Starting phenix.real_space_refine (version: dev) on Fri May 13 22:14:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/05_2022/6oif_20076_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/05_2022/6oif_20076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/05_2022/6oif_20076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/05_2022/6oif_20076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/05_2022/6oif_20076_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/05_2022/6oif_20076_neut_trim_updated.pdb" } resolution = 4.4 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= 0.028 sd= 0.092 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 115025 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "B" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "C" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "D" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "E" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "F" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "G" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "H" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "I" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "J" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "K" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "L" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "M" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "N" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "O" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "P" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "Q" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "R" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "S" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "T" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "U" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "V" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "W" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "X" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "Y" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 273, 'PCIS': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 37.55, per 1000 atoms: 0.33 Number of scatterers: 115025 At special positions: 0 Unit cell: (160.153, 158.984, 202.237, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 225 16.00 P 75 15.00 O 10850 8.00 N 9750 7.00 C 37375 6.00 H 56750 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 319 " distance=2.02 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 319 " distance=2.02 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 319 " distance=2.02 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 319 " distance=2.02 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 319 " distance=2.02 Simple disulfide: pdb=" SG CYS F 280 " - pdb=" SG CYS F 319 " distance=2.02 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 319 " distance=2.02 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 319 " distance=2.02 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 319 " distance=2.02 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 319 " distance=2.02 Simple disulfide: pdb=" SG CYS K 280 " - pdb=" SG CYS K 319 " distance=2.02 Simple disulfide: pdb=" SG CYS L 280 " - pdb=" SG CYS L 319 " distance=2.02 Simple disulfide: pdb=" SG CYS M 280 " - pdb=" SG CYS M 319 " distance=2.02 Simple disulfide: pdb=" SG CYS N 280 " - pdb=" SG CYS N 319 " distance=2.02 Simple disulfide: pdb=" SG CYS O 280 " - pdb=" SG CYS O 319 " distance=2.02 Simple disulfide: pdb=" SG CYS P 280 " - pdb=" SG CYS P 319 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 280 " - pdb=" SG CYS Q 319 " distance=2.02 Simple disulfide: pdb=" SG CYS R 280 " - pdb=" SG CYS R 319 " distance=2.02 Simple disulfide: pdb=" SG CYS S 280 " - pdb=" SG CYS S 319 " distance=2.02 Simple disulfide: pdb=" SG CYS T 280 " - pdb=" SG CYS T 319 " distance=2.02 Simple disulfide: pdb=" SG CYS U 280 " - pdb=" SG CYS U 319 " distance=2.02 Simple disulfide: pdb=" SG CYS V 280 " - pdb=" SG CYS V 319 " distance=2.02 Simple disulfide: pdb=" SG CYS W 280 " - pdb=" SG CYS W 319 " distance=2.02 Simple disulfide: pdb=" SG CYS X 280 " - pdb=" SG CYS X 319 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 280 " - pdb=" SG CYS Y 319 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 47920 OH TYR K 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 38780 OH TYR I 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 61630 OH TYR N 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 29640 OH TYR G 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 84480 OH TYR S 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 93620 OH TYR U 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 2220 OH TYR A 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 98190 OH TYR V 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 66200 OH TYR O 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 70770 OH TYR P 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 57060 OH TYR M 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 43350 OH TYR J 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 79910 OH TYR R 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 6790 OH TYR B 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM A024O OH TYR W 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 34210 OH TYR H 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 75340 OH TYR Q 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 11360 OH TYR C 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 15930 OH TYR D 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 20500 OH TYR E 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 89050 OH TYR T 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 52490 OH TYR L 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM 25070 OH TYR F 189 .*. O " rejected from bonding due to valence issues. Atom "ATOM A05NM OH TYR X 189 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 68.51 Conformation dependent library (CDL) restraints added in 6.6 seconds 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13300 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 300 helices and 50 sheets defined 59.6% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.48 Creating SS restraints... Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 5.841A pdb=" N TYR A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY A 225 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.676A pdb=" N LEU B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 5.841A pdb=" N TYR B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY B 225 " --> pdb=" O PHE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE B 323 " --> pdb=" O CYS B 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN C 88 " --> pdb=" O PHE C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE C 180 " --> pdb=" O HIS C 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 5.841A pdb=" N TYR C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY C 225 " --> pdb=" O PHE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 246 Processing helix chain 'C' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 303 removed outlier: 3.835A pdb=" N VAL C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE C 323 " --> pdb=" O CYS C 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN D 88 " --> pdb=" O PHE D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE D 180 " --> pdb=" O HIS D 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) Proline residue: D 185 - end of helix removed outlier: 5.841A pdb=" N TYR D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY D 225 " --> pdb=" O PHE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 246 Processing helix chain 'D' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA D 301 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE D 323 " --> pdb=" O CYS D 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 69 removed outlier: 3.676A pdb=" N LEU E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 143 through 163 removed outlier: 3.513A pdb=" N ALA E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE E 180 " --> pdb=" O HIS E 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Proline residue: E 185 - end of helix removed outlier: 5.842A pdb=" N TYR E 189 " --> pdb=" O PRO E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE E 214 " --> pdb=" O GLY E 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY E 225 " --> pdb=" O PHE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 246 Processing helix chain 'E' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 303 removed outlier: 3.835A pdb=" N VAL E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA E 301 " --> pdb=" O VAL E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE E 323 " --> pdb=" O CYS E 319 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 69 removed outlier: 3.676A pdb=" N LEU F 61 " --> pdb=" O SER F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN F 88 " --> pdb=" O PHE F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 189 removed outlier: 4.233A pdb=" N ILE F 180 " --> pdb=" O HIS F 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 182 " --> pdb=" O GLY F 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE F 183 " --> pdb=" O LEU F 179 " (cutoff:3.500A) Proline residue: F 185 - end of helix removed outlier: 5.841A pdb=" N TYR F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE F 214 " --> pdb=" O GLY F 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS F 232 " --> pdb=" O ARG F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 246 Processing helix chain 'F' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS F 254 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA F 301 " --> pdb=" O VAL F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE F 323 " --> pdb=" O CYS F 319 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N THR F 324 " --> pdb=" O LYS F 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 removed outlier: 3.674A pdb=" N LEU G 61 " --> pdb=" O SER G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN G 88 " --> pdb=" O PHE G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 Processing helix chain 'G' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA G 163 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 189 removed outlier: 4.233A pdb=" N ILE G 180 " --> pdb=" O HIS G 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 182 " --> pdb=" O GLY G 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Proline residue: G 185 - end of helix removed outlier: 5.841A pdb=" N TYR G 189 " --> pdb=" O PRO G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 225 removed outlier: 3.762A pdb=" N ILE G 214 " --> pdb=" O GLY G 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY G 225 " --> pdb=" O PHE G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 246 Processing helix chain 'G' and resid 248 through 259 removed outlier: 3.680A pdb=" N HIS G 254 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 289 removed outlier: 4.203A pdb=" N GLU G 284 " --> pdb=" O CYS G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL G 297 " --> pdb=" O ASP G 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA G 301 " --> pdb=" O VAL G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL G 322 " --> pdb=" O GLY G 318 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE G 323 " --> pdb=" O CYS G 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR G 324 " --> pdb=" O LYS G 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN H 88 " --> pdb=" O PHE H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 120 Processing helix chain 'H' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA H 163 " --> pdb=" O VAL H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE H 180 " --> pdb=" O HIS H 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA H 182 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE H 183 " --> pdb=" O LEU H 179 " (cutoff:3.500A) Proline residue: H 185 - end of helix removed outlier: 5.841A pdb=" N TYR H 189 " --> pdb=" O PRO H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE H 214 " --> pdb=" O GLY H 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY H 225 " --> pdb=" O PHE H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS H 232 " --> pdb=" O ARG H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 246 Processing helix chain 'H' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS H 254 " --> pdb=" O SER H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 289 removed outlier: 4.203A pdb=" N GLU H 284 " --> pdb=" O CYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL H 297 " --> pdb=" O ASP H 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA H 301 " --> pdb=" O VAL H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL H 322 " --> pdb=" O GLY H 318 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE H 323 " --> pdb=" O CYS H 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR H 324 " --> pdb=" O LYS H 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU I 61 " --> pdb=" O SER I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN I 88 " --> pdb=" O PHE I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 120 Processing helix chain 'I' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA I 163 " --> pdb=" O VAL I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE I 180 " --> pdb=" O HIS I 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA I 182 " --> pdb=" O GLY I 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE I 183 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Proline residue: I 185 - end of helix removed outlier: 5.841A pdb=" N TYR I 189 " --> pdb=" O PRO I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE I 214 " --> pdb=" O GLY I 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY I 225 " --> pdb=" O PHE I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS I 232 " --> pdb=" O ARG I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 246 Processing helix chain 'I' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS I 254 " --> pdb=" O SER I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU I 284 " --> pdb=" O CYS I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL I 297 " --> pdb=" O ASP I 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA I 301 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL I 322 " --> pdb=" O GLY I 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE I 323 " --> pdb=" O CYS I 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR I 324 " --> pdb=" O LYS I 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 69 removed outlier: 3.674A pdb=" N LEU J 61 " --> pdb=" O SER J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN J 88 " --> pdb=" O PHE J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 120 Processing helix chain 'J' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA J 163 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE J 180 " --> pdb=" O HIS J 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA J 182 " --> pdb=" O GLY J 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE J 183 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Proline residue: J 185 - end of helix removed outlier: 5.841A pdb=" N TYR J 189 " --> pdb=" O PRO J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE J 214 " --> pdb=" O GLY J 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY J 225 " --> pdb=" O PHE J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS J 232 " --> pdb=" O ARG J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 246 Processing helix chain 'J' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS J 254 " --> pdb=" O SER J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU J 284 " --> pdb=" O CYS J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL J 297 " --> pdb=" O ASP J 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA J 301 " --> pdb=" O VAL J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL J 322 " --> pdb=" O GLY J 318 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE J 323 " --> pdb=" O CYS J 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR J 324 " --> pdb=" O LYS J 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN K 88 " --> pdb=" O PHE K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 120 Processing helix chain 'K' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA K 163 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE K 180 " --> pdb=" O HIS K 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA K 182 " --> pdb=" O GLY K 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE K 183 " --> pdb=" O LEU K 179 " (cutoff:3.500A) Proline residue: K 185 - end of helix removed outlier: 5.841A pdb=" N TYR K 189 " --> pdb=" O PRO K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 225 removed outlier: 3.762A pdb=" N ILE K 214 " --> pdb=" O GLY K 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY K 225 " --> pdb=" O PHE K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS K 232 " --> pdb=" O ARG K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 246 Processing helix chain 'K' and resid 248 through 259 removed outlier: 3.680A pdb=" N HIS K 254 " --> pdb=" O SER K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 289 removed outlier: 4.205A pdb=" N GLU K 284 " --> pdb=" O CYS K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL K 297 " --> pdb=" O ASP K 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA K 301 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL K 322 " --> pdb=" O GLY K 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE K 323 " --> pdb=" O CYS K 319 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N THR K 324 " --> pdb=" O LYS K 320 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN L 88 " --> pdb=" O PHE L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 120 Processing helix chain 'L' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA L 163 " --> pdb=" O VAL L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE L 180 " --> pdb=" O HIS L 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE L 183 " --> pdb=" O LEU L 179 " (cutoff:3.500A) Proline residue: L 185 - end of helix removed outlier: 5.841A pdb=" N TYR L 189 " --> pdb=" O PRO L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 225 removed outlier: 3.762A pdb=" N ILE L 214 " --> pdb=" O GLY L 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY L 225 " --> pdb=" O PHE L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS L 232 " --> pdb=" O ARG L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 236 through 246 Processing helix chain 'L' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS L 254 " --> pdb=" O SER L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 289 removed outlier: 4.203A pdb=" N GLU L 284 " --> pdb=" O CYS L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL L 297 " --> pdb=" O ASP L 293 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA L 301 " --> pdb=" O VAL L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL L 322 " --> pdb=" O GLY L 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE L 323 " --> pdb=" O CYS L 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR L 324 " --> pdb=" O LYS L 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU M 61 " --> pdb=" O SER M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN M 88 " --> pdb=" O PHE M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 120 Processing helix chain 'M' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE M 180 " --> pdb=" O HIS M 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA M 182 " --> pdb=" O GLY M 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE M 183 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Proline residue: M 185 - end of helix removed outlier: 5.841A pdb=" N TYR M 189 " --> pdb=" O PRO M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE M 214 " --> pdb=" O GLY M 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY M 225 " --> pdb=" O PHE M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 232 removed outlier: 4.794A pdb=" N LYS M 232 " --> pdb=" O ARG M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 246 Processing helix chain 'M' and resid 248 through 259 removed outlier: 3.680A pdb=" N HIS M 254 " --> pdb=" O SER M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 289 removed outlier: 4.203A pdb=" N GLU M 284 " --> pdb=" O CYS M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL M 297 " --> pdb=" O ASP M 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA M 301 " --> pdb=" O VAL M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL M 322 " --> pdb=" O GLY M 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE M 323 " --> pdb=" O CYS M 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR M 324 " --> pdb=" O LYS M 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU N 61 " --> pdb=" O SER N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 89 removed outlier: 3.813A pdb=" N ASN N 88 " --> pdb=" O PHE N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 120 Processing helix chain 'N' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA N 163 " --> pdb=" O VAL N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE N 180 " --> pdb=" O HIS N 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA N 182 " --> pdb=" O GLY N 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE N 183 " --> pdb=" O LEU N 179 " (cutoff:3.500A) Proline residue: N 185 - end of helix removed outlier: 5.841A pdb=" N TYR N 189 " --> pdb=" O PRO N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE N 214 " --> pdb=" O GLY N 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY N 225 " --> pdb=" O PHE N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 232 removed outlier: 4.794A pdb=" N LYS N 232 " --> pdb=" O ARG N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 246 Processing helix chain 'N' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS N 254 " --> pdb=" O SER N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU N 284 " --> pdb=" O CYS N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL N 297 " --> pdb=" O ASP N 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA N 301 " --> pdb=" O VAL N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL N 322 " --> pdb=" O GLY N 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE N 323 " --> pdb=" O CYS N 319 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR N 324 " --> pdb=" O LYS N 320 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU O 61 " --> pdb=" O SER O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN O 88 " --> pdb=" O PHE O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 120 Processing helix chain 'O' and resid 143 through 163 removed outlier: 3.513A pdb=" N ALA O 163 " --> pdb=" O VAL O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE O 180 " --> pdb=" O HIS O 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA O 182 " --> pdb=" O GLY O 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE O 183 " --> pdb=" O LEU O 179 " (cutoff:3.500A) Proline residue: O 185 - end of helix removed outlier: 5.841A pdb=" N TYR O 189 " --> pdb=" O PRO O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.762A pdb=" N ILE O 214 " --> pdb=" O GLY O 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY O 225 " --> pdb=" O PHE O 221 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 232 removed outlier: 4.794A pdb=" N LYS O 232 " --> pdb=" O ARG O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 236 through 246 Processing helix chain 'O' and resid 248 through 259 removed outlier: 3.680A pdb=" N HIS O 254 " --> pdb=" O SER O 250 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU O 284 " --> pdb=" O CYS O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL O 297 " --> pdb=" O ASP O 293 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA O 301 " --> pdb=" O VAL O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL O 322 " --> pdb=" O GLY O 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE O 323 " --> pdb=" O CYS O 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR O 324 " --> pdb=" O LYS O 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU P 61 " --> pdb=" O SER P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN P 88 " --> pdb=" O PHE P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 120 Processing helix chain 'P' and resid 143 through 163 removed outlier: 3.513A pdb=" N ALA P 163 " --> pdb=" O VAL P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 189 removed outlier: 4.233A pdb=" N ILE P 180 " --> pdb=" O HIS P 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA P 182 " --> pdb=" O GLY P 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE P 183 " --> pdb=" O LEU P 179 " (cutoff:3.500A) Proline residue: P 185 - end of helix removed outlier: 5.842A pdb=" N TYR P 189 " --> pdb=" O PRO P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 225 removed outlier: 3.762A pdb=" N ILE P 214 " --> pdb=" O GLY P 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY P 225 " --> pdb=" O PHE P 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 232 removed outlier: 4.794A pdb=" N LYS P 232 " --> pdb=" O ARG P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 246 Processing helix chain 'P' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS P 254 " --> pdb=" O SER P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU P 284 " --> pdb=" O CYS P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL P 297 " --> pdb=" O ASP P 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA P 301 " --> pdb=" O VAL P 297 " (cutoff:3.500A) Processing helix chain 'P' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL P 322 " --> pdb=" O GLY P 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE P 323 " --> pdb=" O CYS P 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR P 324 " --> pdb=" O LYS P 320 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU Q 61 " --> pdb=" O SER Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN Q 88 " --> pdb=" O PHE Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 120 Processing helix chain 'Q' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA Q 163 " --> pdb=" O VAL Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE Q 180 " --> pdb=" O HIS Q 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA Q 182 " --> pdb=" O GLY Q 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE Q 183 " --> pdb=" O LEU Q 179 " (cutoff:3.500A) Proline residue: Q 185 - end of helix removed outlier: 5.841A pdb=" N TYR Q 189 " --> pdb=" O PRO Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 225 removed outlier: 3.762A pdb=" N ILE Q 214 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY Q 225 " --> pdb=" O PHE Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS Q 232 " --> pdb=" O ARG Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 236 through 246 Processing helix chain 'Q' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS Q 254 " --> pdb=" O SER Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU Q 284 " --> pdb=" O CYS Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL Q 297 " --> pdb=" O ASP Q 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA Q 301 " --> pdb=" O VAL Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL Q 322 " --> pdb=" O GLY Q 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE Q 323 " --> pdb=" O CYS Q 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR Q 324 " --> pdb=" O LYS Q 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 69 removed outlier: 3.676A pdb=" N LEU R 61 " --> pdb=" O SER R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 89 removed outlier: 3.813A pdb=" N ASN R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 120 Processing helix chain 'R' and resid 143 through 163 removed outlier: 3.513A pdb=" N ALA R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE R 180 " --> pdb=" O HIS R 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE R 183 " --> pdb=" O LEU R 179 " (cutoff:3.500A) Proline residue: R 185 - end of helix removed outlier: 5.841A pdb=" N TYR R 189 " --> pdb=" O PRO R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 225 removed outlier: 3.762A pdb=" N ILE R 214 " --> pdb=" O GLY R 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY R 225 " --> pdb=" O PHE R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 246 Processing helix chain 'R' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS R 254 " --> pdb=" O SER R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU R 284 " --> pdb=" O CYS R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL R 297 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL R 322 " --> pdb=" O GLY R 318 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE R 323 " --> pdb=" O CYS R 319 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THR R 324 " --> pdb=" O LYS R 320 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU S 61 " --> pdb=" O SER S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN S 88 " --> pdb=" O PHE S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 120 Processing helix chain 'S' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA S 163 " --> pdb=" O VAL S 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE S 180 " --> pdb=" O HIS S 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA S 182 " --> pdb=" O GLY S 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE S 183 " --> pdb=" O LEU S 179 " (cutoff:3.500A) Proline residue: S 185 - end of helix removed outlier: 5.841A pdb=" N TYR S 189 " --> pdb=" O PRO S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 210 through 225 removed outlier: 3.762A pdb=" N ILE S 214 " --> pdb=" O GLY S 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY S 225 " --> pdb=" O PHE S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 232 removed outlier: 4.794A pdb=" N LYS S 232 " --> pdb=" O ARG S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 236 through 246 Processing helix chain 'S' and resid 248 through 259 removed outlier: 3.680A pdb=" N HIS S 254 " --> pdb=" O SER S 250 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU S 284 " --> pdb=" O CYS S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL S 297 " --> pdb=" O ASP S 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA S 301 " --> pdb=" O VAL S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL S 322 " --> pdb=" O GLY S 318 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N PHE S 323 " --> pdb=" O CYS S 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR S 324 " --> pdb=" O LYS S 320 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU T 61 " --> pdb=" O SER T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN T 88 " --> pdb=" O PHE T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 120 Processing helix chain 'T' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA T 163 " --> pdb=" O VAL T 159 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE T 180 " --> pdb=" O HIS T 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA T 182 " --> pdb=" O GLY T 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE T 183 " --> pdb=" O LEU T 179 " (cutoff:3.500A) Proline residue: T 185 - end of helix removed outlier: 5.841A pdb=" N TYR T 189 " --> pdb=" O PRO T 185 " (cutoff:3.500A) Processing helix chain 'T' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE T 214 " --> pdb=" O GLY T 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY T 225 " --> pdb=" O PHE T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 227 through 232 removed outlier: 4.794A pdb=" N LYS T 232 " --> pdb=" O ARG T 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 246 Processing helix chain 'T' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS T 254 " --> pdb=" O SER T 250 " (cutoff:3.500A) Processing helix chain 'T' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU T 284 " --> pdb=" O CYS T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL T 297 " --> pdb=" O ASP T 293 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA T 301 " --> pdb=" O VAL T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL T 322 " --> pdb=" O GLY T 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE T 323 " --> pdb=" O CYS T 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR T 324 " --> pdb=" O LYS T 320 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 69 removed outlier: 3.676A pdb=" N LEU U 61 " --> pdb=" O SER U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN U 88 " --> pdb=" O PHE U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 120 Processing helix chain 'U' and resid 143 through 163 removed outlier: 3.513A pdb=" N ALA U 163 " --> pdb=" O VAL U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE U 180 " --> pdb=" O HIS U 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA U 182 " --> pdb=" O GLY U 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE U 183 " --> pdb=" O LEU U 179 " (cutoff:3.500A) Proline residue: U 185 - end of helix removed outlier: 5.841A pdb=" N TYR U 189 " --> pdb=" O PRO U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE U 214 " --> pdb=" O GLY U 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY U 225 " --> pdb=" O PHE U 221 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 232 removed outlier: 4.794A pdb=" N LYS U 232 " --> pdb=" O ARG U 228 " (cutoff:3.500A) Processing helix chain 'U' and resid 236 through 246 Processing helix chain 'U' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS U 254 " --> pdb=" O SER U 250 " (cutoff:3.500A) Processing helix chain 'U' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU U 284 " --> pdb=" O CYS U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL U 297 " --> pdb=" O ASP U 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA U 301 " --> pdb=" O VAL U 297 " (cutoff:3.500A) Processing helix chain 'U' and resid 318 through 332 removed outlier: 4.309A pdb=" N VAL U 322 " --> pdb=" O GLY U 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE U 323 " --> pdb=" O CYS U 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR U 324 " --> pdb=" O LYS U 320 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU V 61 " --> pdb=" O SER V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN V 88 " --> pdb=" O PHE V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 120 Processing helix chain 'V' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA V 163 " --> pdb=" O VAL V 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE V 180 " --> pdb=" O HIS V 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA V 182 " --> pdb=" O GLY V 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE V 183 " --> pdb=" O LEU V 179 " (cutoff:3.500A) Proline residue: V 185 - end of helix removed outlier: 5.841A pdb=" N TYR V 189 " --> pdb=" O PRO V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE V 214 " --> pdb=" O GLY V 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY V 225 " --> pdb=" O PHE V 221 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 232 removed outlier: 4.794A pdb=" N LYS V 232 " --> pdb=" O ARG V 228 " (cutoff:3.500A) Processing helix chain 'V' and resid 236 through 246 Processing helix chain 'V' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS V 254 " --> pdb=" O SER V 250 " (cutoff:3.500A) Processing helix chain 'V' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU V 284 " --> pdb=" O CYS V 280 " (cutoff:3.500A) Processing helix chain 'V' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL V 297 " --> pdb=" O ASP V 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA V 301 " --> pdb=" O VAL V 297 " (cutoff:3.500A) Processing helix chain 'V' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL V 322 " --> pdb=" O GLY V 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE V 323 " --> pdb=" O CYS V 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR V 324 " --> pdb=" O LYS V 320 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU W 61 " --> pdb=" O SER W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN W 88 " --> pdb=" O PHE W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 120 Processing helix chain 'W' and resid 143 through 163 removed outlier: 3.514A pdb=" N ALA W 163 " --> pdb=" O VAL W 159 " (cutoff:3.500A) Processing helix chain 'W' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE W 180 " --> pdb=" O HIS W 176 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA W 182 " --> pdb=" O GLY W 178 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE W 183 " --> pdb=" O LEU W 179 " (cutoff:3.500A) Proline residue: W 185 - end of helix removed outlier: 5.841A pdb=" N TYR W 189 " --> pdb=" O PRO W 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE W 214 " --> pdb=" O GLY W 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY W 225 " --> pdb=" O PHE W 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS W 232 " --> pdb=" O ARG W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 236 through 246 Processing helix chain 'W' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS W 254 " --> pdb=" O SER W 250 " (cutoff:3.500A) Processing helix chain 'W' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU W 284 " --> pdb=" O CYS W 280 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL W 297 " --> pdb=" O ASP W 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA W 301 " --> pdb=" O VAL W 297 " (cutoff:3.500A) Processing helix chain 'W' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL W 322 " --> pdb=" O GLY W 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE W 323 " --> pdb=" O CYS W 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR W 324 " --> pdb=" O LYS W 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 69 removed outlier: 3.676A pdb=" N LEU X 61 " --> pdb=" O SER X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN X 88 " --> pdb=" O PHE X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 120 Processing helix chain 'X' and resid 143 through 163 removed outlier: 3.513A pdb=" N ALA X 163 " --> pdb=" O VAL X 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 189 removed outlier: 4.234A pdb=" N ILE X 180 " --> pdb=" O HIS X 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA X 182 " --> pdb=" O GLY X 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE X 183 " --> pdb=" O LEU X 179 " (cutoff:3.500A) Proline residue: X 185 - end of helix removed outlier: 5.841A pdb=" N TYR X 189 " --> pdb=" O PRO X 185 " (cutoff:3.500A) Processing helix chain 'X' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE X 214 " --> pdb=" O GLY X 210 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY X 225 " --> pdb=" O PHE X 221 " (cutoff:3.500A) Processing helix chain 'X' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS X 232 " --> pdb=" O ARG X 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 236 through 246 Processing helix chain 'X' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS X 254 " --> pdb=" O SER X 250 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU X 284 " --> pdb=" O CYS X 280 " (cutoff:3.500A) Processing helix chain 'X' and resid 293 through 303 removed outlier: 3.836A pdb=" N VAL X 297 " --> pdb=" O ASP X 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA X 301 " --> pdb=" O VAL X 297 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL X 322 " --> pdb=" O GLY X 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE X 323 " --> pdb=" O CYS X 319 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N THR X 324 " --> pdb=" O LYS X 320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 57 through 69 removed outlier: 3.675A pdb=" N LEU Y 61 " --> pdb=" O SER Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 89 removed outlier: 3.814A pdb=" N ASN Y 88 " --> pdb=" O PHE Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 120 Processing helix chain 'Y' and resid 143 through 163 removed outlier: 3.513A pdb=" N ALA Y 163 " --> pdb=" O VAL Y 159 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 189 removed outlier: 4.233A pdb=" N ILE Y 180 " --> pdb=" O HIS Y 176 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA Y 182 " --> pdb=" O GLY Y 178 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE Y 183 " --> pdb=" O LEU Y 179 " (cutoff:3.500A) Proline residue: Y 185 - end of helix removed outlier: 5.841A pdb=" N TYR Y 189 " --> pdb=" O PRO Y 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 210 through 225 removed outlier: 3.763A pdb=" N ILE Y 214 " --> pdb=" O GLY Y 210 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY Y 225 " --> pdb=" O PHE Y 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 227 through 232 removed outlier: 4.793A pdb=" N LYS Y 232 " --> pdb=" O ARG Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 236 through 246 Processing helix chain 'Y' and resid 248 through 259 removed outlier: 3.681A pdb=" N HIS Y 254 " --> pdb=" O SER Y 250 " (cutoff:3.500A) Processing helix chain 'Y' and resid 273 through 289 removed outlier: 4.204A pdb=" N GLU Y 284 " --> pdb=" O CYS Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 293 through 303 removed outlier: 3.835A pdb=" N VAL Y 297 " --> pdb=" O ASP Y 293 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA Y 301 " --> pdb=" O VAL Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 318 through 332 removed outlier: 4.308A pdb=" N VAL Y 322 " --> pdb=" O GLY Y 318 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N PHE Y 323 " --> pdb=" O CYS Y 319 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N THR Y 324 " --> pdb=" O LYS Y 320 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE A 166 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE A 168 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP A 170 " --> pdb=" O PHE A 132 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU A 100 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY A 102 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 265 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 267 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 101 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 269 " --> pdb=" O HIS A 101 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE B 166 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE B 168 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP B 170 " --> pdb=" O PHE B 132 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU B 100 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 102 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR B 265 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 267 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS B 101 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 269 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE C 166 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE C 168 " --> pdb=" O HIS C 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP C 170 " --> pdb=" O PHE C 132 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU C 100 " --> pdb=" O PHE C 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY C 102 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR C 265 " --> pdb=" O THR C 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 267 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS C 101 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 269 " --> pdb=" O HIS C 101 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE D 166 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE D 168 " --> pdb=" O HIS D 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP D 170 " --> pdb=" O PHE D 132 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 201 through 208 removed outlier: 3.616A pdb=" N LEU D 100 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY D 102 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR D 265 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 267 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS D 101 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 269 " --> pdb=" O HIS D 101 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 128 through 133 removed outlier: 3.831A pdb=" N ILE E 166 " --> pdb=" O TYR E 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE E 168 " --> pdb=" O HIS E 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP E 170 " --> pdb=" O PHE E 132 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU E 100 " --> pdb=" O PHE E 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY E 102 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR E 265 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 267 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS E 101 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 269 " --> pdb=" O HIS E 101 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE F 166 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE F 168 " --> pdb=" O HIS F 130 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP F 170 " --> pdb=" O PHE F 132 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU F 100 " --> pdb=" O PHE F 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY F 102 " --> pdb=" O SER F 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR F 265 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL F 267 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS F 101 " --> pdb=" O VAL F 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 269 " --> pdb=" O HIS F 101 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE G 166 " --> pdb=" O TYR G 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE G 168 " --> pdb=" O HIS G 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP G 170 " --> pdb=" O PHE G 132 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU G 100 " --> pdb=" O PHE G 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY G 102 " --> pdb=" O SER G 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR G 265 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL G 267 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS G 101 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE G 269 " --> pdb=" O HIS G 101 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE H 166 " --> pdb=" O TYR H 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE H 168 " --> pdb=" O HIS H 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP H 170 " --> pdb=" O PHE H 132 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU H 100 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY H 102 " --> pdb=" O SER H 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 265 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 267 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS H 101 " --> pdb=" O VAL H 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE H 269 " --> pdb=" O HIS H 101 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE I 166 " --> pdb=" O TYR I 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE I 168 " --> pdb=" O HIS I 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP I 170 " --> pdb=" O PHE I 132 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU I 100 " --> pdb=" O PHE I 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY I 102 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR I 265 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL I 267 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS I 101 " --> pdb=" O VAL I 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE I 269 " --> pdb=" O HIS I 101 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE J 166 " --> pdb=" O TYR J 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE J 168 " --> pdb=" O HIS J 130 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP J 170 " --> pdb=" O PHE J 132 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU J 100 " --> pdb=" O PHE J 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY J 102 " --> pdb=" O SER J 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR J 265 " --> pdb=" O THR J 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL J 267 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS J 101 " --> pdb=" O VAL J 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE J 269 " --> pdb=" O HIS J 101 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE K 166 " --> pdb=" O TYR K 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE K 168 " --> pdb=" O HIS K 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP K 170 " --> pdb=" O PHE K 132 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 201 through 208 removed outlier: 3.616A pdb=" N LEU K 100 " --> pdb=" O PHE K 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY K 102 " --> pdb=" O SER K 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR K 265 " --> pdb=" O THR K 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL K 267 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS K 101 " --> pdb=" O VAL K 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE K 269 " --> pdb=" O HIS K 101 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE L 166 " --> pdb=" O TYR L 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE L 168 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP L 170 " --> pdb=" O PHE L 132 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 201 through 208 removed outlier: 3.616A pdb=" N LEU L 100 " --> pdb=" O PHE L 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY L 102 " --> pdb=" O SER L 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR L 265 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL L 267 " --> pdb=" O SER L 99 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS L 101 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE L 269 " --> pdb=" O HIS L 101 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE M 166 " --> pdb=" O TYR M 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE M 168 " --> pdb=" O HIS M 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP M 170 " --> pdb=" O PHE M 132 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU M 100 " --> pdb=" O PHE M 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY M 102 " --> pdb=" O SER M 207 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR M 265 " --> pdb=" O THR M 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL M 267 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS M 101 " --> pdb=" O VAL M 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE M 269 " --> pdb=" O HIS M 101 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE N 166 " --> pdb=" O TYR N 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE N 168 " --> pdb=" O HIS N 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP N 170 " --> pdb=" O PHE N 132 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU N 100 " --> pdb=" O PHE N 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY N 102 " --> pdb=" O SER N 207 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR N 265 " --> pdb=" O THR N 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL N 267 " --> pdb=" O SER N 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS N 101 " --> pdb=" O VAL N 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE N 269 " --> pdb=" O HIS N 101 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE O 166 " --> pdb=" O TYR O 128 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE O 168 " --> pdb=" O HIS O 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP O 170 " --> pdb=" O PHE O 132 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU O 100 " --> pdb=" O PHE O 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY O 102 " --> pdb=" O SER O 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR O 265 " --> pdb=" O THR O 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL O 267 " --> pdb=" O SER O 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS O 101 " --> pdb=" O VAL O 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE O 269 " --> pdb=" O HIS O 101 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE P 166 " --> pdb=" O TYR P 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE P 168 " --> pdb=" O HIS P 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP P 170 " --> pdb=" O PHE P 132 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU P 100 " --> pdb=" O PHE P 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY P 102 " --> pdb=" O SER P 207 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR P 265 " --> pdb=" O THR P 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL P 267 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS P 101 " --> pdb=" O VAL P 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE P 269 " --> pdb=" O HIS P 101 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE Q 166 " --> pdb=" O TYR Q 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE Q 168 " --> pdb=" O HIS Q 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP Q 170 " --> pdb=" O PHE Q 132 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 201 through 208 removed outlier: 3.616A pdb=" N LEU Q 100 " --> pdb=" O PHE Q 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY Q 102 " --> pdb=" O SER Q 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR Q 265 " --> pdb=" O THR Q 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL Q 267 " --> pdb=" O SER Q 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS Q 101 " --> pdb=" O VAL Q 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE Q 269 " --> pdb=" O HIS Q 101 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE R 166 " --> pdb=" O TYR R 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE R 168 " --> pdb=" O HIS R 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP R 170 " --> pdb=" O PHE R 132 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 201 through 208 removed outlier: 3.616A pdb=" N LEU R 100 " --> pdb=" O PHE R 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY R 102 " --> pdb=" O SER R 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR R 265 " --> pdb=" O THR R 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL R 267 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS R 101 " --> pdb=" O VAL R 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE R 269 " --> pdb=" O HIS R 101 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 128 through 133 removed outlier: 3.829A pdb=" N ILE S 166 " --> pdb=" O TYR S 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE S 168 " --> pdb=" O HIS S 130 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP S 170 " --> pdb=" O PHE S 132 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU S 100 " --> pdb=" O PHE S 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY S 102 " --> pdb=" O SER S 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR S 265 " --> pdb=" O THR S 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL S 267 " --> pdb=" O SER S 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS S 101 " --> pdb=" O VAL S 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE S 269 " --> pdb=" O HIS S 101 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'T' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE T 166 " --> pdb=" O TYR T 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE T 168 " --> pdb=" O HIS T 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP T 170 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU T 100 " --> pdb=" O PHE T 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY T 102 " --> pdb=" O SER T 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR T 265 " --> pdb=" O THR T 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL T 267 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS T 101 " --> pdb=" O VAL T 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE T 269 " --> pdb=" O HIS T 101 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE U 166 " --> pdb=" O TYR U 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE U 168 " --> pdb=" O HIS U 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP U 170 " --> pdb=" O PHE U 132 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU U 100 " --> pdb=" O PHE U 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY U 102 " --> pdb=" O SER U 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR U 265 " --> pdb=" O THR U 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL U 267 " --> pdb=" O SER U 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS U 101 " --> pdb=" O VAL U 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE U 269 " --> pdb=" O HIS U 101 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE V 166 " --> pdb=" O TYR V 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE V 168 " --> pdb=" O HIS V 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP V 170 " --> pdb=" O PHE V 132 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 201 through 208 removed outlier: 3.616A pdb=" N LEU V 100 " --> pdb=" O PHE V 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY V 102 " --> pdb=" O SER V 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR V 265 " --> pdb=" O THR V 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL V 267 " --> pdb=" O SER V 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS V 101 " --> pdb=" O VAL V 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE V 269 " --> pdb=" O HIS V 101 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE W 166 " --> pdb=" O TYR W 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE W 168 " --> pdb=" O HIS W 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP W 170 " --> pdb=" O PHE W 132 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 201 through 208 removed outlier: 3.616A pdb=" N LEU W 100 " --> pdb=" O PHE W 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY W 102 " --> pdb=" O SER W 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR W 265 " --> pdb=" O THR W 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL W 267 " --> pdb=" O SER W 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS W 101 " --> pdb=" O VAL W 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE W 269 " --> pdb=" O HIS W 101 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'X' and resid 128 through 133 removed outlier: 3.830A pdb=" N ILE X 166 " --> pdb=" O TYR X 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE X 168 " --> pdb=" O HIS X 130 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP X 170 " --> pdb=" O PHE X 132 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'X' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU X 100 " --> pdb=" O PHE X 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY X 102 " --> pdb=" O SER X 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR X 265 " --> pdb=" O THR X 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL X 267 " --> pdb=" O SER X 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS X 101 " --> pdb=" O VAL X 267 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE X 269 " --> pdb=" O HIS X 101 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Y' and resid 128 through 133 removed outlier: 3.829A pdb=" N ILE Y 166 " --> pdb=" O TYR Y 128 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE Y 168 " --> pdb=" O HIS Y 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP Y 170 " --> pdb=" O PHE Y 132 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Y' and resid 201 through 208 removed outlier: 3.615A pdb=" N LEU Y 100 " --> pdb=" O PHE Y 205 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY Y 102 " --> pdb=" O SER Y 207 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR Y 265 " --> pdb=" O THR Y 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL Y 267 " --> pdb=" O SER Y 99 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS Y 101 " --> pdb=" O VAL Y 267 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE Y 269 " --> pdb=" O HIS Y 101 " (cutoff:3.500A) 2700 hydrogen bonds defined for protein. 8100 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: 41.80 Time building geometry restraints manager: 73.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 56725 1.03 - 1.23: 90 1.23 - 1.42: 25785 1.42 - 1.62: 33500 1.62 - 1.82: 375 Bond restraints: 116475 Sorted by residual: bond pdb=" C4 ATP S 401 " pdb=" C5 ATP S 401 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.61e+01 bond pdb=" C4 ATP M 401 " pdb=" C5 ATP M 401 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.59e+01 bond pdb=" C4 ATP O 401 " pdb=" C5 ATP O 401 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.59e+01 bond pdb=" C4 ATP I 401 " pdb=" C5 ATP I 401 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.58e+01 bond pdb=" C4 ATP G 401 " pdb=" C5 ATP G 401 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.57e+01 ... (remaining 116470 not shown) Histogram of bond angle deviations from ideal: 71.88 - 84.65: 150 84.65 - 97.42: 0 97.42 - 110.19: 101566 110.19 - 122.96: 95319 122.96 - 135.73: 13040 Bond angle restraints: 210075 Sorted by residual: angle pdb=" PB ATP G 401 " pdb=" O3B ATP G 401 " pdb=" PG ATP G 401 " ideal model delta sigma weight residual 139.87 117.70 22.17 1.00e+00 1.00e+00 4.92e+02 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 117.70 22.17 1.00e+00 1.00e+00 4.91e+02 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 117.71 22.16 1.00e+00 1.00e+00 4.91e+02 angle pdb=" PB ATP P 401 " pdb=" O3B ATP P 401 " pdb=" PG ATP P 401 " ideal model delta sigma weight residual 139.87 117.72 22.15 1.00e+00 1.00e+00 4.91e+02 angle pdb=" PB ATP X 401 " pdb=" O3B ATP X 401 " pdb=" PG ATP X 401 " ideal model delta sigma weight residual 139.87 117.72 22.15 1.00e+00 1.00e+00 4.91e+02 ... (remaining 210070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 45350 16.35 - 32.69: 1300 32.69 - 49.04: 125 49.04 - 65.38: 25 65.38 - 81.73: 50 Dihedral angle restraints: 46850 sinusoidal: 21250 harmonic: 25600 Sorted by residual: dihedral pdb=" CA VAL Q 297 " pdb=" C VAL Q 297 " pdb=" N SER Q 298 " pdb=" CA SER Q 298 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA VAL E 297 " pdb=" C VAL E 297 " pdb=" N SER E 298 " pdb=" CA SER E 298 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA VAL F 297 " pdb=" C VAL F 297 " pdb=" N SER F 298 " pdb=" CA SER F 298 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 46847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 7195 0.068 - 0.136: 1256 0.136 - 0.204: 99 0.204 - 0.272: 0 0.272 - 0.340: 50 Chirality restraints: 8600 Sorted by residual: chirality pdb=" CA SER T 224 " pdb=" N SER T 224 " pdb=" C SER T 224 " pdb=" CB SER T 224 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA SER O 224 " pdb=" N SER O 224 " pdb=" C SER O 224 " pdb=" CB SER O 224 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA SER E 224 " pdb=" N SER E 224 " pdb=" C SER E 224 " pdb=" CB SER E 224 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 8597 not shown) Planarity restraints: 17025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 261 " -0.058 2.00e-02 2.50e+03 8.47e-02 1.08e+02 pdb=" CG ASN K 261 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN K 261 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN K 261 " -0.019 2.00e-02 2.50e+03 pdb="HD21 ASN K 261 " 0.132 2.00e-02 2.50e+03 pdb="HD22 ASN K 261 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 261 " 0.058 2.00e-02 2.50e+03 8.46e-02 1.07e+02 pdb=" CG ASN C 261 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 261 " -0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN C 261 " 0.019 2.00e-02 2.50e+03 pdb="HD21 ASN C 261 " -0.132 2.00e-02 2.50e+03 pdb="HD22 ASN C 261 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN Q 261 " -0.058 2.00e-02 2.50e+03 8.45e-02 1.07e+02 pdb=" CG ASN Q 261 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN Q 261 " 0.093 2.00e-02 2.50e+03 pdb=" ND2 ASN Q 261 " -0.019 2.00e-02 2.50e+03 pdb="HD21 ASN Q 261 " 0.132 2.00e-02 2.50e+03 pdb="HD22 ASN Q 261 " -0.106 2.00e-02 2.50e+03 ... (remaining 17022 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 2707 2.12 - 2.74: 218183 2.74 - 3.36: 327341 3.36 - 3.98: 408886 3.98 - 4.60: 657450 Nonbonded interactions: 1614567 Sorted by model distance: nonbonded pdb=" HE1 TYR N 189 " pdb=" O2A ATP N 401 " model vdw 1.504 2.450 nonbonded pdb=" HE1 TYR R 189 " pdb=" O2A ATP R 401 " model vdw 1.504 2.450 nonbonded pdb=" HE1 TYR T 189 " pdb=" O2A ATP T 401 " model vdw 1.504 2.450 nonbonded pdb=" HE1 TYR K 189 " pdb=" O2A ATP K 401 " model vdw 1.504 2.450 nonbonded pdb=" HE1 TYR C 189 " pdb=" O2A ATP C 401 " model vdw 1.504 2.450 ... (remaining 1614562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 51 through 332) selection = (chain 'B' and resid 51 through 332) selection = (chain 'C' and resid 51 through 332) selection = (chain 'D' and resid 51 through 332) selection = (chain 'E' and resid 51 through 332) selection = (chain 'F' and resid 51 through 332) selection = (chain 'G' and resid 51 through 332) selection = (chain 'H' and resid 51 through 332) selection = (chain 'I' and resid 51 through 332) selection = (chain 'J' and resid 51 through 332) selection = (chain 'K' and resid 51 through 332) selection = (chain 'L' and resid 51 through 332) selection = (chain 'M' and resid 51 through 332) selection = (chain 'N' and resid 51 through 332) selection = (chain 'O' and resid 51 through 332) selection = (chain 'P' and resid 51 through 332) selection = (chain 'Q' and resid 51 through 332) selection = (chain 'R' and resid 51 through 332) selection = (chain 'S' and resid 51 through 332) selection = (chain 'T' and resid 51 through 332) selection = (chain 'U' and resid 51 through 332) selection = (chain 'V' and resid 51 through 332) selection = (chain 'W' and resid 51 through 332) selection = (chain 'X' and resid 51 through 332) selection = chain 'Y' } 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: 6 Type Number sf(0) Gaussians P 75 5.49 5 S 225 5.16 5 C 37375 2.51 5 N 9750 2.21 5 O 10850 1.98 5 H 56750 0.53 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 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: 1.240 Extract box with map and model: 9.340 Check model and map are aligned: 1.230 Convert atoms to be neutral: 0.730 Process input model: 266.770 Find NCS groups from input model: 5.480 Set up NCS constraints: 0.710 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 288.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 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 : 0.008 0.075 59725 Z= 0.543 Angle : 1.209 22.172 80775 Z= 0.837 Chirality : 0.054 0.340 8600 Planarity : 0.005 0.040 10200 Dihedral : 9.731 81.731 21725 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -4.69 (0.08), residues: 7000 helix: -3.20 (0.06), residues: 3600 sheet: -3.09 (0.16), residues: 800 loop : -2.63 (0.11), residues: 2600 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1573 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1573 time to evaluate : 6.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1573 average time/residue: 1.4912 time to fit residues: 3730.1510 Evaluate side-chains 892 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 892 time to evaluate : 6.640 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 591 optimal weight: 20.0000 chunk 530 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 chunk 548 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 chunk 408 optimal weight: 9.9990 chunk 635 optimal weight: 20.0000 overall best weight: 11.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 130 HIS A 158 ASN A 286 GLN B 72 GLN B 130 HIS B 152 GLN B 286 GLN C 72 GLN C 238 HIS C 286 GLN D 72 GLN D 130 HIS D 152 GLN D 286 GLN E 72 GLN E 130 HIS E 158 ASN E 286 GLN F 72 GLN F 152 GLN F 238 HIS F 286 GLN G 72 GLN G 130 HIS G 158 ASN G 286 GLN H 130 HIS H 152 GLN H 286 GLN I 72 GLN I 158 ASN I 286 GLN J 72 GLN J 152 GLN J 286 GLN K 72 GLN K 109 ASN K 130 HIS K 158 ASN K 286 GLN L 72 GLN L 152 GLN L 286 GLN M 72 GLN M 130 HIS M 158 ASN M 286 GLN N 152 GLN N 286 GLN O 72 GLN O 130 HIS O 158 ASN O 286 GLN P 72 GLN P 152 GLN P 286 GLN Q 72 GLN Q 130 HIS Q 158 ASN Q 286 GLN R 72 GLN R 152 GLN R 238 HIS R 286 GLN S 72 GLN S 130 HIS S 158 ASN S 286 GLN T 72 GLN T 152 GLN T 286 GLN U 72 GLN U 130 HIS U 158 ASN U 286 GLN V 72 GLN V 152 GLN V 158 ASN V 286 GLN W 72 GLN W 130 HIS W 158 ASN W 286 GLN X 72 GLN X 152 GLN X 286 GLN Y 72 GLN ** Y 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 GLN Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 59725 Z= 0.339 Angle : 0.735 10.199 80775 Z= 0.409 Chirality : 0.049 0.388 8600 Planarity : 0.005 0.069 10200 Dihedral : 9.204 85.599 7725 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -3.43 (0.09), residues: 7000 helix: -1.98 (0.07), residues: 3625 sheet: -2.86 (0.16), residues: 800 loop : -2.24 (0.12), residues: 2575 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1090 time to evaluate : 6.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 1093 average time/residue: 1.3762 time to fit residues: 2447.6553 Evaluate side-chains 765 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 765 time to evaluate : 6.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 5.9990 chunk 197 optimal weight: 30.0000 chunk 529 optimal weight: 3.9990 chunk 432 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 636 optimal weight: 6.9990 chunk 687 optimal weight: 10.0000 chunk 567 optimal weight: 8.9990 chunk 631 optimal weight: 20.0000 chunk 217 optimal weight: 30.0000 chunk 510 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 238 HIS I 109 ASN I 130 HIS ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 238 HIS V 158 ASN Y 130 HIS Y 158 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.117 59725 Z= 0.228 Angle : 0.578 5.955 80775 Z= 0.331 Chirality : 0.046 0.367 8600 Planarity : 0.003 0.034 10200 Dihedral : 7.431 62.177 7725 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.73 (0.09), residues: 7000 helix: -1.42 (0.07), residues: 3625 sheet: -2.60 (0.17), residues: 800 loop : -1.84 (0.13), residues: 2575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1008 time to evaluate : 6.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1008 average time/residue: 1.3682 time to fit residues: 2278.5237 Evaluate side-chains 772 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 7.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 629 optimal weight: 7.9990 chunk 478 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 303 optimal weight: 6.9990 chunk 427 optimal weight: 9.9990 chunk 639 optimal weight: 20.0000 chunk 676 optimal weight: 9.9990 chunk 333 optimal weight: 20.0000 chunk 605 optimal weight: 30.0000 chunk 182 optimal weight: 20.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN B 158 ASN C 130 HIS C 158 ASN F 130 HIS ** I 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 ASN ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 59725 Z= 0.262 Angle : 0.597 6.148 80775 Z= 0.340 Chirality : 0.046 0.376 8600 Planarity : 0.004 0.085 10200 Dihedral : 7.255 83.150 7725 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.17 % Favored : 90.81 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.54 (0.09), residues: 7000 helix: -1.25 (0.07), residues: 3800 sheet: -2.70 (0.16), residues: 875 loop : -1.65 (0.13), residues: 2325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 952 time to evaluate : 7.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 952 average time/residue: 1.3236 time to fit residues: 2102.0317 Evaluate side-chains 750 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 750 time to evaluate : 7.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 10.0000 chunk 384 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 chunk 503 optimal weight: 10.0000 chunk 279 optimal weight: 40.0000 chunk 577 optimal weight: 0.8980 chunk 467 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 345 optimal weight: 8.9990 chunk 607 optimal weight: 30.0000 chunk 170 optimal weight: 20.0000 overall best weight: 7.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 137 HIS I 109 ASN K 109 ASN K 137 HIS L 72 GLN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 59725 Z= 0.219 Angle : 0.547 5.381 80775 Z= 0.312 Chirality : 0.045 0.373 8600 Planarity : 0.003 0.041 10200 Dihedral : 6.927 75.109 7725 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.30 (0.10), residues: 7000 helix: -1.07 (0.08), residues: 3850 sheet: -2.58 (0.17), residues: 900 loop : -1.50 (0.14), residues: 2250 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 948 time to evaluate : 6.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 948 average time/residue: 1.3245 time to fit residues: 2084.9064 Evaluate side-chains 762 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 762 time to evaluate : 6.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 227 optimal weight: 20.0000 chunk 609 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 397 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 677 optimal weight: 20.0000 chunk 562 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 56 optimal weight: 60.0000 chunk 224 optimal weight: 50.0000 chunk 355 optimal weight: 30.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 158 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.066 59725 Z= 0.385 Angle : 0.719 6.788 80775 Z= 0.408 Chirality : 0.048 0.397 8600 Planarity : 0.004 0.042 10200 Dihedral : 7.571 88.647 7725 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.96 % Favored : 88.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.83 (0.09), residues: 7000 helix: -1.26 (0.08), residues: 3725 sheet: -2.58 (0.17), residues: 875 loop : -2.35 (0.12), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 870 time to evaluate : 7.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 870 average time/residue: 1.3287 time to fit residues: 1921.3498 Evaluate side-chains 701 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 7.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 385 optimal weight: 9.9990 chunk 494 optimal weight: 20.0000 chunk 383 optimal weight: 10.0000 chunk 570 optimal weight: 9.9990 chunk 378 optimal weight: 0.6980 chunk 674 optimal weight: 20.0000 chunk 422 optimal weight: 30.0000 chunk 411 optimal weight: 20.0000 chunk 311 optimal weight: 20.0000 overall best weight: 6.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN F 143 ASN G 150 GLN M 150 GLN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 125 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.8065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 59725 Z= 0.206 Angle : 0.550 5.663 80775 Z= 0.313 Chirality : 0.045 0.374 8600 Planarity : 0.003 0.041 10200 Dihedral : 7.143 87.277 7725 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.24 (0.10), residues: 7000 helix: -0.92 (0.08), residues: 3725 sheet: -2.35 (0.17), residues: 875 loop : -1.78 (0.13), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 916 time to evaluate : 7.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 916 average time/residue: 1.3114 time to fit residues: 1997.0373 Evaluate side-chains 704 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 6.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.4648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 8.9990 chunk 269 optimal weight: 0.3980 chunk 402 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 428 optimal weight: 5.9990 chunk 459 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 62 optimal weight: 0.0980 chunk 530 optimal weight: 9.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 ASN M 130 HIS ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 HIS R 130 HIS ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 HIS Y 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.8311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 59725 Z= 0.176 Angle : 0.525 6.255 80775 Z= 0.296 Chirality : 0.045 0.369 8600 Planarity : 0.003 0.067 10200 Dihedral : 6.844 83.352 7725 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.10), residues: 7000 helix: -0.83 (0.08), residues: 3875 sheet: -2.19 (0.17), residues: 875 loop : -1.24 (0.14), residues: 2250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 911 time to evaluate : 6.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 911 average time/residue: 1.2747 time to fit residues: 1939.3138 Evaluate side-chains 713 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 713 time to evaluate : 7.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.8005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 7.9990 chunk 646 optimal weight: 20.0000 chunk 589 optimal weight: 30.0000 chunk 628 optimal weight: 20.0000 chunk 378 optimal weight: 8.9990 chunk 273 optimal weight: 20.0000 chunk 493 optimal weight: 1.9990 chunk 192 optimal weight: 30.0000 chunk 568 optimal weight: 20.0000 chunk 594 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 ASN M 130 HIS ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 130 HIS ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 118 ASN T 130 HIS ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.8639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 59725 Z= 0.213 Angle : 0.548 7.244 80775 Z= 0.310 Chirality : 0.045 0.374 8600 Planarity : 0.003 0.091 10200 Dihedral : 6.863 85.793 7725 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.80 (0.10), residues: 7000 helix: -0.69 (0.08), residues: 3775 sheet: -2.14 (0.17), residues: 875 loop : -1.34 (0.14), residues: 2350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 871 time to evaluate : 6.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 871 average time/residue: 1.2995 time to fit residues: 1899.1985 Evaluate side-chains 707 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 6.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 412 optimal weight: 40.0000 chunk 664 optimal weight: 30.0000 chunk 405 optimal weight: 6.9990 chunk 315 optimal weight: 20.0000 chunk 462 optimal weight: 30.0000 chunk 697 optimal weight: 6.9990 chunk 641 optimal weight: 8.9990 chunk 555 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 chunk 340 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 143 ASN M 130 HIS N 130 HIS ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 130 HIS ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.8858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 59725 Z= 0.197 Angle : 0.527 6.141 80775 Z= 0.298 Chirality : 0.045 0.375 8600 Planarity : 0.003 0.037 10200 Dihedral : 6.763 82.876 7725 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.69 (0.10), residues: 7000 helix: -0.60 (0.08), residues: 3775 sheet: -2.20 (0.17), residues: 900 loop : -1.22 (0.14), residues: 2325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14000 Ramachandran restraints generated. 7000 Oldfield, 0 Emsley, 7000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 881 time to evaluate : 6.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 881 average time/residue: 1.2437 time to fit residues: 1833.0148 Evaluate side-chains 705 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 705 time to evaluate : 6.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.7587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 20.0000 chunk 591 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 512 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 556 optimal weight: 20.0000 chunk 232 optimal weight: 20.0000 chunk 571 optimal weight: 20.0000 chunk 70 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN H 158 ASN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN N 158 ASN ** N 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 118 ASN T 130 HIS ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.076699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.065702 restraints weight = 943588.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.068286 restraints weight = 513577.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.070022 restraints weight = 324738.319| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.9418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 59725 Z= 0.354 Angle : 0.663 8.246 80775 Z= 0.377 Chirality : 0.048 0.386 8600 Planarity : 0.004 0.041 10200 Dihedral : 7.300 89.911 7725 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.31 (0.10), residues: 7000 helix: -0.96 (0.08), residues: 3750 sheet: -2.23 (0.17), residues: 875 loop : -1.92 (0.13), residues: 2375 =============================================================================== Job complete usr+sys time: 29136.95 seconds wall clock time: 496 minutes 31.86 seconds (29791.86 seconds total)