (mtmm) REVERT: N 139 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6524 (t) REVERT: N 256 GLN cc_start: 0.6858 (mp10) cc_final: 0.6519 (pm20) REVERT: N 274 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7214 (mt) REVERT: N 321 ARG cc_start: 0.8271 (tmm160) cc_final: 0.8006 (tmm-80) REVERT: O 10 THR cc_start: 0.8664 (p) cc_final: 0.8373 (t) REVERT: O 84 LYS cc_start: 0.4382 (ttpp) cc_final: 0.4055 (mtmm) REVERT: O 139 VAL cc_start: 0.7156 (OUTLIER) cc_final: 0.6894 (t) REVERT: O 164 ILE cc_start: 0.4390 (OUTLIER) cc_final: 0.4112 (tp) REVERT: O 226 VAL cc_start: 0.6513 (OUTLIER) cc_final: 0.6234 (m) REVERT: O 305 MET cc_start: 0.7969 (mmp) cc_final: 0.7563 (mmm) REVERT: O 359 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8316 (mt) REVERT: O 367 PHE cc_start: 0.6038 (OUTLIER) cc_final: 0.5438 (m-80) REVERT: P 59 ASP cc_start: 0.0894 (OUTLIER) cc_final: 0.0593 (m-30) REVERT: P 68 LYS cc_start: 0.5281 (mtmm) cc_final: 0.4079 (mmtt) REVERT: P 139 VAL cc_start: 0.6740 (t) cc_final: 0.6362 (t) REVERT: P 290 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.7957 (p) REVERT: P 341 THR cc_start: 0.8303 (p) cc_final: 0.8050 (t) REVERT: Q 274 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7127 (mt) REVERT: Q 290 SER cc_start: 0.8611 (t) cc_final: 0.7939 (p) REVERT: Q 341 THR cc_start: 0.8293 (p) cc_final: 0.8054 (t) REVERT: R 10 THR cc_start: 0.8684 (p) cc_final: 0.8330 (t) REVERT: R 32 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5353 (tt) REVERT: S 123 ASP cc_start: 0.2460 (OUTLIER) cc_final: 0.1473 (p0) REVERT: S 220 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5694 (pt) REVERT: T 59 ASP cc_start: 0.2267 (OUTLIER) cc_final: 0.1481 (t0) REVERT: T 123 ASP cc_start: 0.2404 (OUTLIER) cc_final: 0.1406 (p0) REVERT: T 133 ASP cc_start: 0.5454 (t0) cc_final: 0.5169 (t70) REVERT: T 169 LYS cc_start: 0.5959 (ttpm) cc_final: 0.5384 (ptmt) REVERT: T 220 ILE cc_start: 0.6148 (OUTLIER) cc_final: 0.5729 (pt) REVERT: T 290 SER cc_start: 0.8756 (t) cc_final: 0.8299 (m) REVERT: T 294 ASN cc_start: 0.7464 (OUTLIER) cc_final: 0.7261 (t0) REVERT: U 23 ARG cc_start: 0.5423 (tpt-90) cc_final: 0.3089 (mtm180) REVERT: U 123 ASP cc_start: 0.2557 (OUTLIER) cc_final: 0.2074 (p0) REVERT: U 286 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6894 (tt0) REVERT: U 288 MET cc_start: 0.7970 (mmt) cc_final: 0.7586 (mmt) REVERT: U 290 SER cc_start: 0.8554 (t) cc_final: 0.8231 (m) REVERT: V 220 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.5740 (pt) REVERT: V 294 ASN cc_start: 0.7562 (OUTLIER) cc_final: 0.7240 (t0) REVERT: W 81 ILE cc_start: 0.4287 (OUTLIER) cc_final: 0.4068 (mt) REVERT: W 208 THR cc_start: 0.3126 (OUTLIER) cc_final: 0.2904 (m) REVERT: W 220 ILE cc_start: 0.6275 (OUTLIER) cc_final: 0.5750 (pt) REVERT: W 288 MET cc_start: 0.8227 (mmt) cc_final: 0.7767 (mmt) REVERT: W 294 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7242 (t0) REVERT: X 164 ILE cc_start: 0.4520 (OUTLIER) cc_final: 0.3903 (tp) REVERT: X 191 MET cc_start: 0.6134 (ttp) cc_final: 0.5698 (ttm) REVERT: X 220 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5838 (pt) REVERT: X 364 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7786 (mm110) REVERT: Y 16 ASP cc_start: 0.7778 (t0) cc_final: 0.7379 (t0) REVERT: Y 112 LYS cc_start: 0.8512 (mttp) cc_final: 0.8237 (mtpt) REVERT: Z 16 ASP cc_start: 0.7965 (t0) cc_final: 0.7534 (t0) REVERT: Z 112 LYS cc_start: 0.8516 (mttp) cc_final: 0.8292 (mtpt) REVERT: m 16 ASP cc_start: 0.7886 (t0) cc_final: 0.7509 (t70) REVERT: m 73 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8010 (ttm-80) REVERT: m 96 ASP cc_start: 0.8265 (t0) cc_final: 0.7933 (t70) REVERT: n 16 ASP cc_start: 0.7802 (t0) cc_final: 0.7393 (t0) REVERT: n 28 ASP cc_start: 0.6917 (p0) cc_final: 0.6682 (p0) REVERT: n 100 ASN cc_start: 0.7855 (m-40) cc_final: 0.7483 (m-40) REVERT: n 112 LYS cc_start: 0.8506 (mttp) cc_final: 0.8190 (mtpt) REVERT: o 12 THR cc_start: 0.8396 (m) cc_final: 0.8165 (m) REVERT: o 16 ASP cc_start: 0.7960 (t0) cc_final: 0.7538 (t0) REVERT: o 41 MET cc_start: 0.8558 (tpp) cc_final: 0.8204 (tpp) REVERT: o 112 LYS cc_start: 0.8495 (mttp) cc_final: 0.8233 (mtpt) REVERT: p 16 ASP cc_start: 0.7893 (t0) cc_final: 0.7511 (t70) REVERT: p 19 ARG cc_start: 0.7636 (ttt-90) cc_final: 0.7259 (ttt180) REVERT: p 96 ASP cc_start: 0.8321 (t0) cc_final: 0.7997 (t70) REVERT: q 18 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6469 (mtt-85) REVERT: q 93 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7379 (t0) REVERT: q 111 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: q 112 LYS cc_start: 0.8538 (mttp) cc_final: 0.8272 (mtpt) REVERT: r 90 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.6836 (p90) REVERT: r 101 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: s 8 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7419 (tpt) REVERT: t 93 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7487 (t0) REVERT: t 97 SER cc_start: 0.8099 (m) cc_final: 0.7421 (p) REVERT: t 111 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: u 1 MET cc_start: 0.1760 (mmm) cc_final: 0.1460 (mmp) REVERT: u 86 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7861 (ttp80) REVERT: u 90 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.6817 (p90) REVERT: u 101 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: v 8 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7469 (tpt) REVERT: w 3 MET cc_start: 0.3101 (tmm) cc_final: 0.2665 (tmt) REVERT: x 93 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7374 (t70) REVERT: x 97 SER cc_start: 0.8303 (m) cc_final: 0.7817 (p) REVERT: x 112 LYS cc_start: 0.8490 (mttp) cc_final: 0.8227 (mtpt) REVERT: y 16 ASP cc_start: 0.7889 (t0) cc_final: 0.7609 (t70) REVERT: y 97 SER cc_start: 0.8246 (m) cc_final: 0.7969 (p) REVERT: y 112 LYS cc_start: 0.8424 (mttp) cc_final: 0.8146 (mtpt) REVERT: y 115 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7757 (m-30) REVERT: z 3 MET cc_start: 0.3095 (tmm) cc_final: 0.2628 (tmt) REVERT: z 97 SER cc_start: 0.8270 (m) cc_final: 0.8053 (p) REVERT: z 112 LYS cc_start: 0.8503 (mttp) cc_final: 0.8270 (mtpt) outliers start: 346 outliers final: 267 residues processed: 1097 average time/residue: 1.1367 time to fit residues: 1631.4762 Evaluate side-chains 1147 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 834 time to evaluate : 4.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 24 MET Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 90 PHE Chi-restraints excluded: chain 1 residue 93 ASP Chi-restraints excluded: chain 1 residue 104 THR Chi-restraints excluded: chain 2 residue 21 ILE Chi-restraints excluded: chain 2 residue 56 ASP Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 90 PHE Chi-restraints excluded: chain 2 residue 104 THR Chi-restraints excluded: chain 2 residue 111 GLN Chi-restraints excluded: chain 2 residue 115 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 119 GLN Chi-restraints excluded: chain M residue 163 VAL Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 264 THR Chi-restraints excluded: chain M residue 343 THR Chi-restraints excluded: chain M residue 365 VAL Chi-restraints excluded: chain M residue 367 PHE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 15 THR Chi-restraints excluded: chain N residue 139 VAL Chi-restraints excluded: chain N residue 162 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 164 ILE Chi-restraints excluded: chain N residue 228 THR Chi-restraints excluded: chain N residue 259 LEU Chi-restraints excluded: chain N residue 260 VAL Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 274 ILE Chi-restraints excluded: chain N residue 289 LEU Chi-restraints excluded: chain N residue 343 THR Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 13 THR Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 139 VAL Chi-restraints excluded: chain O residue 164 ILE Chi-restraints excluded: chain O residue 172 VAL Chi-restraints excluded: chain O residue 202 ASP Chi-restraints excluded: chain O residue 226 VAL Chi-restraints excluded: chain O residue 228 THR Chi-restraints excluded: chain O residue 257 GLU Chi-restraints excluded: chain O residue 260 VAL Chi-restraints excluded: chain O residue 264 THR Chi-restraints excluded: chain O residue 289 LEU Chi-restraints excluded: chain O residue 290 SER Chi-restraints excluded: chain O residue 333 THR Chi-restraints excluded: chain O residue 343 THR Chi-restraints excluded: chain O residue 359 ILE Chi-restraints excluded: chain O residue 367 PHE Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 10 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 59 ASP Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 202 ASP Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 228 THR Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 264 THR Chi-restraints excluded: chain P residue 290 SER Chi-restraints excluded: chain P residue 333 THR Chi-restraints excluded: chain P residue 365 VAL Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 15 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 47 THR Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 163 VAL Chi-restraints excluded: chain Q residue 172 VAL Chi-restraints excluded: chain Q residue 190 SER Chi-restraints excluded: chain Q residue 202 ASP Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 228 THR Chi-restraints excluded: chain Q residue 235 GLU Chi-restraints excluded: chain Q residue 264 THR Chi-restraints excluded: chain Q residue 274 ILE Chi-restraints excluded: chain Q residue 333 THR Chi-restraints excluded: chain Q residue 365 VAL Chi-restraints excluded: chain R residue 13 THR Chi-restraints excluded: chain R residue 15 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 264 THR Chi-restraints excluded: chain R residue 343 THR Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 367 PHE Chi-restraints excluded: chain S residue 59 ASP Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 123 ASP Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 162 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 172 VAL Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 201 ASP Chi-restraints excluded: chain S residue 208 THR Chi-restraints excluded: chain S residue 220 ILE Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 GLU Chi-restraints excluded: chain S residue 266 THR Chi-restraints excluded: chain S residue 343 THR Chi-restraints excluded: chain S residue 383 THR Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 59 ASP Chi-restraints excluded: chain T residue 121 THR Chi-restraints excluded: chain T residue 123 ASP Chi-restraints excluded: chain T residue 161 THR Chi-restraints excluded: chain T residue 162 THR Chi-restraints excluded: chain T residue 163 VAL Chi-restraints excluded: chain T residue 199 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 208 THR Chi-restraints excluded: chain T residue 220 ILE Chi-restraints excluded: chain T residue 226 VAL Chi-restraints excluded: chain T residue 240 SER Chi-restraints excluded: chain T residue 266 THR Chi-restraints excluded: chain T residue 289 LEU Chi-restraints excluded: chain T residue 294 ASN Chi-restraints excluded: chain T residue 383 THR Chi-restraints excluded: chain U residue 4 LEU Chi-restraints excluded: chain U residue 123 ASP Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 163 VAL Chi-restraints excluded: chain U residue 172 VAL Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 199 VAL Chi-restraints excluded: chain U residue 202 ASP Chi-restraints excluded: chain U residue 208 THR Chi-restraints excluded: chain U residue 226 VAL Chi-restraints excluded: chain U residue 266 THR Chi-restraints excluded: chain U residue 289 LEU Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain V residue 13 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 123 ASP Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 163 VAL Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 202 ASP Chi-restraints excluded: chain V residue 208 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 240 SER Chi-restraints excluded: chain V residue 252 ASP Chi-restraints excluded: chain V residue 266 THR Chi-restraints excluded: chain V residue 289 LEU Chi-restraints excluded: chain V residue 294 ASN Chi-restraints excluded: chain V residue 296 ASP Chi-restraints excluded: chain V residue 383 THR Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 123 ASP Chi-restraints excluded: chain W residue 139 VAL Chi-restraints excluded: chain W residue 162 THR Chi-restraints excluded: chain W residue 163 VAL Chi-restraints excluded: chain W residue 172 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 202 ASP Chi-restraints excluded: chain W residue 208 THR Chi-restraints excluded: chain W residue 220 ILE Chi-restraints excluded: chain W residue 226 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 252 ASP Chi-restraints excluded: chain W residue 266 THR Chi-restraints excluded: chain W residue 289 LEU Chi-restraints excluded: chain W residue 294 ASN Chi-restraints excluded: chain W residue 332 LEU Chi-restraints excluded: chain W residue 383 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 64 THR Chi-restraints excluded: chain X residue 121 THR Chi-restraints excluded: chain X residue 123 ASP Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 163 VAL Chi-restraints excluded: chain X residue 164 ILE Chi-restraints excluded: chain X residue 172 VAL Chi-restraints excluded: chain X residue 197 THR Chi-restraints excluded: chain X residue 199 VAL Chi-restraints excluded: chain X residue 201 ASP Chi-restraints excluded: chain X residue 208 THR Chi-restraints excluded: chain X residue 220 ILE Chi-restraints excluded: chain X residue 226 VAL Chi-restraints excluded: chain X residue 264 THR Chi-restraints excluded: chain X residue 266 THR Chi-restraints excluded: chain X residue 364 GLN Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain Y residue 12 THR Chi-restraints excluded: chain Y residue 21 ILE Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 56 ASP Chi-restraints excluded: chain Y residue 90 PHE Chi-restraints excluded: chain Y residue 115 ASP Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 56 ASP Chi-restraints excluded: chain Z residue 90 PHE Chi-restraints excluded: chain Z residue 115 ASP Chi-restraints excluded: chain Z residue 133 GLU Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 14 THR Chi-restraints excluded: chain m residue 40 THR Chi-restraints excluded: chain m residue 52 SER Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 ARG Chi-restraints excluded: chain m residue 90 PHE Chi-restraints excluded: chain m residue 115 ASP Chi-restraints excluded: chain m residue 133 GLU Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain n residue 56 ASP Chi-restraints excluded: chain n residue 90 PHE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain o residue 21 ILE Chi-restraints excluded: chain o residue 56 ASP Chi-restraints excluded: chain o residue 90 PHE Chi-restraints excluded: chain o residue 115 ASP Chi-restraints excluded: chain o residue 133 GLU Chi-restraints excluded: chain p residue 12 THR Chi-restraints excluded: chain p residue 14 THR Chi-restraints excluded: chain p residue 21 ILE Chi-restraints excluded: chain p residue 32 THR Chi-restraints excluded: chain p residue 33 SER Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 90 PHE Chi-restraints excluded: chain p residue 115 ASP Chi-restraints excluded: chain p residue 133 GLU Chi-restraints excluded: chain q residue 12 THR Chi-restraints excluded: chain q residue 18 ARG Chi-restraints excluded: chain q residue 21 ILE Chi-restraints excluded: chain q residue 24 MET Chi-restraints excluded: chain q residue 90 PHE Chi-restraints excluded: chain q residue 93 ASP Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 21 ILE Chi-restraints excluded: chain r residue 40 THR Chi-restraints excluded: chain r residue 90 PHE Chi-restraints excluded: chain r residue 93 ASP Chi-restraints excluded: chain r residue 101 GLU Chi-restraints excluded: chain r residue 110 ILE Chi-restraints excluded: chain r residue 115 ASP Chi-restraints excluded: chain s residue 8 MET Chi-restraints excluded: chain s residue 21 ILE Chi-restraints excluded: chain s residue 40 THR Chi-restraints excluded: chain s residue 56 ASP Chi-restraints excluded: chain s residue 95 ILE Chi-restraints excluded: chain s residue 115 ASP Chi-restraints excluded: chain t residue 21 ILE Chi-restraints excluded: chain t residue 24 MET Chi-restraints excluded: chain t residue 90 PHE Chi-restraints excluded: chain t residue 93 ASP Chi-restraints excluded: chain t residue 95 ILE Chi-restraints excluded: chain t residue 111 GLN Chi-restraints excluded: chain u residue 21 ILE Chi-restraints excluded: chain u residue 40 THR Chi-restraints excluded: chain u residue 56 ASP Chi-restraints excluded: chain u residue 86 ARG Chi-restraints excluded: chain u residue 90 PHE Chi-restraints excluded: chain u residue 93 ASP Chi-restraints excluded: chain u residue 101 GLU Chi-restraints excluded: chain u residue 110 ILE Chi-restraints excluded: chain u residue 111 GLN Chi-restraints excluded: chain v residue 8 MET Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 21 ILE Chi-restraints excluded: chain v residue 56 ASP Chi-restraints excluded: chain v residue 97 SER Chi-restraints excluded: chain v residue 115 ASP Chi-restraints excluded: chain w residue 32 THR Chi-restraints excluded: chain w residue 56 ASP Chi-restraints excluded: chain w residue 61 VAL Chi-restraints excluded: chain w residue 90 PHE Chi-restraints excluded: chain x residue 21 ILE Chi-restraints excluded: chain x residue 56 ASP Chi-restraints excluded: chain x residue 90 PHE Chi-restraints excluded: chain x residue 93 ASP Chi-restraints excluded: chain x residue 104 THR Chi-restraints excluded: chain x residue 115 ASP Chi-restraints excluded: chain y residue 21 ILE Chi-restraints excluded: chain y residue 56 ASP Chi-restraints excluded: chain y residue 61 VAL Chi-restraints excluded: chain y residue 90 PHE Chi-restraints excluded: chain y residue 104 THR Chi-restraints excluded: chain y residue 111 GLN Chi-restraints excluded: chain y residue 115 ASP Chi-restraints excluded: chain z residue 21 ILE Chi-restraints excluded: chain z residue 32 THR Chi-restraints excluded: chain z residue 56 ASP Chi-restraints excluded: chain z residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 446 optimal weight: 8.9990 chunk 598 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 517 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 562 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 577 optimal weight: 8.9990 chunk 71 optimal weight: 0.0470 chunk 103 optimal weight: 5.9990 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN 2 121 ASN ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 294 ASN S 239 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN X 168 HIS Y 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.188486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.176493 restraints weight = 57169.105| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 0.49 r_work: 0.3747 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.309 55668 Z= 0.284 Angle : 0.699 65.885 75798 Z= 0.380 Chirality : 0.045 0.239 8778 Planarity : 0.006 0.297 9822 Dihedral : 7.726 59.846 7851 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 6.00 % Allowed : 27.30 % Favored : 66.70 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 7080 helix: 0.87 (0.14), residues: 1500 sheet: 0.00 (0.13), residues: 1488 loop : -2.31 (0.09), residues: 4092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 127 HIS 0.022 0.001 HIS O 155 PHE 0.029 0.002 PHE q 90 TYR 0.016 0.002 TYR S 67 ARG 0.018 0.000 ARG U 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23377.28 seconds wall clock time: 403 minutes 58.58 seconds (24238.58 seconds total)