Starting phenix.real_space_refine (version: dev) on Sun May 15 00:52:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tup_10593/05_2022/6tup_10593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tup_10593/05_2022/6tup_10593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tup_10593/05_2022/6tup_10593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tup_10593/05_2022/6tup_10593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tup_10593/05_2022/6tup_10593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tup_10593/05_2022/6tup_10593.pdb" } resolution = 3.2 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= 0.002 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 None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 22400 Number of models: 1 Model: "" Number of chains: 100 Chain: "A" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "z" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "B" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "H" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "I" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "J" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "K" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "L" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "N" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "O" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "P" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "Q" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "R" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "S" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "T" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "U" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "V" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "W" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "X" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "Y" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "Z" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "0" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "1" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "2" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "3" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "4" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "5" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "6" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "7" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "8" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "9" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "a" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "b" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "c" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "d" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "e" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "f" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "g" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "h" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "i" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "j" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "k" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "l" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "m" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "n" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "o" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "p" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "q" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "r" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "s" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "t" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "u" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "v" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "w" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "y" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AA" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AB" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AC" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AD" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AE" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AF" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AG" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AH" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AI" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AJ" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AK" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AL" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AM" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AN" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AO" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AP" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AQ" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AR" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AS" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AT" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AU" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AV" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AW" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AX" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "AY" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "AZ" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A0" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "A1" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A2" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "A3" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A4" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "A5" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A6" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "A7" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "A8" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "A9" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "BA" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 322 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "BB" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 12.43, per 1000 atoms: 0.55 Number of scatterers: 22400 At special positions: 0 Unit cell: (75.9, 75.9, 245.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 300 15.00 O 4650 8.00 N 4100 7.00 C 13250 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: 53.74 Conformation dependent library (CDL) restraints added in 2.8 seconds 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3900 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 0 sheets defined 97.8% alpha, 0.0% beta 144 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 25.18 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLU B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 20 removed outlier: 4.127A pdb=" N GLU D 9 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP D 14 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP D 18 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D 20 " --> pdb=" O GLN D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE D 26 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA D 29 " --> pdb=" O TYR D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU D 43 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU F 9 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER F 10 " --> pdb=" O SER F 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP F 14 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS F 20 " --> pdb=" O GLN F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE F 26 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU F 38 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU F 43 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU H 9 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER H 10 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP H 14 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP H 18 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS H 20 " --> pdb=" O GLN H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE H 26 " --> pdb=" O ILE H 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY H 37 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU H 43 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLU J 9 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER J 10 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA J 11 " --> pdb=" O ALA J 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP J 14 " --> pdb=" O SER J 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP J 18 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS J 20 " --> pdb=" O GLN J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE J 26 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA J 29 " --> pdb=" O TYR J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY J 37 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU J 43 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU L 9 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER L 10 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP L 14 " --> pdb=" O SER L 10 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP L 18 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS L 20 " --> pdb=" O GLN L 16 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE L 26 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA L 29 " --> pdb=" O TYR L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY L 37 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU L 38 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU L 43 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU N 9 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER N 10 " --> pdb=" O SER N 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP N 14 " --> pdb=" O SER N 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP N 18 " --> pdb=" O ASP N 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS N 20 " --> pdb=" O GLN N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE N 26 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA N 29 " --> pdb=" O TYR N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY N 37 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU N 38 " --> pdb=" O ALA N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU N 43 " --> pdb=" O ILE N 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU P 9 " --> pdb=" O THR P 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER P 10 " --> pdb=" O SER P 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA P 11 " --> pdb=" O ALA P 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP P 14 " --> pdb=" O SER P 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP P 18 " --> pdb=" O ASP P 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS P 20 " --> pdb=" O GLN P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE P 26 " --> pdb=" O ILE P 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY P 28 " --> pdb=" O GLY P 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA P 29 " --> pdb=" O TYR P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY P 37 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU P 38 " --> pdb=" O ALA P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU P 43 " --> pdb=" O ILE P 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU R 9 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER R 10 " --> pdb=" O SER R 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP R 14 " --> pdb=" O SER R 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP R 18 " --> pdb=" O ASP R 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS R 20 " --> pdb=" O GLN R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE R 26 " --> pdb=" O ILE R 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA R 29 " --> pdb=" O TYR R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU R 38 " --> pdb=" O ALA R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU R 43 " --> pdb=" O ILE R 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU T 9 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER T 10 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA T 11 " --> pdb=" O ALA T 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP T 14 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP T 18 " --> pdb=" O ASP T 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS T 20 " --> pdb=" O GLN T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE T 26 " --> pdb=" O ILE T 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY T 28 " --> pdb=" O GLY T 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA T 29 " --> pdb=" O TYR T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY T 37 " --> pdb=" O LEU T 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU T 38 " --> pdb=" O ALA T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU T 43 " --> pdb=" O ILE T 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU V 9 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER V 10 " --> pdb=" O SER V 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA V 11 " --> pdb=" O ALA V 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP V 14 " --> pdb=" O SER V 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP V 18 " --> pdb=" O ASP V 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS V 20 " --> pdb=" O GLN V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE V 26 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY V 28 " --> pdb=" O GLY V 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA V 29 " --> pdb=" O TYR V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY V 37 " --> pdb=" O LEU V 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU V 38 " --> pdb=" O ALA V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU V 43 " --> pdb=" O ILE V 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU X 9 " --> pdb=" O THR X 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER X 10 " --> pdb=" O SER X 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA X 11 " --> pdb=" O ALA X 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP X 14 " --> pdb=" O SER X 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP X 18 " --> pdb=" O ASP X 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS X 20 " --> pdb=" O GLN X 16 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE X 26 " --> pdb=" O ILE X 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY X 28 " --> pdb=" O GLY X 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA X 29 " --> pdb=" O TYR X 25 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY X 37 " --> pdb=" O LEU X 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU X 38 " --> pdb=" O ALA X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU X 43 " --> pdb=" O ILE X 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLU Z 9 " --> pdb=" O THR Z 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER Z 10 " --> pdb=" O SER Z 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA Z 11 " --> pdb=" O ALA Z 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP Z 14 " --> pdb=" O SER Z 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP Z 18 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS Z 20 " --> pdb=" O GLN Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE Z 26 " --> pdb=" O ILE Z 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY Z 28 " --> pdb=" O GLY Z 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA Z 29 " --> pdb=" O TYR Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY Z 37 " --> pdb=" O LEU Z 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU Z 38 " --> pdb=" O ALA Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU Z 43 " --> pdb=" O ILE Z 39 " (cutoff:3.500A) Processing helix chain '1' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLU 1 9 " --> pdb=" O THR 1 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER 1 10 " --> pdb=" O SER 1 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA 1 11 " --> pdb=" O ALA 1 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP 1 14 " --> pdb=" O SER 1 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP 1 18 " --> pdb=" O ASP 1 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS 1 20 " --> pdb=" O GLN 1 16 " (cutoff:3.500A) Processing helix chain '1' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE 1 26 " --> pdb=" O ILE 1 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 1 28 " --> pdb=" O GLY 1 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA 1 29 " --> pdb=" O TYR 1 25 " (cutoff:3.500A) Processing helix chain '1' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY 1 37 " --> pdb=" O LEU 1 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 1 38 " --> pdb=" O ALA 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU 1 43 " --> pdb=" O ILE 1 39 " (cutoff:3.500A) Processing helix chain '3' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU 3 9 " --> pdb=" O THR 3 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER 3 10 " --> pdb=" O SER 3 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA 3 11 " --> pdb=" O ALA 3 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP 3 14 " --> pdb=" O SER 3 10 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP 3 18 " --> pdb=" O ASP 3 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS 3 20 " --> pdb=" O GLN 3 16 " (cutoff:3.500A) Processing helix chain '3' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE 3 26 " --> pdb=" O ILE 3 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 3 28 " --> pdb=" O GLY 3 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA 3 29 " --> pdb=" O TYR 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY 3 37 " --> pdb=" O LEU 3 33 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU 3 38 " --> pdb=" O ALA 3 34 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU 3 43 " --> pdb=" O ILE 3 39 " (cutoff:3.500A) Processing helix chain '5' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU 5 9 " --> pdb=" O THR 5 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER 5 10 " --> pdb=" O SER 5 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA 5 11 " --> pdb=" O ALA 5 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP 5 14 " --> pdb=" O SER 5 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP 5 18 " --> pdb=" O ASP 5 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS 5 20 " --> pdb=" O GLN 5 16 " (cutoff:3.500A) Processing helix chain '5' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE 5 26 " --> pdb=" O ILE 5 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 5 28 " --> pdb=" O GLY 5 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA 5 29 " --> pdb=" O TYR 5 25 " (cutoff:3.500A) Processing helix chain '5' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY 5 37 " --> pdb=" O LEU 5 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU 5 38 " --> pdb=" O ALA 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU 5 43 " --> pdb=" O ILE 5 39 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLU 7 9 " --> pdb=" O THR 7 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER 7 10 " --> pdb=" O SER 7 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA 7 11 " --> pdb=" O ALA 7 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP 7 14 " --> pdb=" O SER 7 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP 7 18 " --> pdb=" O ASP 7 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS 7 20 " --> pdb=" O GLN 7 16 " (cutoff:3.500A) Processing helix chain '7' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE 7 26 " --> pdb=" O ILE 7 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 7 28 " --> pdb=" O GLY 7 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA 7 29 " --> pdb=" O TYR 7 25 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY 7 37 " --> pdb=" O LEU 7 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU 7 38 " --> pdb=" O ALA 7 34 " (cutoff:3.500A) Processing helix chain '7' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU 7 43 " --> pdb=" O ILE 7 39 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU 9 9 " --> pdb=" O THR 9 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER 9 10 " --> pdb=" O SER 9 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA 9 11 " --> pdb=" O ALA 9 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP 9 14 " --> pdb=" O SER 9 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP 9 18 " --> pdb=" O ASP 9 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS 9 20 " --> pdb=" O GLN 9 16 " (cutoff:3.500A) Processing helix chain '9' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE 9 26 " --> pdb=" O ILE 9 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 9 28 " --> pdb=" O GLY 9 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA 9 29 " --> pdb=" O TYR 9 25 " (cutoff:3.500A) Processing helix chain '9' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY 9 37 " --> pdb=" O LEU 9 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 9 38 " --> pdb=" O ALA 9 34 " (cutoff:3.500A) Processing helix chain '9' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU 9 43 " --> pdb=" O ILE 9 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU b 9 " --> pdb=" O THR b 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA b 11 " --> pdb=" O ALA b 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP b 14 " --> pdb=" O SER b 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP b 18 " --> pdb=" O ASP b 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS b 20 " --> pdb=" O GLN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE b 26 " --> pdb=" O ILE b 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY b 28 " --> pdb=" O GLY b 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA b 29 " --> pdb=" O TYR b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY b 37 " --> pdb=" O LEU b 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU b 38 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU b 43 " --> pdb=" O ILE b 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU d 9 " --> pdb=" O THR d 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER d 10 " --> pdb=" O SER d 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA d 11 " --> pdb=" O ALA d 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP d 14 " --> pdb=" O SER d 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP d 18 " --> pdb=" O ASP d 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS d 20 " --> pdb=" O GLN d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE d 26 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY d 28 " --> pdb=" O GLY d 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA d 29 " --> pdb=" O TYR d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY d 37 " --> pdb=" O LEU d 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU d 38 " --> pdb=" O ALA d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU d 43 " --> pdb=" O ILE d 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU f 9 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER f 10 " --> pdb=" O SER f 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA f 11 " --> pdb=" O ALA f 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP f 14 " --> pdb=" O SER f 10 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP f 18 " --> pdb=" O ASP f 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS f 20 " --> pdb=" O GLN f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE f 26 " --> pdb=" O ILE f 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY f 28 " --> pdb=" O GLY f 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY f 37 " --> pdb=" O LEU f 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU f 38 " --> pdb=" O ALA f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU f 43 " --> pdb=" O ILE f 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU h 9 " --> pdb=" O THR h 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER h 10 " --> pdb=" O SER h 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA h 11 " --> pdb=" O ALA h 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP h 14 " --> pdb=" O SER h 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP h 18 " --> pdb=" O ASP h 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS h 20 " --> pdb=" O GLN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE h 26 " --> pdb=" O ILE h 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY h 28 " --> pdb=" O GLY h 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA h 29 " --> pdb=" O TYR h 25 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY h 37 " --> pdb=" O LEU h 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU h 43 " --> pdb=" O ILE h 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA j 11 " --> pdb=" O ALA j 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP j 14 " --> pdb=" O SER j 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS j 20 " --> pdb=" O GLN j 16 " (cutoff:3.500A) Processing helix chain 'j' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE j 26 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY j 28 " --> pdb=" O GLY j 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA j 29 " --> pdb=" O TYR j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY j 37 " --> pdb=" O LEU j 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU j 38 " --> pdb=" O ALA j 34 " (cutoff:3.500A) Processing helix chain 'j' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU j 43 " --> pdb=" O ILE j 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLU l 9 " --> pdb=" O THR l 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER l 10 " --> pdb=" O SER l 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA l 11 " --> pdb=" O ALA l 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP l 14 " --> pdb=" O SER l 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP l 18 " --> pdb=" O ASP l 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS l 20 " --> pdb=" O GLN l 16 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE l 26 " --> pdb=" O ILE l 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY l 28 " --> pdb=" O GLY l 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA l 29 " --> pdb=" O TYR l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY l 37 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU l 38 " --> pdb=" O ALA l 34 " (cutoff:3.500A) Processing helix chain 'l' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU l 43 " --> pdb=" O ILE l 39 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU n 9 " --> pdb=" O THR n 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER n 10 " --> pdb=" O SER n 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA n 11 " --> pdb=" O ALA n 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP n 14 " --> pdb=" O SER n 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP n 18 " --> pdb=" O ASP n 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS n 20 " --> pdb=" O GLN n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE n 26 " --> pdb=" O ILE n 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY n 28 " --> pdb=" O GLY n 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA n 29 " --> pdb=" O TYR n 25 " (cutoff:3.500A) Processing helix chain 'n' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY n 37 " --> pdb=" O LEU n 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU n 38 " --> pdb=" O ALA n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU n 43 " --> pdb=" O ILE n 39 " (cutoff:3.500A) Processing helix chain 'p' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLU p 9 " --> pdb=" O THR p 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER p 10 " --> pdb=" O SER p 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA p 11 " --> pdb=" O ALA p 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP p 14 " --> pdb=" O SER p 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP p 18 " --> pdb=" O ASP p 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS p 20 " --> pdb=" O GLN p 16 " (cutoff:3.500A) Processing helix chain 'p' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE p 26 " --> pdb=" O ILE p 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY p 28 " --> pdb=" O GLY p 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA p 29 " --> pdb=" O TYR p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY p 37 " --> pdb=" O LEU p 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU p 38 " --> pdb=" O ALA p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 46 removed outlier: 3.797A pdb=" N LEU p 43 " --> pdb=" O ILE p 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU r 9 " --> pdb=" O THR r 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER r 10 " --> pdb=" O SER r 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA r 11 " --> pdb=" O ALA r 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP r 14 " --> pdb=" O SER r 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP r 18 " --> pdb=" O ASP r 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS r 20 " --> pdb=" O GLN r 16 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE r 26 " --> pdb=" O ILE r 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY r 28 " --> pdb=" O GLY r 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA r 29 " --> pdb=" O TYR r 25 " (cutoff:3.500A) Processing helix chain 'r' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU r 38 " --> pdb=" O ALA r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU r 43 " --> pdb=" O ILE r 39 " (cutoff:3.500A) Processing helix chain 't' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU t 9 " --> pdb=" O THR t 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP t 14 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP t 18 " --> pdb=" O ASP t 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS t 20 " --> pdb=" O GLN t 16 " (cutoff:3.500A) Processing helix chain 't' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE t 26 " --> pdb=" O ILE t 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY t 28 " --> pdb=" O GLY t 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA t 29 " --> pdb=" O TYR t 25 " (cutoff:3.500A) Processing helix chain 't' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLY t 37 " --> pdb=" O LEU t 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU t 38 " --> pdb=" O ALA t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEU t 43 " --> pdb=" O ILE t 39 " (cutoff:3.500A) Processing helix chain 'v' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLU v 9 " --> pdb=" O THR v 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER v 10 " --> pdb=" O SER v 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA v 11 " --> pdb=" O ALA v 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP v 14 " --> pdb=" O SER v 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP v 18 " --> pdb=" O ASP v 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS v 20 " --> pdb=" O GLN v 16 " (cutoff:3.500A) Processing helix chain 'v' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILE v 26 " --> pdb=" O ILE v 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY v 28 " --> pdb=" O GLY v 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA v 29 " --> pdb=" O TYR v 25 " (cutoff:3.500A) Processing helix chain 'v' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY v 37 " --> pdb=" O LEU v 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU v 38 " --> pdb=" O ALA v 34 " (cutoff:3.500A) Processing helix chain 'v' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU v 43 " --> pdb=" O ILE v 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLU x 9 " --> pdb=" O THR x 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER x 10 " --> pdb=" O SER x 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA x 11 " --> pdb=" O ALA x 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP x 14 " --> pdb=" O SER x 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP x 18 " --> pdb=" O ASP x 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS x 20 " --> pdb=" O GLN x 16 " (cutoff:3.500A) Processing helix chain 'x' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILE x 26 " --> pdb=" O ILE x 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY x 28 " --> pdb=" O GLY x 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA x 29 " --> pdb=" O TYR x 25 " (cutoff:3.500A) Processing helix chain 'x' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLY x 37 " --> pdb=" O LEU x 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU x 38 " --> pdb=" O ALA x 34 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEU x 43 " --> pdb=" O ILE x 39 " (cutoff:3.500A) Processing helix chain 'AA' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAA 9 " --> pdb=" O THRAA 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SERAA 10 " --> pdb=" O SERAA 6 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALAAA 11 " --> pdb=" O ALAAA 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASPAA 14 " --> pdb=" O SERAA 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAA 18 " --> pdb=" O ASPAA 14 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYSAA 20 " --> pdb=" O GLNAA 16 " (cutoff:3.500A) Processing helix chain 'AA' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAA 26 " --> pdb=" O ILEAA 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYAA 28 " --> pdb=" O GLYAA 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALAAA 29 " --> pdb=" O TYRAA 25 " (cutoff:3.500A) Processing helix chain 'AA' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAA 37 " --> pdb=" O LEUAA 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAA 38 " --> pdb=" O ALAAA 34 " (cutoff:3.500A) Processing helix chain 'AA' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAA 43 " --> pdb=" O ILEAA 39 " (cutoff:3.500A) Processing helix chain 'AC' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAC 9 " --> pdb=" O THRAC 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERAC 10 " --> pdb=" O SERAC 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAC 11 " --> pdb=" O ALAAC 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASPAC 14 " --> pdb=" O SERAC 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAC 18 " --> pdb=" O ASPAC 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSAC 20 " --> pdb=" O GLNAC 16 " (cutoff:3.500A) Processing helix chain 'AC' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAC 26 " --> pdb=" O ILEAC 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYAC 28 " --> pdb=" O GLYAC 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAAC 29 " --> pdb=" O TYRAC 25 " (cutoff:3.500A) Processing helix chain 'AC' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLYAC 37 " --> pdb=" O LEUAC 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAC 38 " --> pdb=" O ALAAC 34 " (cutoff:3.500A) Processing helix chain 'AC' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAC 43 " --> pdb=" O ILEAC 39 " (cutoff:3.500A) Processing helix chain 'AE' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAE 9 " --> pdb=" O THRAE 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERAE 10 " --> pdb=" O SERAE 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAAE 11 " --> pdb=" O ALAAE 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPAE 14 " --> pdb=" O SERAE 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAE 18 " --> pdb=" O ASPAE 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSAE 20 " --> pdb=" O GLNAE 16 " (cutoff:3.500A) Processing helix chain 'AE' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILEAE 26 " --> pdb=" O ILEAE 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYAE 28 " --> pdb=" O GLYAE 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALAAE 29 " --> pdb=" O TYRAE 25 " (cutoff:3.500A) Processing helix chain 'AE' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAE 37 " --> pdb=" O LEUAE 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAE 38 " --> pdb=" O ALAAE 34 " (cutoff:3.500A) Processing helix chain 'AE' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEUAE 43 " --> pdb=" O ILEAE 39 " (cutoff:3.500A) Processing helix chain 'AG' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLUAG 9 " --> pdb=" O THRAG 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERAG 10 " --> pdb=" O SERAG 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAG 11 " --> pdb=" O ALAAG 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASPAG 14 " --> pdb=" O SERAG 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAG 18 " --> pdb=" O ASPAG 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYSAG 20 " --> pdb=" O GLNAG 16 " (cutoff:3.500A) Processing helix chain 'AG' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAG 26 " --> pdb=" O ILEAG 22 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLYAG 28 " --> pdb=" O GLYAG 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALAAG 29 " --> pdb=" O TYRAG 25 " (cutoff:3.500A) Processing helix chain 'AG' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAG 37 " --> pdb=" O LEUAG 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEUAG 38 " --> pdb=" O ALAAG 34 " (cutoff:3.500A) Processing helix chain 'AG' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEUAG 43 " --> pdb=" O ILEAG 39 " (cutoff:3.500A) Processing helix chain 'AI' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAI 9 " --> pdb=" O THRAI 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SERAI 10 " --> pdb=" O SERAI 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAI 11 " --> pdb=" O ALAAI 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASPAI 14 " --> pdb=" O SERAI 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAI 18 " --> pdb=" O ASPAI 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYSAI 20 " --> pdb=" O GLNAI 16 " (cutoff:3.500A) Processing helix chain 'AI' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILEAI 26 " --> pdb=" O ILEAI 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYAI 28 " --> pdb=" O GLYAI 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAAI 29 " --> pdb=" O TYRAI 25 " (cutoff:3.500A) Processing helix chain 'AI' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAI 37 " --> pdb=" O LEUAI 33 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEUAI 38 " --> pdb=" O ALAAI 34 " (cutoff:3.500A) Processing helix chain 'AI' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEUAI 43 " --> pdb=" O ILEAI 39 " (cutoff:3.500A) Processing helix chain 'AK' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAK 9 " --> pdb=" O THRAK 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SERAK 10 " --> pdb=" O SERAK 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAK 11 " --> pdb=" O ALAAK 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASPAK 14 " --> pdb=" O SERAK 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAK 18 " --> pdb=" O ASPAK 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSAK 20 " --> pdb=" O GLNAK 16 " (cutoff:3.500A) Processing helix chain 'AK' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAK 26 " --> pdb=" O ILEAK 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYAK 28 " --> pdb=" O GLYAK 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAAK 29 " --> pdb=" O TYRAK 25 " (cutoff:3.500A) Processing helix chain 'AK' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAK 37 " --> pdb=" O LEUAK 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAK 38 " --> pdb=" O ALAAK 34 " (cutoff:3.500A) Processing helix chain 'AK' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAK 43 " --> pdb=" O ILEAK 39 " (cutoff:3.500A) Processing helix chain 'AM' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAM 9 " --> pdb=" O THRAM 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERAM 10 " --> pdb=" O SERAM 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAM 11 " --> pdb=" O ALAAM 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPAM 14 " --> pdb=" O SERAM 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAM 18 " --> pdb=" O ASPAM 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSAM 20 " --> pdb=" O GLNAM 16 " (cutoff:3.500A) Processing helix chain 'AM' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAM 26 " --> pdb=" O ILEAM 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYAM 28 " --> pdb=" O GLYAM 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAAM 29 " --> pdb=" O TYRAM 25 " (cutoff:3.500A) Processing helix chain 'AM' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAM 37 " --> pdb=" O LEUAM 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAM 38 " --> pdb=" O ALAAM 34 " (cutoff:3.500A) Processing helix chain 'AM' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAM 43 " --> pdb=" O ILEAM 39 " (cutoff:3.500A) Processing helix chain 'AO' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLUAO 9 " --> pdb=" O THRAO 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SERAO 10 " --> pdb=" O SERAO 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAAO 11 " --> pdb=" O ALAAO 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPAO 14 " --> pdb=" O SERAO 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAO 18 " --> pdb=" O ASPAO 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYSAO 20 " --> pdb=" O GLNAO 16 " (cutoff:3.500A) Processing helix chain 'AO' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAO 26 " --> pdb=" O ILEAO 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYAO 28 " --> pdb=" O GLYAO 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAAO 29 " --> pdb=" O TYRAO 25 " (cutoff:3.500A) Processing helix chain 'AO' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLYAO 37 " --> pdb=" O LEUAO 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEUAO 38 " --> pdb=" O ALAAO 34 " (cutoff:3.500A) Processing helix chain 'AO' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAO 43 " --> pdb=" O ILEAO 39 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAQ 9 " --> pdb=" O THRAQ 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERAQ 10 " --> pdb=" O SERAQ 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAQ 11 " --> pdb=" O ALAAQ 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPAQ 14 " --> pdb=" O SERAQ 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASPAQ 18 " --> pdb=" O ASPAQ 14 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYSAQ 20 " --> pdb=" O GLNAQ 16 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILEAQ 26 " --> pdb=" O ILEAQ 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYAQ 28 " --> pdb=" O GLYAQ 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALAAQ 29 " --> pdb=" O TYRAQ 25 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAQ 37 " --> pdb=" O LEUAQ 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAQ 38 " --> pdb=" O ALAAQ 34 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAQ 43 " --> pdb=" O ILEAQ 39 " (cutoff:3.500A) Processing helix chain 'AS' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAS 9 " --> pdb=" O THRAS 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SERAS 10 " --> pdb=" O SERAS 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAS 11 " --> pdb=" O ALAAS 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPAS 14 " --> pdb=" O SERAS 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAS 18 " --> pdb=" O ASPAS 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYSAS 20 " --> pdb=" O GLNAS 16 " (cutoff:3.500A) Processing helix chain 'AS' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAS 26 " --> pdb=" O ILEAS 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYAS 28 " --> pdb=" O GLYAS 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALAAS 29 " --> pdb=" O TYRAS 25 " (cutoff:3.500A) Processing helix chain 'AS' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAS 37 " --> pdb=" O LEUAS 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAS 38 " --> pdb=" O ALAAS 34 " (cutoff:3.500A) Processing helix chain 'AS' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEUAS 43 " --> pdb=" O ILEAS 39 " (cutoff:3.500A) Processing helix chain 'AU' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAU 9 " --> pdb=" O THRAU 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERAU 10 " --> pdb=" O SERAU 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAU 11 " --> pdb=" O ALAAU 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPAU 14 " --> pdb=" O SERAU 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAU 18 " --> pdb=" O ASPAU 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYSAU 20 " --> pdb=" O GLNAU 16 " (cutoff:3.500A) Processing helix chain 'AU' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAU 26 " --> pdb=" O ILEAU 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYAU 28 " --> pdb=" O GLYAU 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAAU 29 " --> pdb=" O TYRAU 25 " (cutoff:3.500A) Processing helix chain 'AU' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLYAU 37 " --> pdb=" O LEUAU 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEUAU 38 " --> pdb=" O ALAAU 34 " (cutoff:3.500A) Processing helix chain 'AU' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAU 43 " --> pdb=" O ILEAU 39 " (cutoff:3.500A) Processing helix chain 'AW' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLUAW 9 " --> pdb=" O THRAW 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERAW 10 " --> pdb=" O SERAW 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAW 11 " --> pdb=" O ALAAW 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPAW 14 " --> pdb=" O SERAW 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAW 18 " --> pdb=" O ASPAW 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSAW 20 " --> pdb=" O GLNAW 16 " (cutoff:3.500A) Processing helix chain 'AW' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAW 26 " --> pdb=" O ILEAW 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYAW 28 " --> pdb=" O GLYAW 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAAW 29 " --> pdb=" O TYRAW 25 " (cutoff:3.500A) Processing helix chain 'AW' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLYAW 37 " --> pdb=" O LEUAW 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAW 38 " --> pdb=" O ALAAW 34 " (cutoff:3.500A) Processing helix chain 'AW' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAW 43 " --> pdb=" O ILEAW 39 " (cutoff:3.500A) Processing helix chain 'AY' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUAY 9 " --> pdb=" O THRAY 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SERAY 10 " --> pdb=" O SERAY 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAAY 11 " --> pdb=" O ALAAY 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPAY 14 " --> pdb=" O SERAY 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPAY 18 " --> pdb=" O ASPAY 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSAY 20 " --> pdb=" O GLNAY 16 " (cutoff:3.500A) Processing helix chain 'AY' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEAY 26 " --> pdb=" O ILEAY 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYAY 28 " --> pdb=" O GLYAY 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAAY 29 " --> pdb=" O TYRAY 25 " (cutoff:3.500A) Processing helix chain 'AY' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYAY 37 " --> pdb=" O LEUAY 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUAY 38 " --> pdb=" O ALAAY 34 " (cutoff:3.500A) Processing helix chain 'AY' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUAY 43 " --> pdb=" O ILEAY 39 " (cutoff:3.500A) Processing helix chain 'A0' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUA0 9 " --> pdb=" O THRA0 5 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SERA0 10 " --> pdb=" O SERA0 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAA0 11 " --> pdb=" O ALAA0 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPA0 14 " --> pdb=" O SERA0 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPA0 18 " --> pdb=" O ASPA0 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSA0 20 " --> pdb=" O GLNA0 16 " (cutoff:3.500A) Processing helix chain 'A0' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEA0 26 " --> pdb=" O ILEA0 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYA0 28 " --> pdb=" O GLYA0 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAA0 29 " --> pdb=" O TYRA0 25 " (cutoff:3.500A) Processing helix chain 'A0' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYA0 37 " --> pdb=" O LEUA0 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUA0 38 " --> pdb=" O ALAA0 34 " (cutoff:3.500A) Processing helix chain 'A0' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUA0 43 " --> pdb=" O ILEA0 39 " (cutoff:3.500A) Processing helix chain 'A2' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLUA2 9 " --> pdb=" O THRA2 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERA2 10 " --> pdb=" O SERA2 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAA2 11 " --> pdb=" O ALAA2 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASPA2 14 " --> pdb=" O SERA2 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPA2 18 " --> pdb=" O ASPA2 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSA2 20 " --> pdb=" O GLNA2 16 " (cutoff:3.500A) Processing helix chain 'A2' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILEA2 26 " --> pdb=" O ILEA2 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYA2 28 " --> pdb=" O GLYA2 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAA2 29 " --> pdb=" O TYRA2 25 " (cutoff:3.500A) Processing helix chain 'A2' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYA2 37 " --> pdb=" O LEUA2 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUA2 38 " --> pdb=" O ALAA2 34 " (cutoff:3.500A) Processing helix chain 'A2' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEUA2 43 " --> pdb=" O ILEA2 39 " (cutoff:3.500A) Processing helix chain 'A4' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUA4 9 " --> pdb=" O THRA4 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERA4 10 " --> pdb=" O SERA4 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAA4 11 " --> pdb=" O ALAA4 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPA4 14 " --> pdb=" O SERA4 10 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASPA4 18 " --> pdb=" O ASPA4 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSA4 20 " --> pdb=" O GLNA4 16 " (cutoff:3.500A) Processing helix chain 'A4' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEA4 26 " --> pdb=" O ILEA4 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYA4 28 " --> pdb=" O GLYA4 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAA4 29 " --> pdb=" O TYRA4 25 " (cutoff:3.500A) Processing helix chain 'A4' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYA4 37 " --> pdb=" O LEUA4 33 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEUA4 38 " --> pdb=" O ALAA4 34 " (cutoff:3.500A) Processing helix chain 'A4' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEUA4 43 " --> pdb=" O ILEA4 39 " (cutoff:3.500A) Processing helix chain 'A6' and resid 5 through 20 removed outlier: 4.126A pdb=" N GLUA6 9 " --> pdb=" O THRA6 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERA6 10 " --> pdb=" O SERA6 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALAA6 11 " --> pdb=" O ALAA6 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASPA6 14 " --> pdb=" O SERA6 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPA6 18 " --> pdb=" O ASPA6 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSA6 20 " --> pdb=" O GLNA6 16 " (cutoff:3.500A) Processing helix chain 'A6' and resid 20 through 31 removed outlier: 4.089A pdb=" N ILEA6 26 " --> pdb=" O ILEA6 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYA6 28 " --> pdb=" O GLYA6 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALAA6 29 " --> pdb=" O TYRA6 25 " (cutoff:3.500A) Processing helix chain 'A6' and resid 31 through 39 removed outlier: 3.832A pdb=" N GLYA6 37 " --> pdb=" O LEUA6 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUA6 38 " --> pdb=" O ALAA6 34 " (cutoff:3.500A) Processing helix chain 'A6' and resid 39 through 46 removed outlier: 3.796A pdb=" N LEUA6 43 " --> pdb=" O ILEA6 39 " (cutoff:3.500A) Processing helix chain 'A8' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLUA8 9 " --> pdb=" O THRA8 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SERA8 10 " --> pdb=" O SERA8 6 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAA8 11 " --> pdb=" O ALAA8 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPA8 14 " --> pdb=" O SERA8 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPA8 18 " --> pdb=" O ASPA8 14 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYSA8 20 " --> pdb=" O GLNA8 16 " (cutoff:3.500A) Processing helix chain 'A8' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEA8 26 " --> pdb=" O ILEA8 22 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLYA8 28 " --> pdb=" O GLYA8 24 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALAA8 29 " --> pdb=" O TYRA8 25 " (cutoff:3.500A) Processing helix chain 'A8' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYA8 37 " --> pdb=" O LEUA8 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUA8 38 " --> pdb=" O ALAA8 34 " (cutoff:3.500A) Processing helix chain 'A8' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEUA8 43 " --> pdb=" O ILEA8 39 " (cutoff:3.500A) Processing helix chain 'BA' and resid 5 through 20 removed outlier: 4.125A pdb=" N GLUBA 9 " --> pdb=" O THRBA 5 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SERBA 10 " --> pdb=" O SERBA 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALABA 11 " --> pdb=" O ALABA 7 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASPBA 14 " --> pdb=" O SERBA 10 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASPBA 18 " --> pdb=" O ASPBA 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYSBA 20 " --> pdb=" O GLNBA 16 " (cutoff:3.500A) Processing helix chain 'BA' and resid 20 through 31 removed outlier: 4.088A pdb=" N ILEBA 26 " --> pdb=" O ILEBA 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLYBA 28 " --> pdb=" O GLYBA 24 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALABA 29 " --> pdb=" O TYRBA 25 " (cutoff:3.500A) Processing helix chain 'BA' and resid 31 through 39 removed outlier: 3.833A pdb=" N GLYBA 37 " --> pdb=" O LEUBA 33 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEUBA 38 " --> pdb=" O ALABA 34 " (cutoff:3.500A) Processing helix chain 'BA' and resid 39 through 46 removed outlier: 3.795A pdb=" N LEUBA 43 " --> pdb=" O ILEBA 39 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 288 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 10.11 Time building geometry restraints manager: 52.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5884 1.33 - 1.45: 5294 1.45 - 1.56: 11372 1.56 - 1.68: 550 1.68 - 1.79: 200 Bond restraints: 23300 Sorted by residual: bond pdb=" CB VALAG 35 " pdb=" CG2 VALAG 35 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" CB VALA2 35 " pdb=" CG2 VALA2 35 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 bond pdb=" CB VAL H 35 " pdb=" CG2 VAL H 35 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 bond pdb=" CB VAL n 35 " pdb=" CG2 VAL n 35 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 bond pdb=" CB VAL L 35 " pdb=" CG2 VAL L 35 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.17e+00 ... (remaining 23295 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.18: 2385 106.18 - 112.74: 12410 112.74 - 119.30: 7307 119.30 - 125.86: 8798 125.86 - 132.43: 1800 Bond angle restraints: 32700 Sorted by residual: angle pdb=" CA LEU L 33 " pdb=" CB LEU L 33 " pdb=" CG LEU L 33 " ideal model delta sigma weight residual 116.30 125.74 -9.44 3.50e+00 8.16e-02 7.28e+00 angle pdb=" CA LEU t 33 " pdb=" CB LEU t 33 " pdb=" CG LEU t 33 " ideal model delta sigma weight residual 116.30 125.74 -9.44 3.50e+00 8.16e-02 7.27e+00 angle pdb=" CA LEUA4 33 " pdb=" CB LEUA4 33 " pdb=" CG LEUA4 33 " ideal model delta sigma weight residual 116.30 125.72 -9.42 3.50e+00 8.16e-02 7.24e+00 angle pdb=" CA LEUAU 33 " pdb=" CB LEUAU 33 " pdb=" CG LEUAU 33 " ideal model delta sigma weight residual 116.30 125.72 -9.42 3.50e+00 8.16e-02 7.24e+00 angle pdb=" CA LEUAA 33 " pdb=" CB LEUAA 33 " pdb=" CG LEUAA 33 " ideal model delta sigma weight residual 116.30 125.71 -9.41 3.50e+00 8.16e-02 7.23e+00 ... (remaining 32695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10600 17.80 - 35.61: 800 35.61 - 53.41: 503 53.41 - 71.21: 447 71.21 - 89.02: 50 Dihedral angle restraints: 12400 sinusoidal: 6150 harmonic: 6250 Sorted by residual: dihedral pdb=" CA LEU p 38 " pdb=" C LEU p 38 " pdb=" N ILE p 39 " pdb=" CA ILE p 39 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEUBA 38 " pdb=" C LEUBA 38 " pdb=" N ILEBA 39 " pdb=" CA ILEBA 39 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU L 38 " pdb=" C LEU L 38 " pdb=" N ILE L 39 " pdb=" CA ILE L 39 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 12397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1826 0.028 - 0.056: 1340 0.056 - 0.085: 633 0.085 - 0.113: 1 0.113 - 0.141: 200 Chirality restraints: 4000 Sorted by residual: chirality pdb=" CA LEU D 38 " pdb=" N LEU D 38 " pdb=" C LEU D 38 " pdb=" CB LEU D 38 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA LEUAU 38 " pdb=" N LEUAU 38 " pdb=" C LEUAU 38 " pdb=" CB LEUAU 38 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA LEU B 38 " pdb=" N LEU B 38 " pdb=" C LEU B 38 " pdb=" CB LEU B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 3997 not shown) Planarity restraints: 3000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 3 27 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C VAL 3 27 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL 3 27 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY 3 28 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALA2 27 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C VALA2 27 " 0.024 2.00e-02 2.50e+03 pdb=" O VALA2 27 " -0.009 2.00e-02 2.50e+03 pdb=" N GLYA2 28 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 27 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C VAL N 27 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL N 27 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY N 28 " -0.008 2.00e-02 2.50e+03 ... (remaining 2997 not shown) Histogram of nonbonded interaction distances: 0.03 - 1.01: 9138 1.01 - 1.98: 33765 1.98 - 2.95: 65342 2.95 - 3.93: 136638 3.93 - 4.90: 223632 Warning: very small nonbonded interaction distances. Nonbonded interactions: 468515 Sorted by model distance: nonbonded pdb=" C5 DA z 5 " pdb=" C5 DA a 2 " model vdw 0.032 3.480 nonbonded pdb=" C5' DA e 6 " pdb=" C5' DAAH 1 " model vdw 0.040 3.840 nonbonded pdb=" O4' DA 2 1 " pdb=" O4' DA 6 6 " model vdw 0.048 3.040 nonbonded pdb=" C2' DA c 4 " pdb=" C2' DA m 2 " model vdw 0.059 3.840 nonbonded pdb=" C4 DAAH 5 " pdb=" C5 DAA7 6 " model vdw 0.062 3.480 ... (remaining 468510 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 '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'A1' selection = chain 'A3' selection = chain 'A5' selection = chain 'A7' selection = chain 'A9' selection = chain 'AB' selection = chain 'AD' selection = chain 'AF' selection = chain 'AH' selection = chain 'AJ' selection = chain 'AL' selection = chain 'AN' selection = chain 'AP' selection = chain 'AR' selection = chain 'AT' selection = chain 'AV' selection = chain 'AX' selection = chain 'AZ' selection = chain 'BB' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A' selection = chain 'A0' selection = chain 'A2' selection = chain 'A4' selection = chain 'A6' selection = chain 'A8' selection = chain 'AA' selection = chain 'AC' selection = chain 'AE' selection = chain 'AG' selection = chain 'AI' selection = chain 'AK' selection = chain 'AM' selection = chain 'AO' selection = chain 'AQ' selection = chain 'AS' selection = chain 'AU' selection = chain 'AW' selection = chain 'AY' selection = chain 'B' selection = chain 'BA' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' selection = chain 'v' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 100 5.16 5 C 13250 2.51 5 N 4100 2.21 5 O 4650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.020 Extract box with map and model: 15.650 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.200 Process input model: 139.260 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.530 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: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4722 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 : 0.011 0.054 23300 Z= 0.637 Angle : 1.016 9.445 32700 Z= 0.506 Chirality : 0.048 0.141 4000 Planarity : 0.004 0.014 3000 Dihedral : 21.231 89.016 8500 Min Nonbonded Distance : 0.032 Molprobity Statistics. All-atom Clashscore : 54.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % 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: -7.04 (0.09), residues: 2200 helix: -4.65 (0.03), residues: 1900 sheet: None (None), residues: 0 loop : -1.87 (0.39), residues: 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 2.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.5361 time to fit residues: 417.5429 Evaluate side-chains 388 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 156 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.0970 chunk 116 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 1.9765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.135 2.007 23300 Z= 8.138 Angle : 6.408 76.891 32700 Z= 3.609 Chirality : 0.536 5.474 4000 Planarity : 0.029 0.457 3000 Dihedral : 30.020 173.126 5300 Min Nonbonded Distance : 1.360 Molprobity Statistics. All-atom Clashscore : 327.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.55 % Favored : 96.14 % Rotamer Outliers : 8.88 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.20 % 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: -5.49 (0.14), residues: 2200 helix: -3.69 (0.08), residues: 1950 sheet: None (None), residues: 0 loop : 0.12 (0.56), residues: 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 635 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 41 residues processed: 689 average time/residue: 0.4126 time to fit residues: 431.9794 Evaluate side-chains 573 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 532 time to evaluate : 2.099 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 2 residues processed: 41 average time/residue: 0.4449 time to fit residues: 28.7576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 196 optimal weight: 0.0970 chunk 162 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 2.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.083 1.847 23300 Z= 4.989 Angle : 4.662 97.976 32700 Z= 2.590 Chirality : 0.389 4.325 4000 Planarity : 0.014 0.166 3000 Dihedral : 30.704 179.311 5300 Min Nonbonded Distance : 1.402 Molprobity Statistics. All-atom Clashscore : 213.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.14 % Favored : 94.82 % Rotamer Outliers : 7.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.17), residues: 2200 helix: -3.12 (0.10), residues: 1803 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 671 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 55 residues processed: 720 average time/residue: 0.3544 time to fit residues: 388.6600 Evaluate side-chains 613 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 558 time to evaluate : 2.085 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 2 residues processed: 55 average time/residue: 0.3378 time to fit residues: 30.8966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 2.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.065 1.497 23300 Z= 3.912 Angle : 3.802 59.748 32700 Z= 2.134 Chirality : 0.326 4.382 4000 Planarity : 0.012 0.154 3000 Dihedral : 30.542 170.912 5300 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 173.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.55 % Rotamer Outliers : 5.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.17), residues: 2200 helix: -2.96 (0.10), residues: 1854 sheet: None (None), residues: 0 loop : 0.12 (0.49), residues: 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 642 time to evaluate : 2.090 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: 80 outliers final: 29 residues processed: 680 average time/residue: 0.3558 time to fit residues: 371.9514 Evaluate side-chains 583 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 554 time to evaluate : 2.146 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 1 residues processed: 29 average time/residue: 0.3034 time to fit residues: 16.5092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 0 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 2.6651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.056 1.403 23300 Z= 3.415 Angle : 3.373 50.013 32700 Z= 1.905 Chirality : 0.325 4.455 4000 Planarity : 0.011 0.123 3000 Dihedral : 30.692 179.944 5300 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 156.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 6.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -3.91 (0.18), residues: 2200 helix: -2.79 (0.10), residues: 1854 sheet: None (None), residues: 0 loop : 0.49 (0.49), residues: 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 606 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 51 residues processed: 660 average time/residue: 0.3495 time to fit residues: 358.1901 Evaluate side-chains 592 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 541 time to evaluate : 2.008 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 51 outliers final: 1 residues processed: 51 average time/residue: 0.2147 time to fit residues: 22.2633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.3980 chunk 174 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 2.7401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.051 1.294 23300 Z= 3.109 Angle : 3.072 49.500 32700 Z= 1.775 Chirality : 0.302 4.332 4000 Planarity : 0.010 0.103 3000 Dihedral : 30.656 178.823 5300 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 144.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 4.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.09 (0.18), residues: 2200 helix: -2.41 (0.11), residues: 1614 sheet: None (None), residues: 0 loop : -0.13 (0.35), residues: 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 596 time to evaluate : 2.320 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 outliers start: 65 outliers final: 37 residues processed: 630 average time/residue: 0.3429 time to fit residues: 334.8345 Evaluate side-chains 575 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 538 time to evaluate : 1.988 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.2549 time to fit residues: 18.5418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 192 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 2.7860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.048 1.308 23300 Z= 2.893 Angle : 2.909 49.101 32700 Z= 1.677 Chirality : 0.285 4.269 4000 Planarity : 0.010 0.133 3000 Dihedral : 30.579 177.960 5300 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 138.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 4.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.19), residues: 2200 helix: -2.32 (0.12), residues: 1468 sheet: None (None), residues: 0 loop : 0.70 (0.31), residues: 732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 577 time to evaluate : 2.209 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 outliers start: 67 outliers final: 38 residues processed: 608 average time/residue: 0.3448 time to fit residues: 323.7976 Evaluate side-chains 557 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 519 time to evaluate : 1.872 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2879 time to fit residues: 20.5080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.0770 chunk 76 optimal weight: 0.0070 chunk 115 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 122 optimal weight: 0.4980 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 2.9112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.046 1.326 23300 Z= 2.762 Angle : 2.777 39.612 32700 Z= 1.600 Chirality : 0.261 4.319 4000 Planarity : 0.010 0.156 3000 Dihedral : 30.377 173.872 5300 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 127.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.19), residues: 2200 helix: -2.19 (0.11), residues: 1638 sheet: None (None), residues: 0 loop : 0.24 (0.35), residues: 562 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 585 time to evaluate : 2.024 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 outliers start: 42 outliers final: 19 residues processed: 608 average time/residue: 0.3317 time to fit residues: 318.5740 Evaluate side-chains 531 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 512 time to evaluate : 2.063 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2423 time to fit residues: 10.4709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.0770 chunk 168 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 108 optimal weight: 0.0060 chunk 78 optimal weight: 0.0070 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5842 moved from start: 2.9933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.043 1.232 23300 Z= 2.581 Angle : 2.675 47.282 32700 Z= 1.540 Chirality : 0.253 4.376 4000 Planarity : 0.010 0.190 3000 Dihedral : 29.976 171.988 5300 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 122.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.18), residues: 2200 helix: -2.04 (0.11), residues: 1654 sheet: None (None), residues: 0 loop : 0.37 (0.35), residues: 546 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 566 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 584 average time/residue: 0.3295 time to fit residues: 305.6676 Evaluate side-chains 532 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 512 time to evaluate : 2.274 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2242 time to fit residues: 10.8609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 132 optimal weight: 0.0270 chunk 199 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 158 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 126 optimal weight: 0.0980 chunk 169 optimal weight: 0.9980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 moved from start: 3.0398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.041 1.245 23300 Z= 2.465 Angle : 2.603 37.017 32700 Z= 1.492 Chirality : 0.242 4.568 4000 Planarity : 0.009 0.148 3000 Dihedral : 29.763 179.461 5300 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 119.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.18), residues: 2200 helix: -1.92 (0.11), residues: 1686 sheet: None (None), residues: 0 loop : 0.49 (0.36), residues: 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 559 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 567 average time/residue: 0.3329 time to fit residues: 299.1048 Evaluate side-chains 517 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 509 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2236 time to fit residues: 5.7329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 0.0570 chunk 158 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 139 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5359 r_free = 0.5359 target = 0.252184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.205891 restraints weight = 43055.078| |-----------------------------------------------------------------------------| r_work (start): 0.4866 rms_B_bonded: 2.75 r_work: 0.4853 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4841 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work: 0.4827 rms_B_bonded: 2.65 restraints_weight: 0.1250 r_work: 0.4814 rms_B_bonded: 2.80 restraints_weight: 0.0625 r_work: 0.4799 rms_B_bonded: 3.01 restraints_weight: 0.0312 r_work: 0.4784 rms_B_bonded: 3.25 restraints_weight: 0.0156 r_work: 0.4768 rms_B_bonded: 3.54 restraints_weight: 0.0078 r_work: 0.4751 rms_B_bonded: 3.87 restraints_weight: 0.0039 r_work: 0.4733 rms_B_bonded: 4.24 restraints_weight: 0.0020 r_work: 0.4714 rms_B_bonded: 4.65 restraints_weight: 0.0010 r_work (final): 0.4714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 3.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.039 1.209 23300 Z= 2.368 Angle : 2.519 37.185 32700 Z= 1.448 Chirality : 0.238 4.532 4000 Planarity : 0.009 0.130 3000 Dihedral : 29.864 176.421 5300 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 116.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.18), residues: 2200 helix: -1.96 (0.11), residues: 1829 sheet: None (None), residues: 0 loop : 0.37 (0.43), residues: 371 =============================================================================== Job complete usr+sys time: 6450.08 seconds wall clock time: 117 minutes 58.35 seconds (7078.35 seconds total)