Starting phenix.real_space_refine (version: dev) on Mon Dec 19 20:39:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7k_22701/12_2022/7k7k_22701_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7k_22701/12_2022/7k7k_22701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7k_22701/12_2022/7k7k_22701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7k_22701/12_2022/7k7k_22701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7k_22701/12_2022/7k7k_22701_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k7k_22701/12_2022/7k7k_22701_neut.pdb" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 30": "OD1" <-> "OD2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "F ASP 30": "OD1" <-> "OD2" Residue "F PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "G ASP 30": "OD1" <-> "OD2" Residue "G PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 159": "OE1" <-> "OE2" Residue "H ASP 30": "OD1" <-> "OD2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H GLU 159": "OE1" <-> "OE2" Residue "I ASP 30": "OD1" <-> "OD2" Residue "I PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 73": "OE1" <-> "OE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "J ASP 30": "OD1" <-> "OD2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "J GLU 159": "OE1" <-> "OE2" Residue "K ASP 30": "OD1" <-> "OD2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "K GLU 159": "OE1" <-> "OE2" Residue "L ASP 30": "OD1" <-> "OD2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 159": "OE1" <-> "OE2" Residue "M ASP 30": "OD1" <-> "OD2" Residue "M PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M GLU 106": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "N ASP 30": "OD1" <-> "OD2" Residue "N PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "N GLU 106": "OE1" <-> "OE2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "O ASP 30": "OD1" <-> "OD2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 73": "OE1" <-> "OE2" Residue "O GLU 106": "OE1" <-> "OE2" Residue "O GLU 159": "OE1" <-> "OE2" Residue "P ASP 30": "OD1" <-> "OD2" Residue "P PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 73": "OE1" <-> "OE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "P GLU 159": "OE1" <-> "OE2" Residue "Q ASP 30": "OD1" <-> "OD2" Residue "Q PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q GLU 159": "OE1" <-> "OE2" Residue "R ASP 30": "OD1" <-> "OD2" Residue "R PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R GLU 159": "OE1" <-> "OE2" Residue "S ASP 30": "OD1" <-> "OD2" Residue "S PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S GLU 106": "OE1" <-> "OE2" Residue "S GLU 159": "OE1" <-> "OE2" Residue "T ASP 30": "OD1" <-> "OD2" Residue "T PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 106": "OE1" <-> "OE2" Residue "T GLU 159": "OE1" <-> "OE2" Residue "U ASP 30": "OD1" <-> "OD2" Residue "U PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 73": "OE1" <-> "OE2" Residue "U GLU 106": "OE1" <-> "OE2" Residue "U GLU 159": "OE1" <-> "OE2" Residue "V ASP 30": "OD1" <-> "OD2" Residue "V PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "V GLU 106": "OE1" <-> "OE2" Residue "V GLU 159": "OE1" <-> "OE2" Residue "W ASP 30": "OD1" <-> "OD2" Residue "W PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 73": "OE1" <-> "OE2" Residue "W GLU 106": "OE1" <-> "OE2" Residue "W GLU 159": "OE1" <-> "OE2" Residue "X ASP 30": "OD1" <-> "OD2" Residue "X PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X GLU 106": "OE1" <-> "OE2" Residue "X GLU 159": "OE1" <-> "OE2" Residue "Y ASP 30": "OD1" <-> "OD2" Residue "Y PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 73": "OE1" <-> "OE2" Residue "Y GLU 106": "OE1" <-> "OE2" Residue "Y GLU 159": "OE1" <-> "OE2" Residue "Z ASP 30": "OD1" <-> "OD2" Residue "Z PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 73": "OE1" <-> "OE2" Residue "Z GLU 106": "OE1" <-> "OE2" Residue "Z GLU 159": "OE1" <-> "OE2" Residue "a ASP 30": "OD1" <-> "OD2" Residue "a PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 73": "OE1" <-> "OE2" Residue "a GLU 106": "OE1" <-> "OE2" Residue "a GLU 159": "OE1" <-> "OE2" Residue "b ASP 30": "OD1" <-> "OD2" Residue "b PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 73": "OE1" <-> "OE2" Residue "b GLU 106": "OE1" <-> "OE2" Residue "b GLU 159": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 36204 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "B" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "C" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "D" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "E" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "F" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "H" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "I" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "J" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "K" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "L" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "M" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "N" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "O" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "P" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "Q" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "R" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "S" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "T" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "U" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "V" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "W" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "X" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "Y" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "Z" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "a" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "b" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1293 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Time building chain proxies: 19.20, per 1000 atoms: 0.53 Number of scatterers: 36204 At special positions: 0 Unit cell: (127.75, 127.75, 231, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 7588 8.00 N 6104 7.00 C 22316 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.55 Conformation dependent library (CDL) restraints added in 5.6 seconds 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9184 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 0 sheets defined 73.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 76 removed outlier: 3.730A pdb=" N ASP A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.541A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 144 through 147' Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 140 " --> pdb=" O GLN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN B 147 " --> pdb=" O ALA B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 147' Processing helix chain 'B' and resid 149 through 156 Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.992A pdb=" N THR B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 167 " --> pdb=" O MET B 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 76 removed outlier: 3.732A pdb=" N ASP C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 140 " --> pdb=" O GLN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN C 147 " --> pdb=" O ALA C 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 144 through 147' Processing helix chain 'C' and resid 149 through 156 Processing helix chain 'C' and resid 157 through 186 removed outlier: 3.994A pdb=" N THR C 166 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN D 147 " --> pdb=" O ALA D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 147' Processing helix chain 'D' and resid 149 through 156 Processing helix chain 'D' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR D 166 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 185 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS E 38 " --> pdb=" O ASP E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 140 " --> pdb=" O GLN E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 removed outlier: 3.717A pdb=" N ASN E 147 " --> pdb=" O ALA E 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 144 through 147' Processing helix chain 'E' and resid 149 through 156 Processing helix chain 'E' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR E 166 " --> pdb=" O GLN E 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 185 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 removed outlier: 3.946A pdb=" N LYS F 38 " --> pdb=" O ASP F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 76 removed outlier: 3.732A pdb=" N ASP F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR F 76 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU F 83 " --> pdb=" O LYS F 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 140 " --> pdb=" O GLN F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN F 147 " --> pdb=" O ALA F 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 144 through 147' Processing helix chain 'F' and resid 149 through 156 Processing helix chain 'F' and resid 157 through 186 removed outlier: 3.994A pdb=" N THR F 166 " --> pdb=" O GLN F 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU F 167 " --> pdb=" O MET F 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER F 179 " --> pdb=" O SER F 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR F 182 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 185 " --> pdb=" O GLN F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.946A pdb=" N LYS G 38 " --> pdb=" O ASP G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 76 removed outlier: 3.732A pdb=" N ASP G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU G 83 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 109 Processing helix chain 'G' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA G 140 " --> pdb=" O GLN G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 147 removed outlier: 3.717A pdb=" N ASN G 147 " --> pdb=" O ALA G 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 144 through 147' Processing helix chain 'G' and resid 149 through 156 Processing helix chain 'G' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG G 174 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER G 179 " --> pdb=" O SER G 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G 185 " --> pdb=" O GLN G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS H 38 " --> pdb=" O ASP H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP H 66 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU H 83 " --> pdb=" O LYS H 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 109 Processing helix chain 'H' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS H 139 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA H 140 " --> pdb=" O GLN H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN H 147 " --> pdb=" O ALA H 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 144 through 147' Processing helix chain 'H' and resid 149 through 156 Processing helix chain 'H' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU H 167 " --> pdb=" O MET H 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG H 174 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER H 179 " --> pdb=" O SER H 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR H 182 " --> pdb=" O GLN H 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE H 185 " --> pdb=" O GLN H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS I 38 " --> pdb=" O ASP I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR I 76 " --> pdb=" O LYS I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 92 removed outlier: 3.541A pdb=" N LEU I 83 " --> pdb=" O LYS I 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS I 87 " --> pdb=" O LEU I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 109 Processing helix chain 'I' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS I 139 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA I 140 " --> pdb=" O GLN I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 147 removed outlier: 3.717A pdb=" N ASN I 147 " --> pdb=" O ALA I 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 144 through 147' Processing helix chain 'I' and resid 149 through 156 Processing helix chain 'I' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR I 166 " --> pdb=" O GLN I 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU I 167 " --> pdb=" O MET I 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG I 174 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR I 182 " --> pdb=" O GLN I 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS J 38 " --> pdb=" O ASP J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 76 removed outlier: 3.732A pdb=" N ASP J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR J 76 " --> pdb=" O LYS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU J 83 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 109 Processing helix chain 'J' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS J 139 " --> pdb=" O LEU J 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA J 140 " --> pdb=" O GLN J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN J 147 " --> pdb=" O ALA J 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 144 through 147' Processing helix chain 'J' and resid 149 through 156 Processing helix chain 'J' and resid 157 through 186 removed outlier: 3.994A pdb=" N THR J 166 " --> pdb=" O GLN J 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG J 174 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP J 176 " --> pdb=" O SER J 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER J 179 " --> pdb=" O SER J 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR J 182 " --> pdb=" O GLN J 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE J 185 " --> pdb=" O GLN J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 40 removed outlier: 3.946A pdb=" N LYS K 38 " --> pdb=" O ASP K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU K 83 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS K 87 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 Processing helix chain 'K' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS K 139 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA K 140 " --> pdb=" O GLN K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN K 147 " --> pdb=" O ALA K 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 144 through 147' Processing helix chain 'K' and resid 149 through 156 Processing helix chain 'K' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR K 166 " --> pdb=" O GLN K 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU K 167 " --> pdb=" O MET K 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG K 174 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER K 179 " --> pdb=" O SER K 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE K 185 " --> pdb=" O GLN K 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS L 38 " --> pdb=" O ASP L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER L 74 " --> pdb=" O ALA L 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR L 76 " --> pdb=" O LYS L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU L 83 " --> pdb=" O LYS L 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS L 87 " --> pdb=" O LEU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 Processing helix chain 'L' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS L 139 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA L 140 " --> pdb=" O GLN L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 147 removed outlier: 3.717A pdb=" N ASN L 147 " --> pdb=" O ALA L 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 144 through 147' Processing helix chain 'L' and resid 149 through 156 Processing helix chain 'L' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR L 166 " --> pdb=" O GLN L 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU L 167 " --> pdb=" O MET L 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG L 174 " --> pdb=" O LEU L 170 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP L 176 " --> pdb=" O SER L 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER L 179 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR L 182 " --> pdb=" O GLN L 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE L 185 " --> pdb=" O GLN L 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 40 removed outlier: 3.946A pdb=" N LYS M 38 " --> pdb=" O ASP M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER M 74 " --> pdb=" O ALA M 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR M 76 " --> pdb=" O LYS M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 92 removed outlier: 3.541A pdb=" N LEU M 83 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS M 87 " --> pdb=" O LEU M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 109 Processing helix chain 'M' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS M 139 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA M 140 " --> pdb=" O GLN M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN M 147 " --> pdb=" O ALA M 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 144 through 147' Processing helix chain 'M' and resid 149 through 156 Processing helix chain 'M' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR M 166 " --> pdb=" O GLN M 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU M 167 " --> pdb=" O MET M 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG M 174 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP M 176 " --> pdb=" O SER M 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER M 179 " --> pdb=" O SER M 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR M 182 " --> pdb=" O GLN M 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE M 185 " --> pdb=" O GLN M 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 40 removed outlier: 3.946A pdb=" N LYS N 38 " --> pdb=" O ASP N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 76 removed outlier: 3.730A pdb=" N ASP N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER N 74 " --> pdb=" O ALA N 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR N 76 " --> pdb=" O LYS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU N 83 " --> pdb=" O LYS N 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 109 Processing helix chain 'N' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS N 139 " --> pdb=" O LEU N 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA N 140 " --> pdb=" O GLN N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN N 147 " --> pdb=" O ALA N 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 144 through 147' Processing helix chain 'N' and resid 149 through 156 Processing helix chain 'N' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR N 166 " --> pdb=" O GLN N 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU N 167 " --> pdb=" O MET N 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP N 176 " --> pdb=" O SER N 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER N 179 " --> pdb=" O SER N 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE N 185 " --> pdb=" O GLN N 181 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS O 38 " --> pdb=" O ASP O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 76 removed outlier: 3.732A pdb=" N ASP O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR O 76 " --> pdb=" O LYS O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU O 83 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 109 Processing helix chain 'O' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS O 139 " --> pdb=" O LEU O 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA O 140 " --> pdb=" O GLN O 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN O 147 " --> pdb=" O ALA O 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 144 through 147' Processing helix chain 'O' and resid 149 through 156 Processing helix chain 'O' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR O 166 " --> pdb=" O GLN O 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU O 167 " --> pdb=" O MET O 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG O 174 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP O 176 " --> pdb=" O SER O 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER O 179 " --> pdb=" O SER O 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR O 182 " --> pdb=" O GLN O 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE O 185 " --> pdb=" O GLN O 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 40 removed outlier: 3.946A pdb=" N LYS P 38 " --> pdb=" O ASP P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 76 removed outlier: 3.732A pdb=" N ASP P 66 " --> pdb=" O ALA P 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER P 74 " --> pdb=" O ALA P 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR P 76 " --> pdb=" O LYS P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU P 83 " --> pdb=" O LYS P 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 109 Processing helix chain 'P' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA P 140 " --> pdb=" O GLN P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN P 147 " --> pdb=" O ALA P 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 144 through 147' Processing helix chain 'P' and resid 149 through 156 Processing helix chain 'P' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR P 166 " --> pdb=" O GLN P 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU P 167 " --> pdb=" O MET P 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG P 174 " --> pdb=" O LEU P 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP P 176 " --> pdb=" O SER P 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER P 179 " --> pdb=" O SER P 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR P 182 " --> pdb=" O GLN P 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE P 185 " --> pdb=" O GLN P 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS Q 38 " --> pdb=" O ASP Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 76 removed outlier: 3.732A pdb=" N ASP Q 66 " --> pdb=" O ALA Q 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER Q 74 " --> pdb=" O ALA Q 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR Q 76 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU Q 83 " --> pdb=" O LYS Q 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 109 Processing helix chain 'Q' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS Q 139 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA Q 140 " --> pdb=" O GLN Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN Q 147 " --> pdb=" O ALA Q 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 144 through 147' Processing helix chain 'Q' and resid 149 through 156 Processing helix chain 'Q' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR Q 166 " --> pdb=" O GLN Q 162 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU Q 167 " --> pdb=" O MET Q 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG Q 174 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP Q 176 " --> pdb=" O SER Q 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER Q 179 " --> pdb=" O SER Q 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR Q 182 " --> pdb=" O GLN Q 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE Q 185 " --> pdb=" O GLN Q 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS R 38 " --> pdb=" O ASP R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER R 74 " --> pdb=" O ALA R 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 92 removed outlier: 3.541A pdb=" N LEU R 83 " --> pdb=" O LYS R 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS R 87 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 109 Processing helix chain 'R' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS R 139 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA R 140 " --> pdb=" O GLN R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN R 147 " --> pdb=" O ALA R 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 144 through 147' Processing helix chain 'R' and resid 149 through 156 Processing helix chain 'R' and resid 157 through 186 removed outlier: 3.994A pdb=" N THR R 166 " --> pdb=" O GLN R 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU R 167 " --> pdb=" O MET R 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG R 174 " --> pdb=" O LEU R 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP R 176 " --> pdb=" O SER R 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER R 179 " --> pdb=" O SER R 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR R 182 " --> pdb=" O GLN R 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE R 185 " --> pdb=" O GLN R 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP S 66 " --> pdb=" O ALA S 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER S 74 " --> pdb=" O ALA S 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR S 76 " --> pdb=" O LYS S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU S 83 " --> pdb=" O LYS S 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS S 87 " --> pdb=" O LEU S 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 109 Processing helix chain 'S' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS S 139 " --> pdb=" O LEU S 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA S 140 " --> pdb=" O GLN S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN S 147 " --> pdb=" O ALA S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 144 through 147' Processing helix chain 'S' and resid 149 through 156 Processing helix chain 'S' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR S 166 " --> pdb=" O GLN S 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU S 167 " --> pdb=" O MET S 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG S 174 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP S 176 " --> pdb=" O SER S 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER S 179 " --> pdb=" O SER S 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR S 182 " --> pdb=" O GLN S 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE S 185 " --> pdb=" O GLN S 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS T 38 " --> pdb=" O ASP T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP T 66 " --> pdb=" O ALA T 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER T 74 " --> pdb=" O ALA T 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR T 76 " --> pdb=" O LYS T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 92 removed outlier: 3.541A pdb=" N LEU T 83 " --> pdb=" O LYS T 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS T 87 " --> pdb=" O LEU T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 109 Processing helix chain 'T' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS T 139 " --> pdb=" O LEU T 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA T 140 " --> pdb=" O GLN T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN T 147 " --> pdb=" O ALA T 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 144 through 147' Processing helix chain 'T' and resid 149 through 156 Processing helix chain 'T' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR T 166 " --> pdb=" O GLN T 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU T 167 " --> pdb=" O MET T 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG T 174 " --> pdb=" O LEU T 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP T 176 " --> pdb=" O SER T 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER T 179 " --> pdb=" O SER T 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR T 182 " --> pdb=" O GLN T 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE T 185 " --> pdb=" O GLN T 181 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS U 38 " --> pdb=" O ASP U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP U 66 " --> pdb=" O ALA U 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER U 74 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR U 76 " --> pdb=" O LYS U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU U 83 " --> pdb=" O LYS U 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS U 87 " --> pdb=" O LEU U 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 109 Processing helix chain 'U' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS U 139 " --> pdb=" O LEU U 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA U 140 " --> pdb=" O GLN U 136 " (cutoff:3.500A) Processing helix chain 'U' and resid 144 through 147 removed outlier: 3.717A pdb=" N ASN U 147 " --> pdb=" O ALA U 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 144 through 147' Processing helix chain 'U' and resid 149 through 156 Processing helix chain 'U' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR U 166 " --> pdb=" O GLN U 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU U 167 " --> pdb=" O MET U 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG U 174 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP U 176 " --> pdb=" O SER U 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER U 179 " --> pdb=" O SER U 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR U 182 " --> pdb=" O GLN U 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE U 185 " --> pdb=" O GLN U 181 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS V 38 " --> pdb=" O ASP V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP V 66 " --> pdb=" O ALA V 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER V 74 " --> pdb=" O ALA V 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR V 76 " --> pdb=" O LYS V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU V 83 " --> pdb=" O LYS V 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 104 through 109 Processing helix chain 'V' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS V 139 " --> pdb=" O LEU V 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA V 140 " --> pdb=" O GLN V 136 " (cutoff:3.500A) Processing helix chain 'V' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN V 147 " --> pdb=" O ALA V 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 144 through 147' Processing helix chain 'V' and resid 149 through 156 Processing helix chain 'V' and resid 157 through 186 removed outlier: 3.992A pdb=" N THR V 166 " --> pdb=" O GLN V 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU V 167 " --> pdb=" O MET V 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP V 176 " --> pdb=" O SER V 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER V 179 " --> pdb=" O SER V 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR V 182 " --> pdb=" O GLN V 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE V 185 " --> pdb=" O GLN V 181 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS W 38 " --> pdb=" O ASP W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP W 66 " --> pdb=" O ALA W 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER W 74 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR W 76 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU W 83 " --> pdb=" O LYS W 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 109 Processing helix chain 'W' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS W 139 " --> pdb=" O LEU W 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA W 140 " --> pdb=" O GLN W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN W 147 " --> pdb=" O ALA W 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 144 through 147' Processing helix chain 'W' and resid 149 through 156 Processing helix chain 'W' and resid 157 through 186 removed outlier: 3.992A pdb=" N THR W 166 " --> pdb=" O GLN W 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU W 167 " --> pdb=" O MET W 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP W 176 " --> pdb=" O SER W 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER W 179 " --> pdb=" O SER W 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR W 182 " --> pdb=" O GLN W 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE W 185 " --> pdb=" O GLN W 181 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS X 38 " --> pdb=" O ASP X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 76 removed outlier: 3.732A pdb=" N ASP X 66 " --> pdb=" O ALA X 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR X 76 " --> pdb=" O LYS X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU X 83 " --> pdb=" O LYS X 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS X 87 " --> pdb=" O LEU X 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 104 through 109 Processing helix chain 'X' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS X 139 " --> pdb=" O LEU X 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA X 140 " --> pdb=" O GLN X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN X 147 " --> pdb=" O ALA X 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 144 through 147' Processing helix chain 'X' and resid 149 through 156 Processing helix chain 'X' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR X 166 " --> pdb=" O GLN X 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU X 167 " --> pdb=" O MET X 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG X 174 " --> pdb=" O LEU X 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP X 176 " --> pdb=" O SER X 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER X 179 " --> pdb=" O SER X 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR X 182 " --> pdb=" O GLN X 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE X 185 " --> pdb=" O GLN X 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 40 removed outlier: 3.946A pdb=" N LYS Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 76 removed outlier: 3.730A pdb=" N ASP Y 66 " --> pdb=" O ALA Y 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER Y 74 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR Y 76 " --> pdb=" O LYS Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 76 through 92 removed outlier: 3.541A pdb=" N LEU Y 83 " --> pdb=" O LYS Y 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS Y 87 " --> pdb=" O LEU Y 83 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 109 Processing helix chain 'Y' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS Y 139 " --> pdb=" O LEU Y 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA Y 140 " --> pdb=" O GLN Y 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN Y 147 " --> pdb=" O ALA Y 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 144 through 147' Processing helix chain 'Y' and resid 149 through 156 Processing helix chain 'Y' and resid 157 through 186 removed outlier: 3.994A pdb=" N THR Y 166 " --> pdb=" O GLN Y 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU Y 167 " --> pdb=" O MET Y 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN Y 168 " --> pdb=" O SER Y 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG Y 174 " --> pdb=" O LEU Y 170 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP Y 176 " --> pdb=" O SER Y 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER Y 179 " --> pdb=" O SER Y 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR Y 182 " --> pdb=" O GLN Y 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE Y 185 " --> pdb=" O GLN Y 181 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 40 removed outlier: 3.944A pdb=" N LYS Z 38 " --> pdb=" O ASP Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP Z 66 " --> pdb=" O ALA Z 62 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR Z 76 " --> pdb=" O LYS Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 92 removed outlier: 3.542A pdb=" N LEU Z 83 " --> pdb=" O LYS Z 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 109 Processing helix chain 'Z' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS Z 139 " --> pdb=" O LEU Z 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA Z 140 " --> pdb=" O GLN Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN Z 147 " --> pdb=" O ALA Z 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 144 through 147' Processing helix chain 'Z' and resid 149 through 156 Processing helix chain 'Z' and resid 157 through 186 removed outlier: 3.992A pdb=" N THR Z 166 " --> pdb=" O GLN Z 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU Z 167 " --> pdb=" O MET Z 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN Z 168 " --> pdb=" O SER Z 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG Z 174 " --> pdb=" O LEU Z 170 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP Z 176 " --> pdb=" O SER Z 172 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER Z 179 " --> pdb=" O SER Z 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR Z 182 " --> pdb=" O GLN Z 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE Z 185 " --> pdb=" O GLN Z 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 40 removed outlier: 3.945A pdb=" N LYS a 38 " --> pdb=" O ASP a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP a 66 " --> pdb=" O ALA a 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER a 74 " --> pdb=" O ALA a 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR a 76 " --> pdb=" O LYS a 72 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 92 removed outlier: 3.541A pdb=" N LEU a 83 " --> pdb=" O LYS a 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS a 87 " --> pdb=" O LEU a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 109 Processing helix chain 'a' and resid 134 through 143 removed outlier: 3.704A pdb=" N LYS a 139 " --> pdb=" O LEU a 135 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA a 140 " --> pdb=" O GLN a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN a 147 " --> pdb=" O ALA a 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 144 through 147' Processing helix chain 'a' and resid 149 through 156 Processing helix chain 'a' and resid 157 through 186 removed outlier: 3.993A pdb=" N THR a 166 " --> pdb=" O GLN a 162 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU a 167 " --> pdb=" O MET a 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN a 168 " --> pdb=" O SER a 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG a 174 " --> pdb=" O LEU a 170 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP a 176 " --> pdb=" O SER a 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER a 179 " --> pdb=" O SER a 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR a 182 " --> pdb=" O GLN a 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE a 185 " --> pdb=" O GLN a 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 40 removed outlier: 3.946A pdb=" N LYS b 38 " --> pdb=" O ASP b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 76 removed outlier: 3.731A pdb=" N ASP b 66 " --> pdb=" O ALA b 62 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER b 74 " --> pdb=" O ALA b 70 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 92 removed outlier: 3.543A pdb=" N LEU b 83 " --> pdb=" O LYS b 79 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS b 87 " --> pdb=" O LEU b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 109 Processing helix chain 'b' and resid 134 through 143 removed outlier: 3.703A pdb=" N LYS b 139 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA b 140 " --> pdb=" O GLN b 136 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 147 removed outlier: 3.716A pdb=" N ASN b 147 " --> pdb=" O ALA b 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 144 through 147' Processing helix chain 'b' and resid 149 through 156 Processing helix chain 'b' and resid 157 through 186 removed outlier: 3.994A pdb=" N THR b 166 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU b 167 " --> pdb=" O MET b 163 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN b 168 " --> pdb=" O SER b 164 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG b 174 " --> pdb=" O LEU b 170 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP b 176 " --> pdb=" O SER b 172 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER b 179 " --> pdb=" O SER b 175 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR b 182 " --> pdb=" O GLN b 178 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE b 185 " --> pdb=" O GLN b 181 " (cutoff:3.500A) 2156 hydrogen bonds defined for protein. 6468 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: 11.17 Time building geometry restraints manager: 15.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12241 1.34 - 1.45: 5336 1.45 - 1.57: 18515 1.57 - 1.69: 0 1.69 - 1.81: 392 Bond restraints: 36484 Sorted by residual: bond pdb=" CB GLN G 181 " pdb=" CG GLN G 181 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.14e+00 bond pdb=" CB GLN Q 181 " pdb=" CG GLN Q 181 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CB GLN C 181 " pdb=" CG GLN C 181 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CB GLN V 181 " pdb=" CG GLN V 181 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CB GLN W 181 " pdb=" CG GLN W 181 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.09e+00 ... (remaining 36479 not shown) Histogram of bond angle deviations from ideal: 100.08 - 105.82: 409 105.82 - 111.55: 15994 111.55 - 117.29: 9397 117.29 - 123.02: 22140 123.02 - 128.76: 1340 Bond angle restraints: 49280 Sorted by residual: angle pdb=" C SER A 121 " pdb=" N GLY A 122 " pdb=" CA GLY A 122 " ideal model delta sigma weight residual 121.41 127.38 -5.97 1.96e+00 2.60e-01 9.28e+00 angle pdb=" C SER Y 121 " pdb=" N GLY Y 122 " pdb=" CA GLY Y 122 " ideal model delta sigma weight residual 121.41 127.37 -5.96 1.96e+00 2.60e-01 9.26e+00 angle pdb=" C SER V 121 " pdb=" N GLY V 122 " pdb=" CA GLY V 122 " ideal model delta sigma weight residual 121.41 127.36 -5.95 1.96e+00 2.60e-01 9.21e+00 angle pdb=" C SER B 121 " pdb=" N GLY B 122 " pdb=" CA GLY B 122 " ideal model delta sigma weight residual 121.41 127.35 -5.94 1.96e+00 2.60e-01 9.17e+00 angle pdb=" C SER O 121 " pdb=" N GLY O 122 " pdb=" CA GLY O 122 " ideal model delta sigma weight residual 121.41 127.34 -5.93 1.96e+00 2.60e-01 9.16e+00 ... (remaining 49275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 19399 16.08 - 32.16: 2693 32.16 - 48.23: 504 48.23 - 64.31: 56 64.31 - 80.39: 112 Dihedral angle restraints: 22764 sinusoidal: 8680 harmonic: 14084 Sorted by residual: dihedral pdb=" CA GLY L 122 " pdb=" C GLY L 122 " pdb=" N ILE L 123 " pdb=" CA ILE L 123 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY O 122 " pdb=" C GLY O 122 " pdb=" N ILE O 123 " pdb=" CA ILE O 123 " ideal model delta harmonic sigma weight residual -180.00 -156.40 -23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLY I 122 " pdb=" C GLY I 122 " pdb=" N ILE I 123 " pdb=" CA ILE I 123 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 22761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2534 0.031 - 0.061: 2186 0.061 - 0.092: 816 0.092 - 0.122: 316 0.122 - 0.153: 56 Chirality restraints: 5908 Sorted by residual: chirality pdb=" CA ILE U 120 " pdb=" N ILE U 120 " pdb=" C ILE U 120 " pdb=" CB ILE U 120 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE Q 120 " pdb=" N ILE Q 120 " pdb=" C ILE Q 120 " pdb=" CB ILE Q 120 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE W 120 " pdb=" N ILE W 120 " pdb=" C ILE W 120 " pdb=" CB ILE W 120 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 5905 not shown) Planarity restraints: 6468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 113 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.32e+00 pdb=" N PRO B 114 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 114 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 114 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Z 113 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO Z 114 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO Z 114 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO Z 114 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP P 113 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO P 114 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO P 114 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO P 114 " 0.033 5.00e-02 4.00e+02 ... (remaining 6465 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 203 2.44 - 3.06: 21689 3.06 - 3.67: 53868 3.67 - 4.29: 77477 4.29 - 4.90: 124112 Nonbonded interactions: 277349 Sorted by model distance: nonbonded pdb=" CD LYS E 72 " pdb=" O LEU X 24 " model vdw 1.827 3.440 nonbonded pdb=" O LEU A 24 " pdb=" CD LYS F 72 " model vdw 1.827 3.440 nonbonded pdb=" O LEU E 24 " pdb=" CD LYS J 72 " model vdw 1.827 3.440 nonbonded pdb=" O LEU H 24 " pdb=" CD LYS M 72 " model vdw 1.827 3.440 nonbonded pdb=" O LEU Q 24 " pdb=" CD LYS V 72 " model vdw 1.828 3.440 ... (remaining 277344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 22316 2.51 5 N 6104 2.21 5 O 7588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.860 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.340 Process input model: 86.560 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 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 : 0.009 0.051 36484 Z= 0.571 Angle : 0.920 5.971 49280 Z= 0.521 Chirality : 0.049 0.153 5908 Planarity : 0.006 0.058 6468 Dihedral : 15.869 80.388 13580 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.33 (0.08), residues: 4732 helix: -4.26 (0.04), residues: 3444 sheet: None (None), residues: 0 loop : -3.17 (0.15), residues: 1288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2482 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 2426 time to evaluate : 4.224 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 outliers start: 56 outliers final: 37 residues processed: 2452 average time/residue: 0.4315 time to fit residues: 1764.3705 Evaluate side-chains 1925 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1888 time to evaluate : 4.329 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3178 time to fit residues: 28.5825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 401 optimal weight: 0.2980 chunk 360 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 373 optimal weight: 0.7980 chunk 144 optimal weight: 0.0270 chunk 226 optimal weight: 0.8980 chunk 277 optimal weight: 0.5980 chunk 432 optimal weight: 9.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 178 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 GLN ** C 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 127 ASN D 43 GLN D 82 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 181 GLN E 43 GLN E 82 ASN E 155 ASN E 162 GLN F 82 ASN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 168 ASN ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN J 56 GLN J 127 ASN J 155 ASN J 168 ASN K 43 GLN K 68 ASN ** K 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 ASN K 168 ASN L 54 GLN L 92 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 ASN L 161 GLN L 162 GLN ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN M 78 GLN ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 ASN ** M 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 GLN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 ASN P 157 GLN Q 43 GLN Q 68 ASN Q 78 GLN Q 154 ASN Q 162 GLN R 68 ASN ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 161 GLN ** R 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 ASN ** S 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 GLN V 68 ASN ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 127 ASN V 154 ASN V 168 ASN W 68 ASN W 78 GLN X 68 ASN Y 56 GLN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 125 ASN ** Y 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 154 ASN Z 181 GLN ** a 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 161 GLN a 165 ASN b 56 GLN ** b 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 154 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 36484 Z= 0.187 Angle : 0.663 7.955 49280 Z= 0.355 Chirality : 0.038 0.173 5908 Planarity : 0.005 0.059 6468 Dihedral : 7.984 78.849 5012 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 4.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.10), residues: 4732 helix: -1.79 (0.07), residues: 3416 sheet: None (None), residues: 0 loop : -2.67 (0.16), residues: 1316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2424 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 2223 time to evaluate : 4.138 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 outliers start: 201 outliers final: 113 residues processed: 2284 average time/residue: 0.4310 time to fit residues: 1620.4646 Evaluate side-chains 2085 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1972 time to evaluate : 4.154 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 0 residues processed: 113 average time/residue: 0.3123 time to fit residues: 72.7067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 240 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 359 optimal weight: 0.6980 chunk 294 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 433 optimal weight: 2.9990 chunk 467 optimal weight: 5.9990 chunk 385 optimal weight: 6.9990 chunk 429 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 347 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN C 43 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN C 162 GLN C 168 ASN C 178 GLN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN E 178 GLN E 181 GLN F 127 ASN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 GLN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN H 168 ASN I 43 GLN ** I 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN I 148 ASN J 56 GLN ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN K 78 GLN K 92 GLN K 162 GLN L 54 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 ASN L 162 GLN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN M 154 ASN M 168 ASN N 82 ASN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 ASN N 165 ASN O 43 GLN O 68 ASN O 78 GLN O 168 ASN ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 ASN P 155 ASN P 157 GLN ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 78 GLN Q 136 GLN Q 154 ASN R 43 GLN R 56 GLN ** R 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 ASN R 162 GLN R 168 ASN ** S 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 GLN ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 ASN T 154 ASN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 162 GLN V 56 GLN V 68 ASN V 78 GLN ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 178 GLN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN Y 165 ASN Z 56 GLN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 78 GLN ** a 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 125 ASN a 127 ASN a 154 ASN a 155 ASN a 165 ASN a 168 ASN ** b 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 36484 Z= 0.259 Angle : 0.655 7.349 49280 Z= 0.346 Chirality : 0.040 0.183 5908 Planarity : 0.004 0.070 6468 Dihedral : 7.738 89.282 5012 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer Outliers : 5.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.12), residues: 4732 helix: -0.36 (0.08), residues: 3416 sheet: None (None), residues: 0 loop : -2.55 (0.17), residues: 1316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2208 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1983 time to evaluate : 4.630 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 outliers start: 225 outliers final: 140 residues processed: 2059 average time/residue: 0.4476 time to fit residues: 1505.9903 Evaluate side-chains 2002 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1862 time to evaluate : 3.947 Switching outliers to nearest non-outliers outliers start: 140 outliers final: 0 residues processed: 140 average time/residue: 0.3262 time to fit residues: 91.6519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 427 optimal weight: 1.9990 chunk 325 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 434 optimal weight: 6.9990 chunk 460 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 411 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 181 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 168 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN E 92 GLN ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 ASN I 68 ASN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 102 GLN ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN K 127 ASN L 54 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 ASN ** M 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN M 92 GLN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 ASN N 56 GLN N 68 ASN ** N 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 GLN O 68 ASN O 162 GLN ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN P 178 GLN Q 68 ASN Q 78 GLN ** R 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 GLN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 43 GLN S 68 ASN S 78 GLN S 154 ASN T 68 ASN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 78 GLN ** U 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 ASN U 162 GLN V 56 GLN V 68 ASN ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 ASN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 ASN Z 56 GLN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 68 ASN a 148 ASN a 155 ASN ** b 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 ASN b 168 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 36484 Z= 0.198 Angle : 0.614 9.033 49280 Z= 0.321 Chirality : 0.039 0.193 5908 Planarity : 0.004 0.066 6468 Dihedral : 7.555 87.476 5012 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 4732 helix: 0.32 (0.09), residues: 3416 sheet: None (None), residues: 0 loop : -2.50 (0.16), residues: 1316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2115 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1952 time to evaluate : 4.101 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 outliers start: 163 outliers final: 101 residues processed: 2005 average time/residue: 0.4451 time to fit residues: 1456.8255 Evaluate side-chains 1947 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1846 time to evaluate : 4.116 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 0 residues processed: 101 average time/residue: 0.2974 time to fit residues: 63.5459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 383 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 342 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 392 optimal weight: 0.8980 chunk 318 optimal weight: 0.0170 chunk 0 optimal weight: 7.9990 chunk 234 optimal weight: 0.4980 chunk 412 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN E 92 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN F 92 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN L 54 GLN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 GLN N 82 ASN ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 ASN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN R 56 GLN R 68 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 GLN S 154 ASN S 162 GLN T 68 ASN T 168 ASN U 68 ASN U 78 GLN ** U 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 ASN ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 ASN W 78 GLN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 ASN Z 56 GLN ** Z 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN a 168 ASN b 56 GLN ** b 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 165 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 36484 Z= 0.170 Angle : 0.603 8.283 49280 Z= 0.312 Chirality : 0.038 0.204 5908 Planarity : 0.004 0.066 6468 Dihedral : 7.417 88.688 5012 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 4732 helix: 0.98 (0.09), residues: 3360 sheet: None (None), residues: 0 loop : -2.27 (0.16), residues: 1372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2104 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 2000 time to evaluate : 4.426 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 outliers start: 104 outliers final: 59 residues processed: 2029 average time/residue: 0.4567 time to fit residues: 1514.9864 Evaluate side-chains 1929 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1870 time to evaluate : 4.551 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.3385 time to fit residues: 43.4010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 154 optimal weight: 1.9990 chunk 414 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 270 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 460 optimal weight: 0.8980 chunk 382 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN D 82 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN E 92 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 92 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN K 92 GLN ** K 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN L 68 ASN ** L 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 ASN ** M 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 ASN N 56 GLN ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 154 ASN Q 162 GLN R 56 GLN ** R 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 168 ASN S 154 ASN S 162 GLN T 168 ASN U 78 GLN ** U 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 ASN Z 56 GLN Z 68 ASN ** Z 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN a 168 ASN ** b 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 68 ASN ** b 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 36484 Z= 0.202 Angle : 0.620 10.207 49280 Z= 0.320 Chirality : 0.039 0.220 5908 Planarity : 0.004 0.060 6468 Dihedral : 7.321 89.670 5012 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.12), residues: 4732 helix: 1.31 (0.09), residues: 3332 sheet: None (None), residues: 0 loop : -1.97 (0.17), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2058 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1923 time to evaluate : 4.534 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 outliers start: 135 outliers final: 94 residues processed: 1946 average time/residue: 0.4422 time to fit residues: 1399.5615 Evaluate side-chains 1951 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1857 time to evaluate : 4.112 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 0.3334 time to fit residues: 64.4314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 444 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 336 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 387 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 458 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 279 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN E 82 ASN E 92 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 ASN F 92 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN H 78 GLN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 ASN J 56 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN K 68 ASN K 92 GLN K 162 GLN L 54 GLN L 68 ASN ** M 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 GLN ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 GLN Q 168 ASN ** R 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 168 ASN S 78 GLN S 154 ASN S 162 GLN T 162 GLN U 82 ASN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 ASN ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 ASN ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 ASN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 ASN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 102 GLN ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN a 161 GLN a 168 ASN ** b 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 36484 Z= 0.247 Angle : 0.657 9.191 49280 Z= 0.340 Chirality : 0.041 0.233 5908 Planarity : 0.004 0.061 6468 Dihedral : 7.253 86.082 5012 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.12), residues: 4732 helix: 1.40 (0.09), residues: 3332 sheet: None (None), residues: 0 loop : -2.02 (0.17), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1994 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1875 time to evaluate : 4.524 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 outliers start: 119 outliers final: 91 residues processed: 1900 average time/residue: 0.4600 time to fit residues: 1422.4828 Evaluate side-chains 1889 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1798 time to evaluate : 4.211 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 0.3214 time to fit residues: 61.0243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 283 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 274 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN E 92 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN L 54 GLN L 68 ASN L 148 ASN M 68 ASN ** M 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN M 147 ASN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 56 GLN ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 GLN ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 155 ASN P 168 ASN R 68 ASN R 147 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 78 GLN S 154 ASN S 162 GLN ** T 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 168 ASN U 43 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 ASN X 181 GLN ** Y 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 ASN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN a 168 ASN ** b 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 36484 Z= 0.204 Angle : 0.644 9.635 49280 Z= 0.332 Chirality : 0.040 0.238 5908 Planarity : 0.004 0.061 6468 Dihedral : 7.181 83.556 5012 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.13), residues: 4732 helix: 1.55 (0.09), residues: 3332 sheet: None (None), residues: 0 loop : -1.97 (0.17), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1973 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1899 time to evaluate : 4.524 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 outliers start: 74 outliers final: 45 residues processed: 1916 average time/residue: 0.4575 time to fit residues: 1432.8761 Evaluate side-chains 1887 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1842 time to evaluate : 4.158 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3124 time to fit residues: 32.6998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 417 optimal weight: 0.3980 chunk 439 optimal weight: 0.9980 chunk 401 optimal weight: 6.9990 chunk 427 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 335 optimal weight: 2.9990 chunk 131 optimal weight: 0.4980 chunk 386 optimal weight: 0.6980 chunk 404 optimal weight: 0.6980 chunk 426 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN E 92 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN L 154 ASN ** M 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN M 147 ASN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 GLN ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 ASN ** P 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN R 147 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 ASN R 168 ASN S 78 GLN S 154 ASN S 162 GLN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 ASN T 168 ASN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 ASN ** X 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 ASN ** Z 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN a 168 ASN b 56 GLN ** b 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 36484 Z= 0.185 Angle : 0.640 9.804 49280 Z= 0.329 Chirality : 0.039 0.241 5908 Planarity : 0.004 0.062 6468 Dihedral : 7.041 79.893 5012 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.13), residues: 4732 helix: 2.06 (0.09), residues: 3164 sheet: None (None), residues: 0 loop : -2.46 (0.15), residues: 1568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1976 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1914 time to evaluate : 4.152 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 outliers start: 62 outliers final: 36 residues processed: 1928 average time/residue: 0.4436 time to fit residues: 1398.0248 Evaluate side-chains 1859 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1823 time to evaluate : 4.503 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3150 time to fit residues: 27.3997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 280 optimal weight: 0.9980 chunk 452 optimal weight: 0.0670 chunk 275 optimal weight: 0.6980 chunk 214 optimal weight: 0.2980 chunk 314 optimal weight: 0.1980 chunk 474 optimal weight: 0.7980 chunk 436 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 291 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN D 82 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN E 92 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN L 54 GLN ** M 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN M 147 ASN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 168 ASN ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN R 147 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 ASN S 78 GLN S 162 GLN ** T 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 56 GLN ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 43 GLN ** Y 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 ASN ** Z 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 GLN a 68 ASN ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN a 168 ASN ** b 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.5836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 36484 Z= 0.178 Angle : 0.660 11.060 49280 Z= 0.336 Chirality : 0.039 0.252 5908 Planarity : 0.004 0.060 6468 Dihedral : 6.960 79.276 5012 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 4732 helix: 2.15 (0.09), residues: 3164 sheet: None (None), residues: 0 loop : -2.43 (0.15), residues: 1568 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9464 Ramachandran restraints generated. 4732 Oldfield, 0 Emsley, 4732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1964 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1937 time to evaluate : 4.194 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 outliers start: 27 outliers final: 16 residues processed: 1952 average time/residue: 0.4521 time to fit residues: 1438.7331 Evaluate side-chains 1870 residues out of total 4032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1854 time to evaluate : 4.173 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3149 time to fit residues: 15.3581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 476 random chunks: chunk 299 optimal weight: 10.0000 chunk 402 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 348 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 378 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 388 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 ASN E 92 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN ** G 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** I 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN K 162 GLN L 54 GLN ** M 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 GLN ** M 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 GLN ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 56 GLN P 168 ASN ** P 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 ASN R 147 ASN ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 ASN R 168 ASN ** S 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 GLN T 54 GLN ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 56 GLN ** U 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 ASN ** X 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 68 ASN Y 127 ASN ** Y 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 168 ASN Z 56 GLN ** Z 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 148 ASN ** b 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111342 restraints weight = 56870.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114252 restraints weight = 25759.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116001 restraints weight = 15964.321| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 36484 Z= 0.231 Angle : 0.698 11.510 49280 Z= 0.354 Chirality : 0.041 0.257 5908 Planarity : 0.004 0.064 6468 Dihedral : 6.940 79.935 5012 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.13), residues: 4732 helix: 2.12 (0.09), residues: 3164 sheet: None (None), residues: 0 loop : -2.27 (0.16), residues: 1568 =============================================================================== Job complete usr+sys time: 18007.01 seconds wall clock time: 316 minutes 1.92 seconds (18961.92 seconds total)