Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 07:22:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/04_2023/6nym_0546.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/04_2023/6nym_0546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/04_2023/6nym_0546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/04_2023/6nym_0546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/04_2023/6nym_0546.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/04_2023/6nym_0546.pdb" } resolution = 3.6 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= 0.008 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 42948 2.51 5 N 12060 2.21 5 O 13512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 68664 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "C" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "D" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "E" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "F" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "G" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "H" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "I" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "J" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "K" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Chain: "L" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5722 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 16, 'TRANS': 733} Chain breaks: 1 Time building chain proxies: 26.50, per 1000 atoms: 0.39 Number of scatterers: 68664 At special positions: 0 Unit cell: (306.34, 276.66, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 13512 8.00 N 12060 7.00 C 42948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.02 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.02 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.02 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 749 " distance=2.02 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 749 " distance=2.02 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 749 " distance=2.02 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 749 " distance=2.02 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 749 " distance=2.02 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 749 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.44 Conformation dependent library (CDL) restraints added in 8.6 seconds 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16080 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 204 sheets defined 6.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU A 720 " --> pdb=" O ASN A 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 720' Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU B 720 " --> pdb=" O ASN B 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 717 through 720' Processing helix chain 'B' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET B 758 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 37 removed outlier: 3.805A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU C 720 " --> pdb=" O ASN C 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 717 through 720' Processing helix chain 'C' and resid 721 through 726 removed outlier: 3.617A pdb=" N LEU C 726 " --> pdb=" O PHE C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET C 758 " --> pdb=" O ASN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 4.129A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU D 720 " --> pdb=" O ASN D 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 717 through 720' Processing helix chain 'D' and resid 721 through 726 removed outlier: 3.617A pdb=" N LEU D 726 " --> pdb=" O PHE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 759 removed outlier: 3.661A pdb=" N MET D 758 " --> pdb=" O ASN D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE E 60 " --> pdb=" O PHE E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 60' Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU E 720 " --> pdb=" O ASN E 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 717 through 720' Processing helix chain 'E' and resid 721 through 726 removed outlier: 3.619A pdb=" N LEU E 726 " --> pdb=" O PHE E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET E 758 " --> pdb=" O ASN E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR E 765 " --> pdb=" O PRO E 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 37 removed outlier: 3.805A pdb=" N ALA F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 71 through 75 Processing helix chain 'F' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU F 720 " --> pdb=" O ASN F 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 717 through 720' Processing helix chain 'F' and resid 721 through 726 removed outlier: 3.619A pdb=" N LEU F 726 " --> pdb=" O PHE F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET F 758 " --> pdb=" O ASN F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR F 765 " --> pdb=" O PRO F 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE G 60 " --> pdb=" O PHE G 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 60' Processing helix chain 'G' and resid 71 through 75 Processing helix chain 'G' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU G 720 " --> pdb=" O ASN G 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 717 through 720' Processing helix chain 'G' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU G 726 " --> pdb=" O PHE G 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) Processing helix chain 'G' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET G 758 " --> pdb=" O ASN G 755 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR G 765 " --> pdb=" O PRO G 762 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE H 60 " --> pdb=" O PHE H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 71 through 75 Processing helix chain 'H' and resid 717 through 720 removed outlier: 3.842A pdb=" N GLU H 720 " --> pdb=" O ASN H 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 717 through 720' Processing helix chain 'H' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU H 726 " --> pdb=" O PHE H 722 " (cutoff:3.500A) Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 759 removed outlier: 3.661A pdb=" N MET H 758 " --> pdb=" O ASN H 755 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR H 765 " --> pdb=" O PRO H 762 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 37 removed outlier: 3.805A pdb=" N ALA I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 4.129A pdb=" N GLU I 59 " --> pdb=" O GLY I 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE I 60 " --> pdb=" O PHE I 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 71 through 75 Processing helix chain 'I' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU I 720 " --> pdb=" O ASN I 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 717 through 720' Processing helix chain 'I' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU I 726 " --> pdb=" O PHE I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) Processing helix chain 'I' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET I 758 " --> pdb=" O ASN I 755 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR I 765 " --> pdb=" O PRO I 762 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU J 59 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE J 60 " --> pdb=" O PHE J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU J 720 " --> pdb=" O ASN J 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 717 through 720' Processing helix chain 'J' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU J 726 " --> pdb=" O PHE J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) Processing helix chain 'J' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET J 758 " --> pdb=" O ASN J 755 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR J 765 " --> pdb=" O PRO J 762 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU K 59 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE K 60 " --> pdb=" O PHE K 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 71 through 75 Processing helix chain 'K' and resid 717 through 720 removed outlier: 3.840A pdb=" N GLU K 720 " --> pdb=" O ASN K 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 717 through 720' Processing helix chain 'K' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU K 726 " --> pdb=" O PHE K 722 " (cutoff:3.500A) Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) Processing helix chain 'K' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET K 758 " --> pdb=" O ASN K 755 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR K 765 " --> pdb=" O PRO K 762 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE L 60 " --> pdb=" O PHE L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 60' Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU L 720 " --> pdb=" O ASN L 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 717 through 720' Processing helix chain 'L' and resid 721 through 726 removed outlier: 3.619A pdb=" N LEU L 726 " --> pdb=" O PHE L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) Processing helix chain 'L' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET L 758 " --> pdb=" O ASN L 755 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR L 765 " --> pdb=" O PRO L 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 8.840A pdb=" N VAL A 48 " --> pdb=" O PRO F 341 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLN F 343 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG A 50 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE F 345 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN A 52 " --> pdb=" O ILE F 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 155 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 211 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY A 108 " --> pdb=" O THR A 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN A 140 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 168 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY A 278 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY A 278 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LYS A 274 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE A 359 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N HIS A 276 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG A 361 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY A 278 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN A 363 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 357 " --> pdb=" O HIS A 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 413 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 288 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU A 407 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU A 379 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 345 removed outlier: 6.539A pdb=" N VAL B 48 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG B 50 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA A 435 " --> pdb=" O ASN A 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 519 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG A 541 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 569 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 543 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 547 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 519 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG A 541 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 569 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 543 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 547 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 567 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 589 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL A 588 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY A 704 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET A 662 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR A 505 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 608 through 609 Processing sheet with id=AB6, first strand: chain 'A' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN A 643 " --> pdb=" O MET A 621 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 691 through 697 removed outlier: 3.649A pdb=" N THR A 691 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 791 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AB9, first strand: chain 'A' and resid 771 through 773 Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 155 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU B 211 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY B 108 " --> pdb=" O THR B 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN B 140 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 168 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.815A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY B 278 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.815A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY B 278 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS B 274 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE B 359 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS B 276 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG B 361 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY B 278 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 363 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 357 " --> pdb=" O HIS B 385 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 413 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 288 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU B 407 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU B 379 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 339 through 345 removed outlier: 6.207A pdb=" N VAL C 48 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG C 50 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA B 435 " --> pdb=" O ASN B 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 470 through 472 Processing sheet with id=AD1, first strand: chain 'B' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 519 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG B 541 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 569 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 543 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 547 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 519 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG B 541 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 569 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 543 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 547 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 567 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 589 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL B 588 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY B 704 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET B 662 " --> pdb=" O GLY B 704 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR B 505 " --> pdb=" O HIS B 531 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD5, first strand: chain 'B' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN B 643 " --> pdb=" O MET B 621 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 691 through 697 removed outlier: 3.649A pdb=" N THR B 691 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR B 791 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD8, first strand: chain 'B' and resid 771 through 773 Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 155 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU C 211 " --> pdb=" O ASN C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY C 108 " --> pdb=" O THR C 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN C 140 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 168 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY C 278 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY C 278 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS C 274 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ILE C 359 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS C 276 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG C 361 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY C 278 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN C 363 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 357 " --> pdb=" O HIS C 385 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 413 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.782A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 288 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU C 407 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU C 379 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 339 through 345 removed outlier: 6.214A pdb=" N VAL D 48 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG D 50 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA C 435 " --> pdb=" O ASN C 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 470 through 472 Processing sheet with id=AE9, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 519 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 541 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 569 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN C 543 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 547 " --> pdb=" O TYR C 573 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 519 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 541 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 569 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN C 543 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 547 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 567 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 589 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL C 588 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY C 704 " --> pdb=" O ALA C 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET C 662 " --> pdb=" O GLY C 704 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR C 505 " --> pdb=" O HIS C 531 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AF4, first strand: chain 'C' and resid 621 through 623 removed outlier: 3.501A pdb=" N ASN C 643 " --> pdb=" O MET C 621 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR C 691 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR C 791 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AF7, first strand: chain 'C' and resid 771 through 773 Processing sheet with id=AF8, first strand: chain 'D' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 155 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 211 " --> pdb=" O ASN D 244 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY D 108 " --> pdb=" O THR D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN D 140 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU D 168 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY D 278 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY D 278 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LYS D 274 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE D 359 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N HIS D 276 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG D 361 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY D 278 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN D 363 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 357 " --> pdb=" O HIS D 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 413 " --> pdb=" O THR D 451 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.782A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU D 288 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 377 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU D 407 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU D 379 " --> pdb=" O GLU D 407 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 339 through 345 removed outlier: 6.175A pdb=" N VAL E 48 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG E 50 " --> pdb=" O PRO D 341 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA D 435 " --> pdb=" O ASN D 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'D' and resid 470 through 472 Processing sheet with id=AG8, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 519 " --> pdb=" O ARG D 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG D 541 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 569 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN D 543 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 547 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 519 " --> pdb=" O ARG D 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG D 541 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 569 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN D 543 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 547 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 567 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 589 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL D 588 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY D 704 " --> pdb=" O ALA D 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET D 662 " --> pdb=" O GLY D 704 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.090A pdb=" N THR D 505 " --> pdb=" O HIS D 531 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 608 through 609 Processing sheet with id=AH3, first strand: chain 'D' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN D 643 " --> pdb=" O MET D 621 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR D 691 " --> pdb=" O TYR D 791 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR D 791 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AH6, first strand: chain 'D' and resid 771 through 773 Processing sheet with id=AH7, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.354A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL E 155 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU E 211 " --> pdb=" O ASN E 244 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.384A pdb=" N ASN E 140 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU E 168 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY E 278 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY E 278 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS E 274 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE E 359 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N HIS E 276 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG E 361 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY E 278 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN E 363 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 357 " --> pdb=" O HIS E 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE E 413 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 288 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA E 377 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU E 407 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU E 379 " --> pdb=" O GLU E 407 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 343 through 345 Processing sheet with id=AI5, first strand: chain 'E' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA E 435 " --> pdb=" O ASN E 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'E' and resid 470 through 472 Processing sheet with id=AI7, first strand: chain 'E' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL E 519 " --> pdb=" O ARG E 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG E 541 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 569 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN E 543 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 547 " --> pdb=" O TYR E 573 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL E 519 " --> pdb=" O ARG E 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG E 541 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 569 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN E 543 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 547 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU E 567 " --> pdb=" O ASN E 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 589 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL E 588 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY E 704 " --> pdb=" O ALA E 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET E 662 " --> pdb=" O GLY E 704 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR E 505 " --> pdb=" O HIS E 531 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 608 through 609 Processing sheet with id=AJ2, first strand: chain 'E' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN E 643 " --> pdb=" O MET E 621 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR E 691 " --> pdb=" O TYR E 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR E 791 " --> pdb=" O THR E 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AJ5, first strand: chain 'E' and resid 771 through 773 Processing sheet with id=AJ6, first strand: chain 'F' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL F 155 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU F 211 " --> pdb=" O ASN F 244 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY F 108 " --> pdb=" O THR F 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.382A pdb=" N ASN F 140 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU F 168 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ8 Processing sheet with id=AJ9, first strand: chain 'F' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY F 278 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY F 278 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LYS F 274 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE F 359 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS F 276 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG F 361 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY F 278 " --> pdb=" O ARG F 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN F 363 " --> pdb=" O GLY F 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 357 " --> pdb=" O HIS F 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE F 413 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU F 288 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA F 377 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU F 407 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU F 379 " --> pdb=" O GLU F 407 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 435 through 436 removed outlier: 7.017A pdb=" N ALA F 435 " --> pdb=" O ASN F 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'F' and resid 470 through 472 Processing sheet with id=AK5, first strand: chain 'F' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 519 " --> pdb=" O ARG F 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG F 541 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE F 569 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN F 543 " --> pdb=" O ILE F 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 547 " --> pdb=" O TYR F 573 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 519 " --> pdb=" O ARG F 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG F 541 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE F 569 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN F 543 " --> pdb=" O ILE F 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 547 " --> pdb=" O TYR F 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 567 " --> pdb=" O ASN F 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU F 589 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL F 588 " --> pdb=" O THR F 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY F 704 " --> pdb=" O ALA F 660 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET F 662 " --> pdb=" O GLY F 704 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'F' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR F 505 " --> pdb=" O HIS F 531 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 608 through 609 Processing sheet with id=AK9, first strand: chain 'F' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN F 643 " --> pdb=" O MET F 621 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR F 691 " --> pdb=" O TYR F 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR F 791 " --> pdb=" O THR F 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AL3, first strand: chain 'F' and resid 771 through 773 Processing sheet with id=AL4, first strand: chain 'G' and resid 48 through 53 removed outlier: 8.861A pdb=" N VAL G 48 " --> pdb=" O PRO L 341 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLN L 343 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG G 50 " --> pdb=" O GLN L 343 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE L 345 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN G 52 " --> pdb=" O ILE L 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'G' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL G 155 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU G 211 " --> pdb=" O ASN G 244 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'G' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY G 108 " --> pdb=" O THR G 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'G' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN G 140 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU G 168 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE G 203 " --> pdb=" O TRP G 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'G' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL G 252 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY G 278 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'G' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL G 252 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY G 278 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS G 274 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE G 359 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS G 276 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG G 361 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY G 278 " --> pdb=" O ARG G 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN G 363 " --> pdb=" O GLY G 278 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL G 357 " --> pdb=" O HIS G 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE G 413 " --> pdb=" O THR G 451 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'G' and resid 269 through 270 removed outlier: 6.782A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU G 288 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA G 377 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU G 407 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU G 379 " --> pdb=" O GLU G 407 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'G' and resid 339 through 345 removed outlier: 6.267A pdb=" N VAL H 48 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG H 50 " --> pdb=" O PRO G 341 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'G' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA G 435 " --> pdb=" O ASN G 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM3 Processing sheet with id=AM4, first strand: chain 'G' and resid 470 through 472 Processing sheet with id=AM5, first strand: chain 'G' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU G 500 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 519 " --> pdb=" O ARG G 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG G 541 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE G 569 " --> pdb=" O ARG G 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN G 543 " --> pdb=" O ILE G 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU G 547 " --> pdb=" O TYR G 573 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'G' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU G 500 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 519 " --> pdb=" O ARG G 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG G 541 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE G 569 " --> pdb=" O ARG G 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN G 543 " --> pdb=" O ILE G 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU G 547 " --> pdb=" O TYR G 573 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU G 567 " --> pdb=" O ASN G 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 589 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL G 588 " --> pdb=" O THR G 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY G 704 " --> pdb=" O ALA G 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET G 662 " --> pdb=" O GLY G 704 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'G' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR G 505 " --> pdb=" O HIS G 531 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'G' and resid 608 through 609 Processing sheet with id=AM9, first strand: chain 'G' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN G 643 " --> pdb=" O MET G 621 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'G' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR G 691 " --> pdb=" O TYR G 791 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR G 791 " --> pdb=" O THR G 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'G' and resid 729 through 730 Processing sheet with id=AN3, first strand: chain 'G' and resid 771 through 773 Processing sheet with id=AN4, first strand: chain 'H' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL H 155 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU H 211 " --> pdb=" O ASN H 244 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'H' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY H 108 " --> pdb=" O THR H 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN H 140 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU H 168 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE H 203 " --> pdb=" O TRP H 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN6 Processing sheet with id=AN7, first strand: chain 'H' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL H 252 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY H 278 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'H' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL H 252 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY H 278 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LYS H 274 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE H 359 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N HIS H 276 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ARG H 361 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY H 278 " --> pdb=" O ARG H 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN H 363 " --> pdb=" O GLY H 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL H 357 " --> pdb=" O HIS H 385 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE H 413 " --> pdb=" O THR H 451 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'H' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU H 288 " --> pdb=" O THR H 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA H 377 " --> pdb=" O LEU H 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU H 407 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU H 379 " --> pdb=" O GLU H 407 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'H' and resid 339 through 345 removed outlier: 6.417A pdb=" N VAL I 48 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG I 50 " --> pdb=" O PRO H 341 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'H' and resid 435 through 436 removed outlier: 7.017A pdb=" N ALA H 435 " --> pdb=" O ASN H 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'H' and resid 470 through 472 Processing sheet with id=AO4, first strand: chain 'H' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU H 500 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H 519 " --> pdb=" O ARG H 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG H 541 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 569 " --> pdb=" O ARG H 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN H 543 " --> pdb=" O ILE H 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU H 547 " --> pdb=" O TYR H 573 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'H' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU H 500 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H 519 " --> pdb=" O ARG H 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG H 541 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 569 " --> pdb=" O ARG H 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN H 543 " --> pdb=" O ILE H 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU H 547 " --> pdb=" O TYR H 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU H 567 " --> pdb=" O ASN H 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU H 589 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL H 588 " --> pdb=" O THR H 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY H 704 " --> pdb=" O ALA H 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET H 662 " --> pdb=" O GLY H 704 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'H' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR H 505 " --> pdb=" O HIS H 531 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'H' and resid 608 through 609 Processing sheet with id=AO8, first strand: chain 'H' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN H 643 " --> pdb=" O MET H 621 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'H' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR H 691 " --> pdb=" O TYR H 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR H 791 " --> pdb=" O THR H 691 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'H' and resid 729 through 730 Processing sheet with id=AP2, first strand: chain 'H' and resid 771 through 773 Processing sheet with id=AP3, first strand: chain 'I' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL I 155 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU I 211 " --> pdb=" O ASN I 244 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'I' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY I 108 " --> pdb=" O THR I 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP4 Processing sheet with id=AP5, first strand: chain 'I' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN I 140 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU I 168 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE I 203 " --> pdb=" O TRP I 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP5 Processing sheet with id=AP6, first strand: chain 'I' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL I 252 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY I 278 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'I' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL I 252 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY I 278 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS I 274 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE I 359 " --> pdb=" O LYS I 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS I 276 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG I 361 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY I 278 " --> pdb=" O ARG I 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN I 363 " --> pdb=" O GLY I 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL I 357 " --> pdb=" O HIS I 385 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE I 413 " --> pdb=" O THR I 451 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'I' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU I 288 " --> pdb=" O THR I 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA I 377 " --> pdb=" O LEU I 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU I 407 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU I 379 " --> pdb=" O GLU I 407 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'I' and resid 339 through 345 removed outlier: 6.225A pdb=" N VAL J 48 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG J 50 " --> pdb=" O PRO I 341 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'I' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA I 435 " --> pdb=" O ASN I 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ1 Processing sheet with id=AQ2, first strand: chain 'I' and resid 470 through 472 Processing sheet with id=AQ3, first strand: chain 'I' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU I 500 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL I 519 " --> pdb=" O ARG I 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG I 541 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE I 569 " --> pdb=" O ARG I 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN I 543 " --> pdb=" O ILE I 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU I 547 " --> pdb=" O TYR I 573 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'I' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU I 500 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL I 519 " --> pdb=" O ARG I 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG I 541 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE I 569 " --> pdb=" O ARG I 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN I 543 " --> pdb=" O ILE I 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU I 547 " --> pdb=" O TYR I 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU I 567 " --> pdb=" O ASN I 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU I 589 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL I 588 " --> pdb=" O THR I 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY I 704 " --> pdb=" O ALA I 660 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET I 662 " --> pdb=" O GLY I 704 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'I' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR I 505 " --> pdb=" O HIS I 531 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'I' and resid 608 through 609 Processing sheet with id=AQ7, first strand: chain 'I' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN I 643 " --> pdb=" O MET I 621 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'I' and resid 691 through 697 removed outlier: 3.647A pdb=" N THR I 691 " --> pdb=" O TYR I 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR I 791 " --> pdb=" O THR I 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'I' and resid 729 through 730 Processing sheet with id=AR1, first strand: chain 'I' and resid 771 through 773 Processing sheet with id=AR2, first strand: chain 'J' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL J 155 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU J 211 " --> pdb=" O ASN J 244 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'J' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY J 108 " --> pdb=" O THR J 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR3 Processing sheet with id=AR4, first strand: chain 'J' and resid 140 through 142 removed outlier: 6.384A pdb=" N ASN J 140 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU J 168 " --> pdb=" O SER J 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE J 203 " --> pdb=" O TRP J 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR4 Processing sheet with id=AR5, first strand: chain 'J' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL J 252 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY J 278 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'J' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL J 252 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY J 278 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS J 274 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ILE J 359 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N HIS J 276 " --> pdb=" O ILE J 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG J 361 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY J 278 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN J 363 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL J 357 " --> pdb=" O HIS J 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE J 413 " --> pdb=" O THR J 451 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'J' and resid 269 through 270 removed outlier: 6.782A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU J 288 " --> pdb=" O THR J 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA J 377 " --> pdb=" O LEU J 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU J 407 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU J 379 " --> pdb=" O GLU J 407 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'J' and resid 339 through 345 removed outlier: 6.481A pdb=" N VAL K 48 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG K 50 " --> pdb=" O PRO J 341 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'J' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA J 435 " --> pdb=" O ASN J 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR9 Processing sheet with id=AS1, first strand: chain 'J' and resid 470 through 472 Processing sheet with id=AS2, first strand: chain 'J' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU J 500 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL J 519 " --> pdb=" O ARG J 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG J 541 " --> pdb=" O LEU J 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE J 569 " --> pdb=" O ARG J 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN J 543 " --> pdb=" O ILE J 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU J 547 " --> pdb=" O TYR J 573 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'J' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU J 500 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL J 519 " --> pdb=" O ARG J 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG J 541 " --> pdb=" O LEU J 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE J 569 " --> pdb=" O ARG J 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN J 543 " --> pdb=" O ILE J 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU J 547 " --> pdb=" O TYR J 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU J 567 " --> pdb=" O ASN J 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU J 589 " --> pdb=" O LEU J 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL J 588 " --> pdb=" O THR J 614 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLY J 704 " --> pdb=" O ALA J 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET J 662 " --> pdb=" O GLY J 704 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'J' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR J 505 " --> pdb=" O HIS J 531 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'J' and resid 608 through 609 Processing sheet with id=AS6, first strand: chain 'J' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN J 643 " --> pdb=" O MET J 621 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'J' and resid 691 through 697 removed outlier: 3.647A pdb=" N THR J 691 " --> pdb=" O TYR J 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR J 791 " --> pdb=" O THR J 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'J' and resid 729 through 730 Processing sheet with id=AS9, first strand: chain 'J' and resid 771 through 773 Processing sheet with id=AT1, first strand: chain 'K' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL K 155 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU K 211 " --> pdb=" O ASN K 244 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY K 108 " --> pdb=" O THR K 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT2 Processing sheet with id=AT3, first strand: chain 'K' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN K 140 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU K 168 " --> pdb=" O SER K 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE K 203 " --> pdb=" O TRP K 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT3 Processing sheet with id=AT4, first strand: chain 'K' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL K 252 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY K 278 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'K' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL K 252 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY K 278 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LYS K 274 " --> pdb=" O VAL K 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE K 359 " --> pdb=" O LYS K 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS K 276 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG K 361 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY K 278 " --> pdb=" O ARG K 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN K 363 " --> pdb=" O GLY K 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL K 357 " --> pdb=" O HIS K 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE K 413 " --> pdb=" O THR K 451 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU K 288 " --> pdb=" O THR K 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA K 377 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU K 407 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU K 379 " --> pdb=" O GLU K 407 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'K' and resid 339 through 345 removed outlier: 6.339A pdb=" N VAL L 48 " --> pdb=" O VAL K 339 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG L 50 " --> pdb=" O PRO K 341 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'K' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA K 435 " --> pdb=" O ASN K 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT8 Processing sheet with id=AT9, first strand: chain 'K' and resid 470 through 472 Processing sheet with id=AU1, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU K 500 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL K 519 " --> pdb=" O ARG K 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG K 541 " --> pdb=" O LEU K 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE K 569 " --> pdb=" O ARG K 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN K 543 " --> pdb=" O ILE K 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU K 547 " --> pdb=" O TYR K 573 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU K 500 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL K 519 " --> pdb=" O ARG K 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG K 541 " --> pdb=" O LEU K 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE K 569 " --> pdb=" O ARG K 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN K 543 " --> pdb=" O ILE K 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU K 547 " --> pdb=" O TYR K 573 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU K 567 " --> pdb=" O ASN K 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU K 589 " --> pdb=" O LEU K 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL K 588 " --> pdb=" O THR K 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY K 704 " --> pdb=" O ALA K 660 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET K 662 " --> pdb=" O GLY K 704 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'K' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR K 505 " --> pdb=" O HIS K 531 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'K' and resid 608 through 609 Processing sheet with id=AU5, first strand: chain 'K' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN K 643 " --> pdb=" O MET K 621 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'K' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR K 691 " --> pdb=" O TYR K 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR K 791 " --> pdb=" O THR K 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 'K' and resid 729 through 730 Processing sheet with id=AU8, first strand: chain 'K' and resid 771 through 773 Processing sheet with id=AU9, first strand: chain 'L' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL L 155 " --> pdb=" O THR L 188 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU L 211 " --> pdb=" O ASN L 244 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'L' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY L 108 " --> pdb=" O THR L 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV1 Processing sheet with id=AV2, first strand: chain 'L' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN L 140 " --> pdb=" O GLU L 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU L 168 " --> pdb=" O SER L 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE L 203 " --> pdb=" O TRP L 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV2 Processing sheet with id=AV3, first strand: chain 'L' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL L 252 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY L 278 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AV4, first strand: chain 'L' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL L 252 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY L 278 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS L 274 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ILE L 359 " --> pdb=" O LYS L 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS L 276 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG L 361 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY L 278 " --> pdb=" O ARG L 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN L 363 " --> pdb=" O GLY L 278 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 357 " --> pdb=" O HIS L 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE L 413 " --> pdb=" O THR L 451 " (cutoff:3.500A) Processing sheet with id=AV5, first strand: chain 'L' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU L 288 " --> pdb=" O THR L 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA L 377 " --> pdb=" O LEU L 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU L 407 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU L 379 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'L' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA L 435 " --> pdb=" O ASN L 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV6 Processing sheet with id=AV7, first strand: chain 'L' and resid 470 through 472 Processing sheet with id=AV8, first strand: chain 'L' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU L 500 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL L 519 " --> pdb=" O ARG L 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG L 541 " --> pdb=" O LEU L 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE L 569 " --> pdb=" O ARG L 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN L 543 " --> pdb=" O ILE L 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU L 547 " --> pdb=" O TYR L 573 " (cutoff:3.500A) Processing sheet with id=AV9, first strand: chain 'L' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU L 500 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL L 519 " --> pdb=" O ARG L 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG L 541 " --> pdb=" O LEU L 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE L 569 " --> pdb=" O ARG L 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN L 543 " --> pdb=" O ILE L 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU L 547 " --> pdb=" O TYR L 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU L 567 " --> pdb=" O ASN L 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU L 589 " --> pdb=" O LEU L 567 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL L 588 " --> pdb=" O THR L 614 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLY L 704 " --> pdb=" O ALA L 660 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET L 662 " --> pdb=" O GLY L 704 " (cutoff:3.500A) Processing sheet with id=AW1, first strand: chain 'L' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR L 505 " --> pdb=" O HIS L 531 " (cutoff:3.500A) Processing sheet with id=AW2, first strand: chain 'L' and resid 608 through 609 Processing sheet with id=AW3, first strand: chain 'L' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN L 643 " --> pdb=" O MET L 621 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'L' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR L 691 " --> pdb=" O TYR L 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR L 791 " --> pdb=" O THR L 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'L' and resid 729 through 730 Processing sheet with id=AW6, first strand: chain 'L' and resid 771 through 773 809 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 42.36 Time building geometry restraints manager: 24.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22641 1.34 - 1.45: 10887 1.45 - 1.57: 36048 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" N LYS F 129 " pdb=" CA LYS F 129 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.88e+00 bond pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.85e+00 bond pdb=" N LYS D 129 " pdb=" CA LYS D 129 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.81e+00 bond pdb=" N LYS E 129 " pdb=" CA LYS E 129 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" N LYS K 129 " pdb=" CA LYS K 129 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.75e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.55: 804 105.55 - 112.68: 35766 112.68 - 119.80: 22965 119.80 - 126.92: 34322 126.92 - 134.04: 727 Bond angle restraints: 94584 Sorted by residual: angle pdb=" C GLY E 83 " pdb=" N ASN E 84 " pdb=" CA ASN E 84 " ideal model delta sigma weight residual 122.46 130.70 -8.24 1.41e+00 5.03e-01 3.41e+01 angle pdb=" C GLY D 83 " pdb=" N ASN D 84 " pdb=" CA ASN D 84 " ideal model delta sigma weight residual 122.46 130.69 -8.23 1.41e+00 5.03e-01 3.41e+01 angle pdb=" C GLY A 83 " pdb=" N ASN A 84 " pdb=" CA ASN A 84 " ideal model delta sigma weight residual 122.46 130.68 -8.22 1.41e+00 5.03e-01 3.40e+01 angle pdb=" C GLY L 83 " pdb=" N ASN L 84 " pdb=" CA ASN L 84 " ideal model delta sigma weight residual 122.46 130.67 -8.21 1.41e+00 5.03e-01 3.39e+01 angle pdb=" C GLY H 83 " pdb=" N ASN H 84 " pdb=" CA ASN H 84 " ideal model delta sigma weight residual 122.46 130.67 -8.21 1.41e+00 5.03e-01 3.39e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 38618 15.99 - 31.99: 2131 31.99 - 47.98: 363 47.98 - 63.97: 24 63.97 - 79.96: 36 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: dihedral pdb=" CB CYS G 738 " pdb=" SG CYS G 738 " pdb=" SG CYS G 749 " pdb=" CB CYS G 749 " ideal model delta sinusoidal sigma weight residual 93.00 172.96 -79.96 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS I 738 " pdb=" SG CYS I 738 " pdb=" SG CYS I 749 " pdb=" CB CYS I 749 " ideal model delta sinusoidal sigma weight residual 93.00 172.94 -79.94 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS J 738 " pdb=" SG CYS J 738 " pdb=" SG CYS J 749 " pdb=" CB CYS J 749 " ideal model delta sinusoidal sigma weight residual 93.00 172.94 -79.94 1 1.00e+01 1.00e-02 7.92e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 6261 0.043 - 0.086: 2845 0.086 - 0.129: 1192 0.129 - 0.172: 274 0.172 - 0.215: 48 Chirality restraints: 10620 Sorted by residual: chirality pdb=" CA ASN C 273 " pdb=" N ASN C 273 " pdb=" C ASN C 273 " pdb=" CB ASN C 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN L 273 " pdb=" N ASN L 273 " pdb=" C ASN L 273 " pdb=" CB ASN L 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN K 273 " pdb=" N ASN K 273 " pdb=" C ASN K 273 " pdb=" CB ASN K 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 574 " 0.018 2.00e-02 2.50e+03 1.46e-02 4.24e+00 pdb=" CG TYR I 574 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR I 574 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR I 574 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR I 574 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I 574 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR I 574 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 574 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 574 " -0.018 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR A 574 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 574 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 574 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 574 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 574 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 574 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 574 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 574 " 0.018 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR G 574 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR G 574 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR G 574 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 574 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR G 574 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G 574 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 574 " 0.006 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 16111 2.79 - 3.32: 63105 3.32 - 3.84: 117525 3.84 - 4.37: 134784 4.37 - 4.90: 234226 Nonbonded interactions: 565751 Sorted by model distance: nonbonded pdb=" OG1 THR L 153 " pdb=" OG1 THR L 185 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR G 153 " pdb=" OG1 THR G 185 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR C 153 " pdb=" OG1 THR C 185 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR I 153 " pdb=" OG1 THR I 185 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR H 153 " pdb=" OG1 THR H 185 " model vdw 2.261 2.440 ... (remaining 565746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 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: 0.090 Extract box with map and model: 16.070 Check model and map are aligned: 0.780 Set scattering table: 0.490 Process input model: 156.630 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.005 0.051 69840 Z= 0.333 Angle : 0.935 11.187 94584 Z= 0.534 Chirality : 0.057 0.215 10620 Planarity : 0.005 0.049 12396 Dihedral : 10.432 70.751 25056 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer Outliers : 0.32 % 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: -5.10 (0.07), residues: 8952 helix: -4.39 (0.13), residues: 288 sheet: -3.69 (0.09), residues: 2076 loop : -3.50 (0.06), residues: 6588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 383 time to evaluate : 6.403 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: 24 outliers final: 8 residues processed: 403 average time/residue: 0.6078 time to fit residues: 437.8380 Evaluate side-chains 189 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 6.343 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5095 time to fit residues: 16.3901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 5.9990 chunk 682 optimal weight: 5.9990 chunk 378 optimal weight: 9.9990 chunk 233 optimal weight: 0.0570 chunk 460 optimal weight: 4.9990 chunk 364 optimal weight: 50.0000 chunk 705 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 428 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 817 optimal weight: 0.7980 overall best weight: 3.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 543 ASN A 685 GLN A 730 ASN A 755 ASN B 289 ASN B 543 ASN B 685 GLN B 730 ASN B 755 ASN C 289 ASN C 543 ASN C 685 GLN C 730 ASN C 755 ASN D 289 ASN D 543 ASN D 685 GLN D 730 ASN D 755 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 543 ASN E 618 ASN E 685 GLN E 730 ASN E 755 ASN F 289 ASN F 543 ASN F 685 GLN F 730 ASN F 755 ASN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 ASN G 543 ASN G 685 GLN G 730 ASN G 755 ASN H 289 ASN H 543 ASN H 665 ASN H 685 GLN H 730 ASN H 755 ASN I 289 ASN I 543 ASN I 685 GLN I 730 ASN I 755 ASN J 289 ASN J 543 ASN J 685 GLN J 730 ASN J 755 ASN K 289 ASN K 543 ASN K 685 GLN K 730 ASN K 755 ASN L 289 ASN L 543 ASN L 685 GLN L 730 ASN L 755 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 69840 Z= 0.290 Angle : 0.640 7.974 94584 Z= 0.342 Chirality : 0.048 0.151 10620 Planarity : 0.004 0.043 12396 Dihedral : 6.121 21.143 9516 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer Outliers : 1.50 % 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: -4.79 (0.07), residues: 8952 helix: -3.38 (0.17), residues: 384 sheet: -3.45 (0.09), residues: 1980 loop : -3.34 (0.06), residues: 6588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 224 time to evaluate : 6.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 58 residues processed: 297 average time/residue: 0.5644 time to fit residues: 313.0064 Evaluate side-chains 238 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 180 time to evaluate : 6.378 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4959 time to fit residues: 63.1571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 0.0370 chunk 253 optimal weight: 4.9990 chunk 680 optimal weight: 20.0000 chunk 556 optimal weight: 0.0970 chunk 225 optimal weight: 10.0000 chunk 818 optimal weight: 20.0000 chunk 884 optimal weight: 10.0000 chunk 729 optimal weight: 10.0000 chunk 811 optimal weight: 30.0000 chunk 279 optimal weight: 10.0000 chunk 656 optimal weight: 20.0000 overall best weight: 5.0266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 340 GLN B 62 ASN B 256 HIS B 340 GLN B 385 HIS B 618 ASN ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 340 GLN C 385 HIS C 469 HIS D 256 HIS D 340 GLN D 385 HIS ** D 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 HIS F 340 GLN F 385 HIS G 256 HIS G 340 GLN H 62 ASN H 256 HIS H 340 GLN H 385 HIS I 256 HIS I 340 GLN I 385 HIS I 469 HIS J 256 HIS J 340 GLN J 385 HIS J 469 HIS K 62 ASN K 256 HIS K 340 GLN K 385 HIS ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 HIS L 340 GLN L 385 HIS L 803 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 69840 Z= 0.393 Angle : 0.705 7.314 94584 Z= 0.379 Chirality : 0.050 0.200 10620 Planarity : 0.004 0.036 12396 Dihedral : 6.212 22.872 9516 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.23 % Favored : 81.77 % Rotamer Outliers : 1.59 % 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: -4.68 (0.07), residues: 8952 helix: -2.54 (0.20), residues: 384 sheet: -3.54 (0.10), residues: 1872 loop : -3.26 (0.06), residues: 6696 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 230 time to evaluate : 6.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 64 residues processed: 323 average time/residue: 0.5767 time to fit residues: 347.0452 Evaluate side-chains 250 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 186 time to evaluate : 6.457 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.5179 time to fit residues: 71.6862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 40.0000 chunk 615 optimal weight: 0.9990 chunk 424 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 390 optimal weight: 8.9990 chunk 549 optimal weight: 0.8980 chunk 821 optimal weight: 50.0000 chunk 869 optimal weight: 5.9990 chunk 429 optimal weight: 9.9990 chunk 778 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN D 62 ASN ** D 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN E 385 HIS ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 385 HIS ** G 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 618 ASN ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 69840 Z= 0.342 Angle : 0.664 7.706 94584 Z= 0.356 Chirality : 0.049 0.178 10620 Planarity : 0.003 0.031 12396 Dihedral : 6.034 21.842 9516 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.59 % Favored : 83.41 % Rotamer Outliers : 2.01 % 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: -4.50 (0.08), residues: 8952 helix: -2.02 (0.23), residues: 384 sheet: -3.38 (0.10), residues: 1740 loop : -3.20 (0.07), residues: 6828 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 230 time to evaluate : 6.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 102 residues processed: 343 average time/residue: 0.5586 time to fit residues: 357.6749 Evaluate side-chains 299 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 197 time to evaluate : 6.358 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 0.5049 time to fit residues: 107.3333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 20.0000 chunk 493 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 647 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 742 optimal weight: 40.0000 chunk 601 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 444 optimal weight: 0.3980 chunk 780 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 ASN ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN ** J 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 764 ASN K 803 ASN ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 69840 Z= 0.305 Angle : 0.649 7.488 94584 Z= 0.344 Chirality : 0.048 0.205 10620 Planarity : 0.003 0.030 12396 Dihedral : 5.859 20.996 9516 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.02 % Favored : 82.98 % Rotamer Outliers : 1.40 % 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: -4.45 (0.08), residues: 8952 helix: -1.89 (0.24), residues: 384 sheet: -3.36 (0.10), residues: 1824 loop : -3.16 (0.07), residues: 6744 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 223 time to evaluate : 6.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 54 residues processed: 312 average time/residue: 0.5811 time to fit residues: 338.7273 Evaluate side-chains 249 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 195 time to evaluate : 6.322 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.5241 time to fit residues: 63.5123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 40.0000 chunk 783 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 510 optimal weight: 9.9990 chunk 214 optimal weight: 0.3980 chunk 870 optimal weight: 6.9990 chunk 722 optimal weight: 9.9990 chunk 403 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 288 optimal weight: 40.0000 chunk 457 optimal weight: 2.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 803 ASN ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 803 ASN ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 803 ASN ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 803 ASN K 618 ASN ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 69840 Z= 0.253 Angle : 0.614 7.739 94584 Z= 0.324 Chirality : 0.048 0.226 10620 Planarity : 0.003 0.030 12396 Dihedral : 5.603 20.338 9516 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.74 % Favored : 84.26 % Rotamer Outliers : 0.89 % 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: -4.38 (0.08), residues: 8952 helix: -1.71 (0.24), residues: 384 sheet: -3.38 (0.10), residues: 1944 loop : -3.06 (0.07), residues: 6624 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 6.408 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: 66 outliers final: 39 residues processed: 267 average time/residue: 0.6092 time to fit residues: 299.7664 Evaluate side-chains 234 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 6.358 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.5317 time to fit residues: 47.7028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 496 optimal weight: 7.9990 chunk 635 optimal weight: 10.0000 chunk 492 optimal weight: 10.0000 chunk 733 optimal weight: 10.0000 chunk 486 optimal weight: 5.9990 chunk 867 optimal weight: 10.0000 chunk 542 optimal weight: 6.9990 chunk 528 optimal weight: 7.9990 chunk 400 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 803 ASN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN E 62 ASN ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN H 803 ASN I 803 ASN ** I 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 69840 Z= 0.423 Angle : 0.719 8.424 94584 Z= 0.384 Chirality : 0.051 0.180 10620 Planarity : 0.004 0.035 12396 Dihedral : 6.042 22.422 9516 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.40 % Favored : 79.60 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.08), residues: 8952 helix: -1.54 (0.25), residues: 384 sheet: -3.68 (0.10), residues: 1980 loop : -3.15 (0.07), residues: 6588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 215 time to evaluate : 6.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 65 residues processed: 319 average time/residue: 0.6224 time to fit residues: 363.3350 Evaluate side-chains 261 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 196 time to evaluate : 6.292 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.5445 time to fit residues: 76.5106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 1.9990 chunk 346 optimal weight: 6.9990 chunk 518 optimal weight: 30.0000 chunk 261 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 551 optimal weight: 2.9990 chunk 590 optimal weight: 0.0030 chunk 428 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 681 optimal weight: 9.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 764 ASN ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 69840 Z= 0.217 Angle : 0.620 12.205 94584 Z= 0.322 Chirality : 0.047 0.209 10620 Planarity : 0.003 0.030 12396 Dihedral : 5.527 21.058 9516 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer Outliers : 1.01 % 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: -4.32 (0.08), residues: 8952 helix: -1.57 (0.25), residues: 384 sheet: -3.32 (0.10), residues: 2028 loop : -3.02 (0.07), residues: 6540 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 219 time to evaluate : 6.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 40 residues processed: 268 average time/residue: 0.6199 time to fit residues: 305.4249 Evaluate side-chains 236 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 6.424 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5654 time to fit residues: 49.8022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 3.9990 chunk 831 optimal weight: 8.9990 chunk 758 optimal weight: 10.0000 chunk 808 optimal weight: 30.0000 chunk 830 optimal weight: 8.9990 chunk 486 optimal weight: 0.5980 chunk 352 optimal weight: 20.0000 chunk 634 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 730 optimal weight: 2.9990 chunk 764 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 69840 Z= 0.248 Angle : 0.636 12.382 94584 Z= 0.328 Chirality : 0.048 0.243 10620 Planarity : 0.003 0.030 12396 Dihedral : 5.450 21.002 9516 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.26 % Favored : 83.74 % Rotamer Outliers : 0.47 % 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: -4.30 (0.08), residues: 8952 helix: -1.71 (0.24), residues: 384 sheet: -3.25 (0.10), residues: 1944 loop : -3.03 (0.07), residues: 6624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 209 time to evaluate : 6.372 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 outliers start: 35 outliers final: 21 residues processed: 231 average time/residue: 0.6182 time to fit residues: 264.1018 Evaluate side-chains 221 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 200 time to evaluate : 6.380 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5232 time to fit residues: 30.0742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 9.9990 chunk 530 optimal weight: 0.9990 chunk 854 optimal weight: 6.9990 chunk 521 optimal weight: 8.9990 chunk 405 optimal weight: 4.9990 chunk 594 optimal weight: 0.0070 chunk 896 optimal weight: 7.9990 chunk 825 optimal weight: 5.9990 chunk 713 optimal weight: 4.9990 chunk 74 optimal weight: 40.0000 chunk 551 optimal weight: 3.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 764 ASN ** I 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 69840 Z= 0.251 Angle : 0.638 15.000 94584 Z= 0.327 Chirality : 0.047 0.158 10620 Planarity : 0.003 0.028 12396 Dihedral : 5.398 21.125 9516 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer Outliers : 0.34 % 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: -4.29 (0.08), residues: 8952 helix: -1.74 (0.24), residues: 384 sheet: -3.31 (0.10), residues: 1884 loop : -3.01 (0.07), residues: 6684 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 6.567 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 outliers start: 25 outliers final: 15 residues processed: 219 average time/residue: 0.6453 time to fit residues: 261.7771 Evaluate side-chains 208 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 6.397 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5562 time to fit residues: 24.3462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 0.0270 chunk 567 optimal weight: 9.9990 chunk 760 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 658 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 715 optimal weight: 6.9990 chunk 299 optimal weight: 50.0000 chunk 734 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN B 756 GLN ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 764 ASN ** H 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 764 ASN ** L 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.160770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.091350 restraints weight = 238570.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.096612 restraints weight = 114926.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.098283 restraints weight = 79909.144| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 69840 Z= 0.428 Angle : 0.751 14.643 94584 Z= 0.393 Chirality : 0.051 0.251 10620 Planarity : 0.004 0.035 12396 Dihedral : 5.957 24.959 9516 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.34 % Favored : 79.66 % Rotamer Outliers : 0.32 % 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: -4.50 (0.08), residues: 8952 helix: -1.72 (0.24), residues: 384 sheet: -3.55 (0.10), residues: 2028 loop : -3.10 (0.07), residues: 6540 =============================================================================== Job complete usr+sys time: 9018.95 seconds wall clock time: 165 minutes 19.00 seconds (9919.00 seconds total)