Starting phenix.real_space_refine (version: dev) on Wed Feb 22 08:02:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2023/8hdw_34681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2023/8hdw_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_2023/8hdw_34681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2023/8hdw_34681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2023/8hdw_34681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdw_34681/02_2023/8hdw_34681.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 21.99, per 1000 atoms: 0.40 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: 15.75 Conformation dependent library (CDL) restraints added in 5.9 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: 2.30 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: 16.68 Time building geometry restraints manager: 17.40 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 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. 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: 1.600 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: 0.030 Extract box with map and model: 9.330 Check model and map are aligned: 0.590 Process input model: 100.170 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Set scattering table: 0.360 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 % 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 *********************** 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 : 4.699 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: symmetry clash revert: symmetry clash outliers start: 645 outliers final: 260 residues processed: 1728 average time/residue: 1.1966 time to fit residues: 2679.7271 Evaluate side-chains 1113 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 853 time to evaluate : 4.549 Switching outliers to nearest non-outliers outliers start: 260 outliers final: 218 residues processed: 42 average time/residue: 0.8515 time to fit residues: 56.7867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 297 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 361 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 chunk 554 optimal weight: 20.0000 chunk 214 optimal weight: 0.7980 chunk 337 optimal weight: 0.0070 chunk 413 optimal weight: 9.9990 chunk 642 optimal weight: 9.9990 overall best weight: 3.3604 ------------------------------------------------------------------------------- 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 2 100 ASN 2 121 ASN ** M 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 307 GLN N 364 GLN O 307 GLN O 364 GLN P 295 ASN ** Q 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 GLN S 76 GLN T 40 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN U 317 GLN V 40 GLN W 40 GLN X 40 GLN X 76 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: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 55668 Z= 0.219 Angle : 0.660 8.703 75798 Z= 0.357 Chirality : 0.047 0.203 8778 Planarity : 0.005 0.045 9822 Dihedral : 5.876 25.001 7680 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 9.87 % 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: -2.08 (0.09), residues: 7080 helix: -0.08 (0.14), residues: 1476 sheet: -0.11 (0.13), residues: 1446 loop : -2.49 (0.09), residues: 4158 *********************** 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 1532 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 569 poor density : 963 time to evaluate : 4.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 569 outliers final: 283 residues processed: 1355 average time/residue: 1.0540 time to fit residues: 1914.0823 Evaluate side-chains 1128 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 845 time to evaluate : 4.586 Switching outliers to nearest non-outliers outliers start: 283 outliers final: 222 residues processed: 62 average time/residue: 0.5191 time to fit residues: 60.3957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 357 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 535 optimal weight: 9.9990 chunk 437 optimal weight: 9.9990 chunk 177 optimal weight: 0.0270 chunk 644 optimal weight: 5.9990 chunk 695 optimal weight: 9.9990 chunk 573 optimal weight: 9.9990 chunk 638 optimal weight: 7.9990 chunk 219 optimal weight: 20.0000 chunk 516 optimal weight: 10.0000 overall best weight: 5.8046 ------------------------------------------------------------------------------- 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 63 ASN N 295 ASN N 307 GLN O 295 ASN O 307 GLN P 29 GLN P 364 GLN R 119 GLN T 76 GLN T 119 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 119 GLN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 63 ASN W 76 GLN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** X 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 374 HIS Y 100 ASN r 120 ASN u 120 ASN v 121 ASN w 121 ASN x 121 ASN z 100 ASN z 121 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 55668 Z= 0.321 Angle : 0.730 8.462 75798 Z= 0.393 Chirality : 0.049 0.246 8778 Planarity : 0.006 0.050 9822 Dihedral : 6.323 28.302 7680 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.05 % Favored : 88.91 % Rotamer Outliers : 9.49 % 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: 0.06 (0.14), residues: 1452 sheet: 0.29 (0.13), residues: 1212 loop : -2.54 (0.08), residues: 4416 *********************** 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 1441 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 547 poor density : 894 time to evaluate : 4.664 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 outliers start: 547 outliers final: 329 residues processed: 1282 average time/residue: 1.1003 time to fit residues: 1874.6037 Evaluate side-chains 1165 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 836 time to evaluate : 4.580 Switching outliers to nearest non-outliers outliers start: 329 outliers final: 261 residues processed: 68 average time/residue: 0.5208 time to fit residues: 65.6381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 9.9990 chunk 484 optimal weight: 0.4980 chunk 334 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 chunk 307 optimal weight: 9.9990 chunk 432 optimal weight: 5.9990 chunk 646 optimal weight: 4.9990 chunk 684 optimal weight: 0.9980 chunk 337 optimal weight: 0.4980 chunk 612 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 121 ASN M 119 GLN ** N 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 ASN R 119 GLN S 119 GLN ** S 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 317 GLN ** U 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 317 GLN V 76 GLN ** V 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN ** 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** Y 100 ASN m 121 ASN n 100 ASN r 120 ASN u 120 ASN v 121 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 55668 Z= 0.148 Angle : 0.582 7.416 75798 Z= 0.311 Chirality : 0.043 0.189 8778 Planarity : 0.004 0.048 9822 Dihedral : 5.223 22.471 7680 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer Outliers : 7.72 % 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: -1.70 (0.09), residues: 7080 helix: 0.84 (0.14), residues: 1476 sheet: -0.10 (0.13), residues: 1278 loop : -2.32 (0.08), residues: 4326 *********************** 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 1341 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 445 poor density : 896 time to evaluate : 4.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 445 outliers final: 276 residues processed: 1250 average time/residue: 1.1023 time to fit residues: 1827.2975 Evaluate side-chains 1099 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 823 time to evaluate : 4.556 Switching outliers to nearest non-outliers outliers start: 276 outliers final: 233 residues processed: 45 average time/residue: 0.4516 time to fit residues: 42.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 9.9990 chunk 388 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 509 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 583 optimal weight: 7.9990 chunk 473 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 614 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 63 ASN M 119 GLN O 239 GLN P 29 GLN P 180 HIS Q 29 GLN Q 239 GLN R 239 GLN S 119 GLN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 168 HIS ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 239 GLN ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** X 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 GLN Y 100 ASN n 100 ASN v 121 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 55668 Z= 0.249 Angle : 0.658 8.103 75798 Z= 0.350 Chirality : 0.046 0.219 8778 Planarity : 0.005 0.044 9822 Dihedral : 5.678 23.761 7680 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer Outliers : 7.91 % 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: -1.66 (0.10), residues: 7080 helix: 0.88 (0.14), residues: 1440 sheet: -0.07 (0.13), residues: 1422 loop : -2.34 (0.09), residues: 4218 *********************** 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 1300 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 456 poor density : 844 time to evaluate : 4.597 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 outliers start: 456 outliers final: 321 residues processed: 1188 average time/residue: 1.1033 time to fit residues: 1739.2756 Evaluate side-chains 1152 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 831 time to evaluate : 4.577 Switching outliers to nearest non-outliers outliers start: 321 outliers final: 255 residues processed: 68 average time/residue: 0.5631 time to fit residues: 69.0030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 230 optimal weight: 6.9990 chunk 616 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 401 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 685 optimal weight: 9.9990 chunk 568 optimal weight: 20.0000 chunk 317 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 226 optimal weight: 30.0000 chunk 359 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** M 239 GLN P 294 ASN Q 119 GLN ** S 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 168 HIS ** W 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 HIS X 63 ASN X 119 GLN Y 100 ASN n 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 55668 Z= 0.410 Angle : 0.808 11.268 75798 Z= 0.433 Chirality : 0.052 0.261 8778 Planarity : 0.007 0.071 9822 Dihedral : 6.629 29.743 7680 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.12 % Favored : 88.69 % Rotamer Outliers : 8.88 % 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: -1.98 (0.09), residues: 7080 helix: 0.35 (0.14), residues: 1440 sheet: -0.14 (0.13), residues: 1350 loop : -2.45 (0.08), residues: 4290 *********************** 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 1379 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 512 poor density : 867 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 512 outliers final: 353 residues processed: 1245 average time/residue: 1.1266 time to fit residues: 1856.3140 Evaluate side-chains 1197 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 844 time to evaluate : 4.611 Switching outliers to nearest non-outliers outliers start: 353 outliers final: 273 residues processed: 80 average time/residue: 0.5615 time to fit residues: 79.5268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 660 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 390 optimal weight: 4.9990 chunk 500 optimal weight: 10.0000 chunk 387 optimal weight: 9.9990 chunk 576 optimal weight: 4.9990 chunk 382 optimal weight: 10.0000 chunk 682 optimal weight: 5.9990 chunk 427 optimal weight: 9.9990 chunk 416 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 ASN Q 294 ASN S 168 HIS T 77 ASN ** T 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 63 ASN ** X 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 100 ASN n 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 55668 Z= 0.277 Angle : 0.698 10.854 75798 Z= 0.372 Chirality : 0.047 0.258 8778 Planarity : 0.006 0.061 9822 Dihedral : 6.089 25.217 7680 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer Outliers : 7.60 % 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: -1.87 (0.09), residues: 7080 helix: 0.45 (0.14), residues: 1476 sheet: -0.11 (0.13), residues: 1422 loop : -2.44 (0.09), residues: 4182 *********************** 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 1296 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 438 poor density : 858 time to evaluate : 4.621 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 outliers start: 438 outliers final: 338 residues processed: 1197 average time/residue: 1.1187 time to fit residues: 1770.3261 Evaluate side-chains 1181 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 843 time to evaluate : 5.624 Switching outliers to nearest non-outliers outliers start: 338 outliers final: 277 residues processed: 64 average time/residue: 0.5073 time to fit residues: 63.1459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 422 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 407 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 433 optimal weight: 9.9990 chunk 464 optimal weight: 5.9990 chunk 337 optimal weight: 5.9990 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 ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 330 ASN P 294 ASN Q 294 ASN R 29 GLN T 77 ASN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 GLN U 63 ASN V 40 GLN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 GLN ** W 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN ** X 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 100 ASN n 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 55668 Z= 0.304 Angle : 0.725 8.979 75798 Z= 0.386 Chirality : 0.048 0.263 8778 Planarity : 0.006 0.059 9822 Dihedral : 6.188 25.462 7680 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 11.24 % Favored : 88.74 % Rotamer Outliers : 7.46 % 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: -1.90 (0.09), residues: 7080 helix: 0.43 (0.14), residues: 1476 sheet: -0.15 (0.13), residues: 1422 loop : -2.44 (0.09), residues: 4182 *********************** 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 1271 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 430 poor density : 841 time to evaluate : 4.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 430 outliers final: 342 residues processed: 1176 average time/residue: 1.1256 time to fit residues: 1754.8136 Evaluate side-chains 1171 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 829 time to evaluate : 4.610 Switching outliers to nearest non-outliers outliers start: 342 outliers final: 285 residues processed: 57 average time/residue: 0.5866 time to fit residues: 60.3288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 620 optimal weight: 5.9990 chunk 653 optimal weight: 0.8980 chunk 596 optimal weight: 9.9990 chunk 635 optimal weight: 8.9990 chunk 382 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 499 optimal weight: 0.0980 chunk 195 optimal weight: 30.0000 chunk 574 optimal weight: 9.9990 chunk 601 optimal weight: 8.9990 chunk 633 optimal weight: 0.7980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 256 GLN Q 294 ASN ** S 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 77 ASN ** 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** ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN X 168 HIS X 239 GLN Y 100 ASN n 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 55668 Z= 0.171 Angle : 0.616 10.438 75798 Z= 0.327 Chirality : 0.044 0.226 8778 Planarity : 0.005 0.055 9822 Dihedral : 5.373 22.771 7680 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 6.24 % 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: -1.64 (0.10), residues: 7080 helix: 0.91 (0.14), residues: 1476 sheet: -0.10 (0.13), residues: 1446 loop : -2.35 (0.09), residues: 4158 *********************** 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 1203 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 843 time to evaluate : 4.664 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 outliers start: 360 outliers final: 294 residues processed: 1148 average time/residue: 1.1398 time to fit residues: 1728.8621 Evaluate side-chains 1101 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 807 time to evaluate : 4.544 Switching outliers to nearest non-outliers outliers start: 294 outliers final: 256 residues processed: 40 average time/residue: 0.5824 time to fit residues: 44.0325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 417 optimal weight: 50.0000 chunk 672 optimal weight: 0.0270 chunk 410 optimal weight: 20.0000 chunk 318 optimal weight: 7.9990 chunk 467 optimal weight: 9.9990 chunk 705 optimal weight: 8.9990 chunk 649 optimal weight: 1.9990 chunk 561 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 433 optimal weight: 0.2980 chunk 344 optimal weight: 30.0000 overall best weight: 2.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 294 ASN Q 294 ASN S 239 GLN T 77 ASN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 63 ASN Y 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 55668 Z= 0.191 Angle : 0.631 10.740 75798 Z= 0.333 Chirality : 0.044 0.219 8778 Planarity : 0.005 0.054 9822 Dihedral : 5.363 22.557 7680 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer Outliers : 5.43 % 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: -1.59 (0.10), residues: 7080 helix: 0.99 (0.14), residues: 1476 sheet: -0.11 (0.13), residues: 1374 loop : -2.28 (0.09), residues: 4230 ********************** 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 1131 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 818 time to evaluate : 5.775 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 outliers start: 313 outliers final: 285 residues processed: 1090 average time/residue: 1.1780 time to fit residues: 1701.9201 Evaluate side-chains 1092 residues out of total 5766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 807 time to evaluate : 4.584 Switching outliers to nearest non-outliers outliers start: 285 outliers final: 256 residues processed: 30 average time/residue: 0.5854 time to fit residues: 35.2584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 172 optimal weight: 10.0000 chunk 517 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 562 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 577 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 121 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 180 HIS P 294 ASN Q 294 ASN S 239 GLN T 77 ASN ** T 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** V 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 40 GLN X 63 ASN X 119 GLN Y 100 ASN w 121 ASN x 121 ASN z 121 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.185512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.171942 restraints weight = 57333.157| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 0.57 r_work: 0.3680 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4514 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= 0.260 Angle : 0.686 10.787 75798 Z= 0.363 Chirality : 0.047 0.233 8778 Planarity : 0.005 0.066 9822 Dihedral : 5.777 23.644 7680 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer Outliers : 5.71 % 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: -1.64 (0.10), residues: 7080 helix: 0.80 (0.14), residues: 1476 sheet: -0.05 (0.13), residues: 1422 loop : -2.32 (0.09), residues: 4182 =============================================================================== Job complete usr+sys time: 23496.35 seconds wall clock time: 405 minutes 49.56 seconds (24349.56 seconds total)