Starting phenix.real_space_refine on Fri Jan 19 04:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/01_2024/6oif_20076_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/01_2024/6oif_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_20076/01_2024/6oif_20076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/01_2024/6oif_20076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/01_2024/6oif_20076_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oif_20076/01_2024/6oif_20076_neut_trim_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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. 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-1.21-5211/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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 273} 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: 34.60, per 1000 atoms: 0.30 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: 69.95 Conformation dependent library (CDL) restraints added in 8.0 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 for structures that cannot fit in PDB format. 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: 21.02 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: 37.04 Time building geometry restraints manager: 74.01 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: 52100 16.35 - 32.69: 1850 32.69 - 49.04: 325 49.04 - 65.38: 25 65.38 - 81.73: 75 Dihedral angle restraints: 54375 sinusoidal: 28775 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 54372 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 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: 0.410 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: 1.170 Extract box with map and model: 6.190 Check model and map are aligned: 1.190 Set scattering table: 0.730 Process input model: 271.450 Find NCS groups from input model: 4.950 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 288.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 : 10.767 81.731 22500 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 % Allowed : 0.00 % Favored : 100.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 253 HIS 0.006 0.002 HIS U 73 PHE 0.036 0.002 PHE Q 110 TYR 0.028 0.004 TYR X 290 ARG 0.010 0.001 ARG G 260 *********************** 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 : 6.647 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 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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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 274 TYR cc_start: 0.7268 (p90) cc_final: 0.6993 (p90) REVERT: D 97 THR cc_start: 0.7755 (p) cc_final: 0.7472 (p) REVERT: E 184 LYS cc_start: 0.8439 (mttt) cc_final: 0.8182 (ttpp) REVERT: F 96 LEU cc_start: 0.9238 (tp) cc_final: 0.8979 (tp) REVERT: G 184 LYS cc_start: 0.8063 (mttt) cc_final: 0.7691 (ttpt) REVERT: I 304 MET cc_start: 0.7569 (tpp) cc_final: 0.7309 (tpp) REVERT: L 274 TYR cc_start: 0.7562 (p90) cc_final: 0.7213 (p90) REVERT: N 260 ARG cc_start: 0.6186 (mmp-170) cc_final: 0.5982 (mmt180) REVERT: N 265 TYR cc_start: 0.8142 (m-10) cc_final: 0.7925 (m-80) REVERT: N 329 TYR cc_start: 0.4789 (m-10) cc_final: 0.4554 (m-10) REVERT: P 260 ARG cc_start: 0.4965 (mmp-170) cc_final: 0.4661 (mmt180) REVERT: R 183 ILE cc_start: 0.6411 (pt) cc_final: 0.5879 (pt) REVERT: S 204 ILE cc_start: 0.7767 (mt) cc_final: 0.7457 (mt) REVERT: T 183 ILE cc_start: 0.5869 (pt) cc_final: 0.5494 (pt) REVERT: U 204 ILE cc_start: 0.7722 (mt) cc_final: 0.7492 (mt) REVERT: W 151 LEU cc_start: 0.9005 (tp) cc_final: 0.8778 (tt) REVERT: X 304 MET cc_start: 0.6516 (tpp) cc_final: 0.6140 (tpp) REVERT: Y 304 MET cc_start: 0.3885 (tpp) cc_final: 0.3671 (tpp) outliers start: 0 outliers final: 0 residues processed: 1573 average time/residue: 1.5023 time to fit residues: 3728.9797 Evaluate side-chains 902 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 902 time to evaluate : 6.524 ------------------------------------------------------------------------------- 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: 9.9990 chunk 294 optimal weight: 20.0000 chunk 181 optimal weight: 0.9990 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: 9.9990 chunk 408 optimal weight: 9.9990 chunk 635 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 152 GLN A 286 GLN B 72 GLN B 152 GLN B 286 GLN C 72 GLN C 238 HIS C 286 GLN D 72 GLN D 152 GLN D 286 GLN E 72 GLN E 286 GLN F 72 GLN F 152 GLN F 238 HIS F 286 GLN G 72 GLN G 152 GLN G 286 GLN H 72 GLN H 152 GLN H 286 GLN I 72 GLN I 286 GLN J 72 GLN J 152 GLN J 286 GLN K 72 GLN K 158 ASN K 286 GLN L 72 GLN L 152 GLN L 286 GLN M 72 GLN M 109 ASN M 158 ASN M 286 GLN N 152 GLN N 286 GLN O 72 GLN O 158 ASN O 286 GLN P 72 GLN P 152 GLN P 286 GLN Q 72 GLN Q 158 ASN Q 286 GLN R 72 GLN R 152 GLN R 238 HIS R 286 GLN S 72 GLN S 158 ASN S 286 GLN T 72 GLN T 152 GLN T 286 GLN U 72 GLN U 158 ASN V 72 GLN V 152 GLN V 158 ASN V 286 GLN W 72 GLN W 158 ASN W 286 GLN X 72 GLN X 152 GLN X 158 ASN X 286 GLN Y 72 GLN Y 158 ASN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 59725 Z= 0.268 Angle : 0.661 6.943 80775 Z= 0.375 Chirality : 0.047 0.374 8600 Planarity : 0.004 0.048 10200 Dihedral : 12.610 89.200 8500 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.05 % Allowed : 0.96 % Favored : 98.99 % 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: -3.33 (0.09), residues: 7000 helix: -1.94 (0.07), residues: 3625 sheet: -2.75 (0.16), residues: 800 loop : -2.12 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 253 HIS 0.011 0.002 HIS F 73 PHE 0.027 0.002 PHE U 110 TYR 0.024 0.002 TYR O 328 ARG 0.026 0.001 ARG C 213 *********************** 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 1149 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1146 time to evaluate : 6.581 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: A 304 MET cc_start: 0.8176 (tpp) cc_final: 0.7966 (tpp) REVERT: B 261 ASN cc_start: 0.8840 (m-40) cc_final: 0.8639 (m-40) REVERT: C 264 ASP cc_start: 0.8847 (t0) cc_final: 0.8510 (t70) REVERT: D 212 GLU cc_start: 0.8769 (pm20) cc_final: 0.8448 (pm20) REVERT: E 304 MET cc_start: 0.7931 (tpp) cc_final: 0.7467 (tpp) REVERT: F 127 ASP cc_start: 0.8464 (p0) cc_final: 0.7892 (t0) REVERT: G 184 LYS cc_start: 0.8695 (mttt) cc_final: 0.8297 (ttpt) REVERT: G 264 ASP cc_start: 0.8763 (t0) cc_final: 0.8455 (t70) REVERT: H 329 TYR cc_start: 0.4264 (m-10) cc_final: 0.3816 (m-10) REVERT: J 96 LEU cc_start: 0.9109 (tp) cc_final: 0.8865 (tp) REVERT: J 172 MET cc_start: 0.8108 (mmp) cc_final: 0.7865 (mmm) REVERT: J 274 TYR cc_start: 0.7506 (p90) cc_final: 0.7240 (p90) REVERT: L 274 TYR cc_start: 0.7726 (p90) cc_final: 0.7388 (p90) REVERT: M 212 GLU cc_start: 0.8214 (pm20) cc_final: 0.7958 (pm20) REVERT: M 279 MET cc_start: 0.8750 (mtt) cc_final: 0.8538 (mmm) REVERT: R 171 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6845 (mm-30) REVERT: S 144 ILE cc_start: 0.9109 (pt) cc_final: 0.8875 (tp) REVERT: S 212 GLU cc_start: 0.7887 (pm20) cc_final: 0.7446 (pm20) REVERT: U 113 LYS cc_start: 0.9052 (ttpt) cc_final: 0.8710 (ttpt) REVERT: U 114 ILE cc_start: 0.8864 (mt) cc_final: 0.8171 (tp) REVERT: W 144 ILE cc_start: 0.9090 (pt) cc_final: 0.8797 (tp) REVERT: Y 173 ASP cc_start: 0.6008 (m-30) cc_final: 0.5728 (m-30) outliers start: 3 outliers final: 0 residues processed: 1149 average time/residue: 1.4332 time to fit residues: 2664.5663 Evaluate side-chains 821 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 821 time to evaluate : 6.631 ------------------------------------------------------------------------------- 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: 6.9990 chunk 197 optimal weight: 30.0000 chunk 529 optimal weight: 30.0000 chunk 432 optimal weight: 30.0000 chunk 175 optimal weight: 20.0000 chunk 636 optimal weight: 5.9990 chunk 687 optimal weight: 20.0000 chunk 567 optimal weight: 20.0000 chunk 631 optimal weight: 10.0000 chunk 217 optimal weight: 30.0000 chunk 510 optimal weight: 10.0000 overall best weight: 10.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 158 ASN C 130 HIS C 158 ASN D 130 HIS E 158 ASN F 130 HIS F 238 HIS G 109 ASN G 130 HIS G 137 HIS G 158 ASN I 109 ASN I 130 HIS I 150 GLN I 158 ASN K 130 HIS K 137 HIS M 109 ASN M 130 HIS O 130 HIS Q 130 HIS S 130 HIS U 130 HIS V 158 ASN W 130 HIS Y 130 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 59725 Z= 0.309 Angle : 0.660 16.076 80775 Z= 0.377 Chirality : 0.046 0.375 8600 Planarity : 0.004 0.044 10200 Dihedral : 10.610 88.309 8500 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.23 % Favored : 90.76 % Rotamer: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.73 % Cbeta Deviations : 0.02 % 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: -2.87 (0.09), residues: 7000 helix: -1.62 (0.07), residues: 3775 sheet: -2.56 (0.17), residues: 800 loop : -1.78 (0.13), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 253 HIS 0.009 0.002 HIS T 101 PHE 0.027 0.002 PHE Y 110 TYR 0.075 0.002 TYR O 290 ARG 0.005 0.001 ARG R 164 *********************** 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 1007 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1001 time to evaluate : 6.745 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: B 149 ASP cc_start: 0.8876 (m-30) cc_final: 0.8634 (m-30) REVERT: B 261 ASN cc_start: 0.9057 (m-40) cc_final: 0.8845 (m110) REVERT: B 265 TYR cc_start: 0.8314 (m-10) cc_final: 0.8015 (m-10) REVERT: C 264 ASP cc_start: 0.9169 (t0) cc_final: 0.8659 (t70) REVERT: C 274 TYR cc_start: 0.7444 (p90) cc_final: 0.7179 (p90) REVERT: D 212 GLU cc_start: 0.8920 (pm20) cc_final: 0.8601 (pm20) REVERT: E 264 ASP cc_start: 0.9020 (t0) cc_final: 0.8447 (t70) REVERT: E 304 MET cc_start: 0.7984 (tpp) cc_final: 0.7592 (tpp) REVERT: F 127 ASP cc_start: 0.8563 (p0) cc_final: 0.8071 (t0) REVERT: G 184 LYS cc_start: 0.8997 (mttt) cc_final: 0.8737 (ttpt) REVERT: H 127 ASP cc_start: 0.8322 (p0) cc_final: 0.7877 (t0) REVERT: H 330 TYR cc_start: 0.6640 (t80) cc_final: 0.6372 (t80) REVERT: I 261 ASN cc_start: 0.8539 (m-40) cc_final: 0.8250 (m110) REVERT: I 264 ASP cc_start: 0.9106 (t70) cc_final: 0.8850 (t70) REVERT: J 274 TYR cc_start: 0.7587 (p90) cc_final: 0.7368 (p90) REVERT: M 212 GLU cc_start: 0.8549 (pm20) cc_final: 0.8247 (pm20) REVERT: S 117 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7928 (mt-10) REVERT: S 204 ILE cc_start: 0.7661 (mt) cc_final: 0.7059 (mt) REVERT: S 212 GLU cc_start: 0.8187 (pm20) cc_final: 0.7701 (pm20) REVERT: U 212 GLU cc_start: 0.8283 (pm20) cc_final: 0.8059 (pm20) REVERT: W 144 ILE cc_start: 0.9190 (pt) cc_final: 0.8927 (tp) REVERT: W 150 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8560 (tp-100) REVERT: W 204 ILE cc_start: 0.7775 (mt) cc_final: 0.7160 (mt) REVERT: X 127 ASP cc_start: 0.6990 (p0) cc_final: 0.6646 (t0) outliers start: 6 outliers final: 1 residues processed: 1007 average time/residue: 1.3499 time to fit residues: 2228.1321 Evaluate side-chains 763 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 762 time to evaluate : 6.666 ------------------------------------------------------------------------------- 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: 6.9990 chunk 478 optimal weight: 30.0000 chunk 330 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 427 optimal weight: 20.0000 chunk 639 optimal weight: 30.0000 chunk 676 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 chunk 605 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN B 158 ASN D 150 GLN F 158 ASN H 130 HIS M 150 GLN R 109 ASN ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 286 GLN X 118 ASN X 158 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 59725 Z= 0.284 Angle : 0.626 7.267 80775 Z= 0.356 Chirality : 0.047 0.381 8600 Planarity : 0.004 0.093 10200 Dihedral : 10.827 89.728 8500 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.20 % Favored : 90.79 % Rotamer: Outliers : 0.02 % Allowed : 1.50 % Favored : 98.48 % 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: -2.65 (0.09), residues: 7000 helix: -1.33 (0.07), residues: 3800 sheet: -2.68 (0.17), residues: 875 loop : -1.75 (0.13), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 253 HIS 0.010 0.002 HIS X 101 PHE 0.040 0.002 PHE X 186 TYR 0.063 0.002 TYR O 290 ARG 0.007 0.001 ARG M 223 *********************** 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 958 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 957 time to evaluate : 6.780 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: A 149 ASP cc_start: 0.8869 (m-30) cc_final: 0.8580 (m-30) REVERT: A 181 ASP cc_start: 0.8751 (m-30) cc_final: 0.8492 (m-30) REVERT: B 149 ASP cc_start: 0.8766 (m-30) cc_final: 0.8459 (m-30) REVERT: C 150 GLN cc_start: 0.9315 (mt0) cc_final: 0.9020 (mt0) REVERT: C 233 LEU cc_start: 0.8333 (tp) cc_final: 0.8094 (tp) REVERT: C 304 MET cc_start: 0.7920 (tpp) cc_final: 0.7708 (tpp) REVERT: D 149 ASP cc_start: 0.8864 (m-30) cc_final: 0.8610 (m-30) REVERT: F 127 ASP cc_start: 0.8704 (p0) cc_final: 0.8131 (t0) REVERT: F 149 ASP cc_start: 0.8981 (m-30) cc_final: 0.8723 (m-30) REVERT: G 264 ASP cc_start: 0.9002 (t70) cc_final: 0.8537 (t70) REVERT: G 304 MET cc_start: 0.8202 (tpp) cc_final: 0.7686 (tpp) REVERT: H 127 ASP cc_start: 0.8586 (p0) cc_final: 0.8038 (t0) REVERT: H 143 ASN cc_start: 0.8165 (m110) cc_final: 0.7929 (m110) REVERT: J 304 MET cc_start: 0.8074 (tpp) cc_final: 0.7856 (tpp) REVERT: K 184 LYS cc_start: 0.8927 (mttm) cc_final: 0.8251 (tmmt) REVERT: L 149 ASP cc_start: 0.8794 (m-30) cc_final: 0.8553 (m-30) REVERT: M 212 GLU cc_start: 0.8541 (pm20) cc_final: 0.8228 (pm20) REVERT: Q 175 MET cc_start: 0.8646 (mmm) cc_final: 0.8426 (mmm) REVERT: R 150 GLN cc_start: 0.8957 (pt0) cc_final: 0.8731 (pt0) REVERT: R 187 LEU cc_start: 0.8980 (mt) cc_final: 0.8722 (mm) REVERT: R 262 LEU cc_start: 0.8187 (mt) cc_final: 0.7936 (mt) REVERT: T 121 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7192 (mt-10) REVERT: U 114 ILE cc_start: 0.8677 (mt) cc_final: 0.8212 (mt) REVERT: U 212 GLU cc_start: 0.8446 (pm20) cc_final: 0.8140 (pm20) REVERT: W 144 ILE cc_start: 0.9221 (pt) cc_final: 0.9014 (tp) REVERT: X 127 ASP cc_start: 0.7587 (p0) cc_final: 0.7377 (t0) outliers start: 1 outliers final: 1 residues processed: 958 average time/residue: 1.3178 time to fit residues: 2074.4866 Evaluate side-chains 765 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 764 time to evaluate : 7.351 ------------------------------------------------------------------------------- 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: 40.0000 chunk 9 optimal weight: 9.9990 chunk 503 optimal weight: 8.9990 chunk 279 optimal weight: 30.0000 chunk 577 optimal weight: 9.9990 chunk 467 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 345 optimal weight: 20.0000 chunk 607 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 109 ASN H 158 ASN X 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.7147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 59725 Z= 0.302 Angle : 0.619 8.764 80775 Z= 0.354 Chirality : 0.046 0.387 8600 Planarity : 0.004 0.065 10200 Dihedral : 10.234 89.009 8500 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -2.61 (0.09), residues: 7000 helix: -1.30 (0.07), residues: 3875 sheet: -2.59 (0.17), residues: 875 loop : -1.78 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP J 154 HIS 0.010 0.002 HIS X 101 PHE 0.027 0.002 PHE B 245 TYR 0.026 0.002 TYR B 290 ARG 0.007 0.001 ARG V 228 *********************** 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 922 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 922 time to evaluate : 6.753 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: A 181 ASP cc_start: 0.8711 (m-30) cc_final: 0.8385 (m-30) REVERT: B 113 LYS cc_start: 0.9303 (ttpt) cc_final: 0.9089 (ttpt) REVERT: B 149 ASP cc_start: 0.8814 (m-30) cc_final: 0.8515 (m-30) REVERT: C 274 TYR cc_start: 0.7603 (p90) cc_final: 0.7216 (p90) REVERT: D 149 ASP cc_start: 0.8978 (m-30) cc_final: 0.8754 (m-30) REVERT: E 79 ILE cc_start: 0.9310 (mm) cc_final: 0.9039 (tt) REVERT: F 127 ASP cc_start: 0.8817 (p0) cc_final: 0.8154 (t0) REVERT: F 143 ASN cc_start: 0.8213 (m110) cc_final: 0.8002 (m-40) REVERT: F 149 ASP cc_start: 0.8930 (m-30) cc_final: 0.8710 (m-30) REVERT: F 150 GLN cc_start: 0.8884 (mp10) cc_final: 0.8603 (mp10) REVERT: G 264 ASP cc_start: 0.8954 (t70) cc_final: 0.8353 (t70) REVERT: G 265 TYR cc_start: 0.8287 (m-10) cc_final: 0.8014 (m-10) REVERT: G 304 MET cc_start: 0.8306 (tpp) cc_final: 0.7671 (tpp) REVERT: H 127 ASP cc_start: 0.8714 (p0) cc_final: 0.8210 (t0) REVERT: H 143 ASN cc_start: 0.8178 (m110) cc_final: 0.7974 (m110) REVERT: I 172 MET cc_start: 0.8557 (mmm) cc_final: 0.8246 (mmm) REVERT: J 170 ASP cc_start: 0.7688 (p0) cc_final: 0.6932 (t0) REVERT: K 184 LYS cc_start: 0.8924 (mttm) cc_final: 0.8554 (ttpt) REVERT: L 149 ASP cc_start: 0.8831 (m-30) cc_final: 0.8589 (m-30) REVERT: L 262 LEU cc_start: 0.8373 (mt) cc_final: 0.8168 (mt) REVERT: L 288 ARG cc_start: 0.3968 (ttt180) cc_final: 0.3536 (tpt-90) REVERT: N 143 ASN cc_start: 0.7858 (m-40) cc_final: 0.7584 (m110) REVERT: N 149 ASP cc_start: 0.8733 (m-30) cc_final: 0.8453 (m-30) REVERT: Q 149 ASP cc_start: 0.8919 (m-30) cc_final: 0.8707 (m-30) REVERT: R 262 LEU cc_start: 0.8251 (mt) cc_final: 0.8012 (mt) REVERT: T 150 GLN cc_start: 0.7913 (pp30) cc_final: 0.7687 (pp30) REVERT: T 262 LEU cc_start: 0.8147 (mt) cc_final: 0.7847 (mt) REVERT: U 184 LYS cc_start: 0.8025 (mttt) cc_final: 0.7754 (mttp) REVERT: U 204 ILE cc_start: 0.8172 (mt) cc_final: 0.7673 (mt) REVERT: U 212 GLU cc_start: 0.8517 (pm20) cc_final: 0.8301 (pm20) REVERT: W 62 GLN cc_start: 0.9098 (pt0) cc_final: 0.8873 (pt0) REVERT: W 150 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8583 (tp-100) outliers start: 0 outliers final: 0 residues processed: 922 average time/residue: 1.3277 time to fit residues: 2028.7151 Evaluate side-chains 733 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 733 time to evaluate : 6.614 ------------------------------------------------------------------------------- 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: 30.0000 chunk 609 optimal weight: 6.9990 chunk 133 optimal weight: 30.0000 chunk 397 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 677 optimal weight: 20.0000 chunk 562 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 56 optimal weight: 60.0000 chunk 224 optimal weight: 40.0000 chunk 355 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 109 ASN L 158 ASN ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.8012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 59725 Z= 0.321 Angle : 0.641 6.454 80775 Z= 0.366 Chirality : 0.047 0.396 8600 Planarity : 0.004 0.045 10200 Dihedral : 10.301 86.739 8500 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -2.66 (0.09), residues: 7000 helix: -1.21 (0.08), residues: 3775 sheet: -2.57 (0.17), residues: 875 loop : -2.07 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 253 HIS 0.010 0.002 HIS R 101 PHE 0.030 0.002 PHE P 323 TYR 0.029 0.002 TYR D 290 ARG 0.010 0.001 ARG H 228 *********************** 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 889 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 889 time to evaluate : 6.630 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: A 181 ASP cc_start: 0.8786 (m-30) cc_final: 0.8553 (m-30) REVERT: C 150 GLN cc_start: 0.9286 (mt0) cc_final: 0.8923 (mt0) REVERT: C 274 TYR cc_start: 0.7644 (p90) cc_final: 0.7389 (p90) REVERT: D 149 ASP cc_start: 0.8994 (m-30) cc_final: 0.8775 (m-30) REVERT: F 149 ASP cc_start: 0.9015 (m-30) cc_final: 0.8734 (m-30) REVERT: G 187 LEU cc_start: 0.9067 (mm) cc_final: 0.8844 (mm) REVERT: G 264 ASP cc_start: 0.8890 (t70) cc_final: 0.8227 (t70) REVERT: G 265 TYR cc_start: 0.8281 (m-10) cc_final: 0.8004 (m-10) REVERT: G 304 MET cc_start: 0.8285 (tpp) cc_final: 0.7761 (tpp) REVERT: H 143 ASN cc_start: 0.8277 (m110) cc_final: 0.8068 (m110) REVERT: H 288 ARG cc_start: 0.5168 (ttt-90) cc_final: 0.3626 (ttp-170) REVERT: J 170 ASP cc_start: 0.7741 (p0) cc_final: 0.7028 (t70) REVERT: K 150 GLN cc_start: 0.9421 (mt0) cc_final: 0.9066 (mt0) REVERT: K 184 LYS cc_start: 0.9049 (mttm) cc_final: 0.8784 (tmmt) REVERT: L 149 ASP cc_start: 0.8946 (m-30) cc_final: 0.8700 (m-30) REVERT: M 279 MET cc_start: 0.8205 (tpp) cc_final: 0.7901 (tpp) REVERT: N 143 ASN cc_start: 0.8013 (m-40) cc_final: 0.7728 (m110) REVERT: N 149 ASP cc_start: 0.8771 (m-30) cc_final: 0.8485 (m-30) REVERT: O 184 LYS cc_start: 0.8760 (mttp) cc_final: 0.8050 (ttpp) REVERT: P 143 ASN cc_start: 0.8040 (m-40) cc_final: 0.7817 (m110) REVERT: P 149 ASP cc_start: 0.8760 (m-30) cc_final: 0.8504 (m-30) REVERT: P 202 MET cc_start: 0.7530 (pmm) cc_final: 0.7305 (pmm) REVERT: R 143 ASN cc_start: 0.8195 (m-40) cc_final: 0.7901 (m-40) REVERT: R 262 LEU cc_start: 0.8460 (mt) cc_final: 0.8259 (mt) REVERT: T 171 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7823 (mm-30) REVERT: T 262 LEU cc_start: 0.8309 (mt) cc_final: 0.8086 (mt) REVERT: V 96 LEU cc_start: 0.9074 (tp) cc_final: 0.8803 (tp) REVERT: V 125 ASN cc_start: 0.8533 (m-40) cc_final: 0.8225 (m110) REVERT: V 149 ASP cc_start: 0.8692 (m-30) cc_final: 0.8420 (m-30) REVERT: W 62 GLN cc_start: 0.9108 (pt0) cc_final: 0.8874 (pt0) REVERT: W 321 THR cc_start: 0.7497 (p) cc_final: 0.6771 (t) outliers start: 0 outliers final: 0 residues processed: 889 average time/residue: 1.3029 time to fit residues: 1906.9358 Evaluate side-chains 711 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 711 time to evaluate : 5.976 ------------------------------------------------------------------------------- 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: 0.0040 chunk 76 optimal weight: 40.0000 chunk 385 optimal weight: 6.9990 chunk 494 optimal weight: 7.9990 chunk 383 optimal weight: 20.0000 chunk 570 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 674 optimal weight: 7.9990 chunk 422 optimal weight: 20.0000 chunk 411 optimal weight: 30.0000 chunk 311 optimal weight: 30.0000 overall best weight: 6.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 150 GLN ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.8217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 59725 Z= 0.199 Angle : 0.539 5.223 80775 Z= 0.309 Chirality : 0.045 0.370 8600 Planarity : 0.003 0.045 10200 Dihedral : 9.710 83.219 8500 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -2.19 (0.10), residues: 7000 helix: -1.05 (0.08), residues: 3925 sheet: -2.39 (0.17), residues: 875 loop : -1.41 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 253 HIS 0.005 0.001 HIS W 176 PHE 0.012 0.001 PHE P 323 TYR 0.022 0.001 TYR O 290 ARG 0.011 0.001 ARG W 223 *********************** 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 898 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 898 time to evaluate : 6.811 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: A 181 ASP cc_start: 0.8747 (m-30) cc_final: 0.8490 (m-30) REVERT: C 150 GLN cc_start: 0.9257 (mt0) cc_final: 0.8885 (mt0) REVERT: C 274 TYR cc_start: 0.7387 (p90) cc_final: 0.7076 (p90) REVERT: D 149 ASP cc_start: 0.8966 (m-30) cc_final: 0.8735 (m-30) REVERT: F 149 ASP cc_start: 0.8918 (m-30) cc_final: 0.8547 (m-30) REVERT: F 150 GLN cc_start: 0.8971 (mp10) cc_final: 0.8665 (mp10) REVERT: G 304 MET cc_start: 0.8313 (tpp) cc_final: 0.7801 (tpp) REVERT: H 143 ASN cc_start: 0.8232 (m110) cc_final: 0.8004 (m110) REVERT: H 288 ARG cc_start: 0.5152 (ttt-90) cc_final: 0.3599 (ttp-170) REVERT: I 261 ASN cc_start: 0.8658 (m-40) cc_final: 0.8342 (m-40) REVERT: J 170 ASP cc_start: 0.7515 (p0) cc_final: 0.6870 (t70) REVERT: K 150 GLN cc_start: 0.9399 (mt0) cc_final: 0.9055 (mt0) REVERT: K 184 LYS cc_start: 0.8996 (mttm) cc_final: 0.8737 (ttpt) REVERT: M 184 LYS cc_start: 0.8771 (mttt) cc_final: 0.8417 (ttpt) REVERT: M 279 MET cc_start: 0.8039 (tpp) cc_final: 0.7815 (tpp) REVERT: N 143 ASN cc_start: 0.7994 (m-40) cc_final: 0.7711 (m110) REVERT: N 149 ASP cc_start: 0.8669 (m-30) cc_final: 0.8379 (m-30) REVERT: O 62 GLN cc_start: 0.8743 (pt0) cc_final: 0.8461 (pp30) REVERT: O 150 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8667 (tp-100) REVERT: O 184 LYS cc_start: 0.8761 (mttp) cc_final: 0.8146 (ttpt) REVERT: P 149 ASP cc_start: 0.8696 (m-30) cc_final: 0.8345 (m-30) REVERT: R 121 GLU cc_start: 0.7328 (tt0) cc_final: 0.7009 (tp30) REVERT: T 262 LEU cc_start: 0.8302 (mt) cc_final: 0.8070 (mt) REVERT: V 125 ASN cc_start: 0.8533 (m-40) cc_final: 0.8203 (m110) REVERT: V 149 ASP cc_start: 0.8629 (m-30) cc_final: 0.8396 (m-30) REVERT: W 62 GLN cc_start: 0.9089 (pt0) cc_final: 0.8869 (pt0) REVERT: W 150 GLN cc_start: 0.8883 (tp-100) cc_final: 0.8566 (tp-100) REVERT: W 321 THR cc_start: 0.7551 (p) cc_final: 0.6837 (t) REVERT: Y 187 LEU cc_start: 0.8125 (mt) cc_final: 0.7848 (tt) outliers start: 0 outliers final: 0 residues processed: 898 average time/residue: 1.2460 time to fit residues: 1843.5638 Evaluate side-chains 709 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 709 time to evaluate : 5.961 ------------------------------------------------------------------------------- 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: 9.9990 chunk 269 optimal weight: 6.9990 chunk 402 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 132 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 chunk 428 optimal weight: 10.0000 chunk 459 optimal weight: 2.9990 chunk 333 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 530 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 143 ASN L 150 GLN P 130 HIS ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.8526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 59725 Z= 0.205 Angle : 0.537 10.311 80775 Z= 0.306 Chirality : 0.045 0.374 8600 Planarity : 0.003 0.097 10200 Dihedral : 9.557 82.944 8500 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 8.47 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -1.97 (0.10), residues: 7000 helix: -0.79 (0.08), residues: 3775 sheet: -2.26 (0.17), residues: 875 loop : -1.48 (0.14), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 253 HIS 0.005 0.001 HIS W 176 PHE 0.016 0.001 PHE P 323 TYR 0.035 0.001 TYR C 290 ARG 0.009 0.001 ARG G 228 *********************** 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 875 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 875 time to evaluate : 6.748 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: A 181 ASP cc_start: 0.8785 (m-30) cc_final: 0.8545 (m-30) REVERT: C 150 GLN cc_start: 0.9276 (mt0) cc_final: 0.8891 (mt0) REVERT: C 274 TYR cc_start: 0.7418 (p90) cc_final: 0.7195 (p90) REVERT: C 329 TYR cc_start: 0.5871 (m-10) cc_final: 0.4907 (m-10) REVERT: D 149 ASP cc_start: 0.8946 (m-30) cc_final: 0.8705 (m-30) REVERT: F 149 ASP cc_start: 0.8896 (m-30) cc_final: 0.8570 (m-30) REVERT: F 261 ASN cc_start: 0.8817 (m-40) cc_final: 0.8545 (m-40) REVERT: G 304 MET cc_start: 0.8386 (tpp) cc_final: 0.7787 (tpp) REVERT: H 212 GLU cc_start: 0.8703 (pm20) cc_final: 0.8488 (pm20) REVERT: H 288 ARG cc_start: 0.5028 (ttt-90) cc_final: 0.3546 (ttp-170) REVERT: H 330 TYR cc_start: 0.6145 (t80) cc_final: 0.5741 (t80) REVERT: I 261 ASN cc_start: 0.8719 (m-40) cc_final: 0.8353 (m-40) REVERT: I 290 TYR cc_start: 0.0229 (t80) cc_final: -0.0096 (t80) REVERT: J 170 ASP cc_start: 0.7613 (p0) cc_final: 0.6941 (t70) REVERT: K 150 GLN cc_start: 0.9400 (mt0) cc_final: 0.9059 (mt0) REVERT: L 127 ASP cc_start: 0.8872 (p0) cc_final: 0.8480 (t0) REVERT: M 184 LYS cc_start: 0.8786 (mttt) cc_final: 0.8506 (ttpt) REVERT: M 279 MET cc_start: 0.8156 (tpp) cc_final: 0.7942 (tpp) REVERT: N 143 ASN cc_start: 0.8023 (m-40) cc_final: 0.7784 (m110) REVERT: N 149 ASP cc_start: 0.8732 (m-30) cc_final: 0.8449 (m-30) REVERT: O 62 GLN cc_start: 0.8915 (pt0) cc_final: 0.8464 (pp30) REVERT: O 150 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8629 (tp-100) REVERT: O 184 LYS cc_start: 0.8872 (mttp) cc_final: 0.8333 (ttpt) REVERT: P 143 ASN cc_start: 0.7854 (m110) cc_final: 0.7646 (m110) REVERT: P 149 ASP cc_start: 0.8778 (m-30) cc_final: 0.8476 (m-30) REVERT: Q 184 LYS cc_start: 0.9015 (mttp) cc_final: 0.8364 (ttpt) REVERT: R 121 GLU cc_start: 0.7290 (tt0) cc_final: 0.7075 (tp30) REVERT: R 143 ASN cc_start: 0.7910 (m110) cc_final: 0.7629 (m-40) REVERT: T 149 ASP cc_start: 0.8820 (m-30) cc_final: 0.8548 (m-30) REVERT: V 149 ASP cc_start: 0.8698 (m-30) cc_final: 0.8448 (m-30) REVERT: W 62 GLN cc_start: 0.9084 (pt0) cc_final: 0.8878 (pt0) REVERT: W 150 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8578 (tp-100) REVERT: W 321 THR cc_start: 0.7569 (p) cc_final: 0.6870 (t) REVERT: X 149 ASP cc_start: 0.8619 (m-30) cc_final: 0.8405 (m-30) REVERT: Y 150 GLN cc_start: 0.8925 (tp-100) cc_final: 0.8611 (tp-100) REVERT: Y 187 LEU cc_start: 0.8205 (mt) cc_final: 0.7970 (tt) REVERT: Y 304 MET cc_start: 0.7191 (tpp) cc_final: 0.6967 (tpp) REVERT: Y 328 TYR cc_start: 0.5762 (t80) cc_final: 0.5496 (t80) outliers start: 0 outliers final: 0 residues processed: 875 average time/residue: 1.3011 time to fit residues: 1887.0374 Evaluate side-chains 713 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 713 time to evaluate : 6.654 ------------------------------------------------------------------------------- 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: 10.0000 chunk 646 optimal weight: 20.0000 chunk 589 optimal weight: 30.0000 chunk 628 optimal weight: 7.9990 chunk 378 optimal weight: 20.0000 chunk 273 optimal weight: 7.9990 chunk 493 optimal weight: 20.0000 chunk 192 optimal weight: 5.9990 chunk 568 optimal weight: 8.9990 chunk 594 optimal weight: 5.9990 chunk 626 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** A 261 ASN B 150 GLN R 130 HIS ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.8753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 59725 Z= 0.204 Angle : 0.535 6.978 80775 Z= 0.305 Chirality : 0.045 0.372 8600 Planarity : 0.003 0.044 10200 Dihedral : 9.440 84.364 8500 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -1.85 (0.10), residues: 7000 helix: -0.72 (0.08), residues: 3775 sheet: -2.19 (0.17), residues: 875 loop : -1.39 (0.14), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP O 253 HIS 0.006 0.001 HIS X 101 PHE 0.014 0.001 PHE O 252 TYR 0.022 0.001 TYR O 290 ARG 0.010 0.001 ARG L 228 *********************** 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 884 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 884 time to evaluate : 6.803 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: A 181 ASP cc_start: 0.8815 (m-30) cc_final: 0.8547 (m-30) REVERT: C 150 GLN cc_start: 0.9278 (mt0) cc_final: 0.8904 (mt0) REVERT: C 274 TYR cc_start: 0.7390 (p90) cc_final: 0.7172 (p90) REVERT: C 329 TYR cc_start: 0.5694 (m-10) cc_final: 0.4804 (m-10) REVERT: D 149 ASP cc_start: 0.8937 (m-30) cc_final: 0.8720 (m-30) REVERT: E 79 ILE cc_start: 0.9348 (mm) cc_final: 0.9126 (tt) REVERT: F 149 ASP cc_start: 0.8900 (m-30) cc_final: 0.8600 (m-30) REVERT: F 261 ASN cc_start: 0.8734 (m-40) cc_final: 0.8476 (m-40) REVERT: G 304 MET cc_start: 0.8388 (tpp) cc_final: 0.7785 (tpp) REVERT: H 143 ASN cc_start: 0.8163 (m110) cc_final: 0.7944 (m110) REVERT: H 212 GLU cc_start: 0.8725 (pm20) cc_final: 0.8502 (pm20) REVERT: H 288 ARG cc_start: 0.5041 (ttt-90) cc_final: 0.3551 (ttp-170) REVERT: H 330 TYR cc_start: 0.6075 (t80) cc_final: 0.5651 (t80) REVERT: I 261 ASN cc_start: 0.8574 (m-40) cc_final: 0.8263 (m-40) REVERT: J 170 ASP cc_start: 0.7757 (p0) cc_final: 0.7169 (t70) REVERT: K 150 GLN cc_start: 0.9396 (mt0) cc_final: 0.9052 (mt0) REVERT: L 127 ASP cc_start: 0.8911 (p0) cc_final: 0.8480 (t0) REVERT: M 184 LYS cc_start: 0.8755 (mttt) cc_final: 0.8549 (ttpt) REVERT: M 279 MET cc_start: 0.8163 (tpp) cc_final: 0.7948 (tpp) REVERT: N 143 ASN cc_start: 0.8079 (m-40) cc_final: 0.7866 (m110) REVERT: N 149 ASP cc_start: 0.8756 (m-30) cc_final: 0.8505 (m-30) REVERT: O 62 GLN cc_start: 0.8945 (pt0) cc_final: 0.8559 (pp30) REVERT: O 150 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8632 (tp-100) REVERT: O 184 LYS cc_start: 0.8834 (mttp) cc_final: 0.8391 (ttpt) REVERT: P 143 ASN cc_start: 0.7903 (m110) cc_final: 0.7664 (m110) REVERT: P 149 ASP cc_start: 0.8800 (m-30) cc_final: 0.8486 (m-30) REVERT: R 121 GLU cc_start: 0.7303 (tt0) cc_final: 0.7067 (tp30) REVERT: R 143 ASN cc_start: 0.7942 (m110) cc_final: 0.7685 (m-40) REVERT: S 62 GLN cc_start: 0.8963 (pt0) cc_final: 0.8621 (pp30) REVERT: S 181 ASP cc_start: 0.8969 (m-30) cc_final: 0.8701 (m-30) REVERT: S 265 TYR cc_start: 0.8220 (m-80) cc_final: 0.7767 (m-10) REVERT: T 149 ASP cc_start: 0.8877 (m-30) cc_final: 0.8602 (m-30) REVERT: V 149 ASP cc_start: 0.8764 (m-30) cc_final: 0.8519 (m-30) REVERT: W 150 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8606 (tp-100) REVERT: W 321 THR cc_start: 0.7499 (p) cc_final: 0.6805 (t) REVERT: Y 150 GLN cc_start: 0.8996 (tp-100) cc_final: 0.8681 (tp-100) REVERT: Y 187 LEU cc_start: 0.8202 (mt) cc_final: 0.7912 (tt) REVERT: Y 304 MET cc_start: 0.7280 (tpp) cc_final: 0.7062 (tpp) outliers start: 0 outliers final: 0 residues processed: 884 average time/residue: 1.3153 time to fit residues: 1937.7367 Evaluate side-chains 718 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 718 time to evaluate : 6.681 ------------------------------------------------------------------------------- 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: 3.9990 chunk 664 optimal weight: 30.0000 chunk 405 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 chunk 462 optimal weight: 10.0000 chunk 697 optimal weight: 30.0000 chunk 641 optimal weight: 6.9990 chunk 555 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 428 optimal weight: 8.9990 chunk 340 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** N 130 HIS ** R 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.8949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 59725 Z= 0.190 Angle : 0.524 7.818 80775 Z= 0.298 Chirality : 0.045 0.373 8600 Planarity : 0.003 0.042 10200 Dihedral : 9.286 85.554 8500 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -0.62 (0.08), residues: 3775 sheet: -2.12 (0.18), residues: 875 loop : -1.24 (0.14), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP K 253 HIS 0.007 0.001 HIS O 176 PHE 0.029 0.001 PHE F 306 TYR 0.022 0.001 TYR O 290 ARG 0.010 0.001 ARG L 228 ********************** 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 874 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 874 time to evaluate : 6.650 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 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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: A 181 ASP cc_start: 0.8830 (m-30) cc_final: 0.8471 (m-30) REVERT: A 253 TRP cc_start: 0.5165 (t-100) cc_final: 0.4629 (t-100) REVERT: C 150 GLN cc_start: 0.9280 (mt0) cc_final: 0.8888 (mt0) REVERT: C 274 TYR cc_start: 0.7451 (p90) cc_final: 0.7226 (p90) REVERT: C 329 TYR cc_start: 0.5506 (m-10) cc_final: 0.4733 (m-10) REVERT: D 149 ASP cc_start: 0.8918 (m-30) cc_final: 0.8700 (m-30) REVERT: E 79 ILE cc_start: 0.9357 (mm) cc_final: 0.9136 (tt) REVERT: F 149 ASP cc_start: 0.8900 (m-30) cc_final: 0.8585 (m-30) REVERT: F 261 ASN cc_start: 0.8792 (m-40) cc_final: 0.8454 (m-40) REVERT: G 304 MET cc_start: 0.8393 (tpp) cc_final: 0.7904 (tpp) REVERT: H 212 GLU cc_start: 0.8679 (pm20) cc_final: 0.8459 (pm20) REVERT: H 288 ARG cc_start: 0.5060 (ttt-90) cc_final: 0.3621 (ttp-170) REVERT: H 304 MET cc_start: 0.8238 (tpp) cc_final: 0.7916 (tpp) REVERT: H 330 TYR cc_start: 0.6086 (t80) cc_final: 0.5656 (t80) REVERT: I 261 ASN cc_start: 0.8596 (m-40) cc_final: 0.8291 (m-40) REVERT: I 265 TYR cc_start: 0.8204 (m-10) cc_final: 0.7997 (m-10) REVERT: J 170 ASP cc_start: 0.7723 (p0) cc_final: 0.7210 (t70) REVERT: K 150 GLN cc_start: 0.9386 (mt0) cc_final: 0.9057 (mt0) REVERT: L 127 ASP cc_start: 0.8984 (p0) cc_final: 0.8494 (t0) REVERT: O 62 GLN cc_start: 0.8933 (pt0) cc_final: 0.8518 (pp30) REVERT: O 150 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8610 (tp-100) REVERT: P 143 ASN cc_start: 0.7911 (m110) cc_final: 0.7687 (m110) REVERT: P 149 ASP cc_start: 0.8849 (m-30) cc_final: 0.8524 (m-30) REVERT: R 121 GLU cc_start: 0.7270 (tt0) cc_final: 0.7036 (tp30) REVERT: R 143 ASN cc_start: 0.7939 (m110) cc_final: 0.7700 (m-40) REVERT: S 62 GLN cc_start: 0.8988 (pt0) cc_final: 0.8679 (pp30) REVERT: S 181 ASP cc_start: 0.8957 (m-30) cc_final: 0.8711 (m-30) REVERT: S 265 TYR cc_start: 0.8298 (m-80) cc_final: 0.7838 (m-10) REVERT: T 149 ASP cc_start: 0.8914 (m-30) cc_final: 0.8604 (m-30) REVERT: V 149 ASP cc_start: 0.8731 (m-30) cc_final: 0.8495 (m-30) REVERT: W 150 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8617 (tp-100) REVERT: W 261 ASN cc_start: 0.8036 (t0) cc_final: 0.7831 (t0) REVERT: Y 150 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8654 (tp-100) REVERT: Y 184 LYS cc_start: 0.8600 (mttt) cc_final: 0.7910 (ttpt) REVERT: Y 187 LEU cc_start: 0.8172 (mt) cc_final: 0.7864 (tt) REVERT: Y 253 TRP cc_start: 0.4446 (t-100) cc_final: 0.4245 (t-100) outliers start: 0 outliers final: 0 residues processed: 874 average time/residue: 1.3007 time to fit residues: 1885.7263 Evaluate side-chains 722 residues out of total 6250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 722 time to evaluate : 6.649 ------------------------------------------------------------------------------- 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: 7.9990 chunk 591 optimal weight: 20.0000 chunk 170 optimal weight: 7.9990 chunk 512 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 154 optimal weight: 7.9990 chunk 556 optimal weight: 30.0000 chunk 232 optimal weight: 20.0000 chunk 571 optimal weight: 30.0000 chunk 70 optimal weight: 0.0070 chunk 102 optimal weight: 4.9990 overall best weight: 5.8006 ------------------------------------------------------------------------------- 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** P 130 HIS ** T 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 118 ASN ** U 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 130 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.079970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068340 restraints weight = 910987.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.071116 restraints weight = 488315.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.072987 restraints weight = 306079.254| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.9137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 59725 Z= 0.178 Angle : 0.516 7.081 80775 Z= 0.293 Chirality : 0.045 0.373 8600 Planarity : 0.003 0.039 10200 Dihedral : 9.119 87.261 8500 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -1.54 (0.10), residues: 7000 helix: -0.51 (0.08), residues: 3775 sheet: -2.17 (0.18), residues: 900 loop : -1.07 (0.14), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP K 253 HIS 0.005 0.001 HIS Q 176 PHE 0.026 0.001 PHE F 245 TYR 0.023 0.001 TYR B 290 ARG 0.010 0.001 ARG L 228 =============================================================================== Job complete usr+sys time: 29224.71 seconds wall clock time: 503 minutes 47.80 seconds (30227.80 seconds total)