Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 05:38:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/04_2023/6nyj_0544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/04_2023/6nyj_0544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/04_2023/6nyj_0544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/04_2023/6nyj_0544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/04_2023/6nyj_0544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyj_0544/04_2023/6nyj_0544.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.090 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 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s 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: 25.81, per 1000 atoms: 0.38 Number of scatterers: 68664 At special positions: 0 Unit cell: (299.98, 293.62, 119.78, 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=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 749 " distance=2.03 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 749 " distance=2.03 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 749 " distance=2.03 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 749 " distance=2.03 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: 20.44 Conformation dependent library (CDL) restraints added in 7.9 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: 84 helices and 180 sheets defined 6.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.991A 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 removed outlier: 3.808A pdb=" N SER A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 765' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 4.212A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.991A 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 removed outlier: 3.808A pdb=" N SER B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 761 through 765' Processing helix chain 'C' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.991A 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 removed outlier: 3.808A pdb=" N SER C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN C 764 " --> pdb=" O ASN C 761 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 761 through 765' Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 3.991A 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 removed outlier: 3.809A pdb=" N SER D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 720 removed outlier: 3.855A 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 Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.326A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN D 764 " --> pdb=" O ASN D 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 761 through 765' Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 3.992A 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 removed outlier: 3.808A pdb=" N SER E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 717 through 720 removed outlier: 3.855A 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 Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN E 764 " --> pdb=" O ASN E 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR E 765 " --> pdb=" O PRO E 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 761 through 765' Processing helix chain 'F' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.991A 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 removed outlier: 3.808A pdb=" N SER F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN F 764 " --> pdb=" O ASN F 761 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR F 765 " --> pdb=" O PRO F 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 761 through 765' Processing helix chain 'G' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.992A 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 removed outlier: 3.809A pdb=" N SER G 74 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN G 764 " --> pdb=" O ASN G 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR G 765 " --> pdb=" O PRO G 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 761 through 765' Processing helix chain 'H' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 3.991A 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 removed outlier: 3.808A pdb=" N SER H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.326A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.523A pdb=" N ASN H 764 " --> pdb=" O ASN H 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR H 765 " --> pdb=" O PRO H 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 761 through 765' Processing helix chain 'I' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 4.210A pdb=" N GLU I 59 " --> pdb=" O GLY I 56 " (cutoff:3.500A) removed outlier: 3.992A 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 removed outlier: 3.809A pdb=" N SER I 74 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN I 764 " --> pdb=" O ASN I 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR I 765 " --> pdb=" O PRO I 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 761 through 765' Processing helix chain 'J' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU J 59 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 3.991A 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 removed outlier: 3.808A pdb=" N SER J 74 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 717 through 720 removed outlier: 3.857A 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 Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN J 764 " --> pdb=" O ASN J 761 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR J 765 " --> pdb=" O PRO J 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 761 through 765' Processing helix chain 'K' and resid 29 through 38 removed outlier: 3.668A pdb=" N ALA K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU K 59 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 3.992A 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 removed outlier: 3.808A pdb=" N SER K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.325A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN K 764 " --> pdb=" O ASN K 761 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR K 765 " --> pdb=" O PRO K 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 761 through 765' Processing helix chain 'L' and resid 29 through 38 removed outlier: 3.667A pdb=" N ALA L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 4.211A pdb=" N GLU L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 3.991A 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 removed outlier: 3.808A pdb=" N SER L 74 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 717 through 720 removed outlier: 3.856A 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 Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.324A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.524A pdb=" N ASN L 764 " --> pdb=" O ASN L 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR L 765 " --> pdb=" O PRO L 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 761 through 765' Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN A 126 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP A 49 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP A 102 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 51 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG A 50 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE B 345 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN A 52 " --> pdb=" O ILE B 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS A 88 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN A 140 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 168 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 224 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 257 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL A 155 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 187 " --> pdb=" O ASN A 212 " (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: 6.296A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 381 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 345 removed outlier: 6.368A pdb=" N TRP F 49 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP F 102 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE F 51 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN F 126 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU A 517 " --> pdb=" O ARG A 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS A 562 " --> pdb=" O PHE A 532 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU A 534 " --> pdb=" O LYS A 562 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU A 567 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 589 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL A 588 " --> pdb=" O THR A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE A 572 " --> pdb=" O ALA A 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU A 645 " --> pdb=" O TYR A 623 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 642 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN A 682 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR A 644 " --> pdb=" O ASN A 682 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 662 through 664 Processing sheet with id=AB5, first strand: chain 'A' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR A 691 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR A 791 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AB7, first strand: chain 'A' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP A 773 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 771 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 125 through 126 removed outlier: 8.279A pdb=" N ASN B 126 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP B 49 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP B 102 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE B 51 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG B 50 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE C 345 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 52 " --> pdb=" O ILE C 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS B 88 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN B 140 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 168 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 224 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU B 257 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL B 155 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU B 187 " --> pdb=" O ASN B 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 381 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU B 517 " --> pdb=" O ARG B 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS B 562 " --> pdb=" O PHE B 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU B 534 " --> pdb=" O LYS B 562 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU B 567 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 589 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL B 588 " --> pdb=" O THR B 614 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 572 through 573 removed outlier: 6.284A pdb=" N PHE B 572 " --> pdb=" O ALA B 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU B 645 " --> pdb=" O TYR B 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 642 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN B 682 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR B 644 " --> pdb=" O ASN B 682 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 662 through 664 Processing sheet with id=AD2, first strand: chain 'B' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR B 691 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR B 791 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD4, first strand: chain 'B' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP B 773 " --> pdb=" O CYS B 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 771 " --> pdb=" O VAL B 740 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN C 126 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP C 49 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP C 102 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 51 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG C 50 " --> pdb=" O GLN D 343 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE D 345 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN C 52 " --> pdb=" O ILE D 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS C 88 " --> pdb=" O GLY C 79 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN C 140 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU C 168 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 224 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU C 257 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL C 155 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU C 187 " --> pdb=" O ASN C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.296A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 381 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 517 " --> pdb=" O ARG C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS C 562 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU C 534 " --> pdb=" O LYS C 562 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU C 567 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 589 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL C 588 " --> pdb=" O THR C 614 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE C 572 " --> pdb=" O ALA C 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU C 645 " --> pdb=" O TYR C 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE C 642 " --> pdb=" O LYS C 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN C 682 " --> pdb=" O ILE C 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR C 644 " --> pdb=" O ASN C 682 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 662 through 664 Processing sheet with id=AE8, first strand: chain 'C' and resid 691 through 697 removed outlier: 4.068A pdb=" N THR C 691 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR C 791 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AF1, first strand: chain 'C' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP C 773 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 771 " --> pdb=" O VAL C 740 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN D 126 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP D 49 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP D 102 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE D 51 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ARG D 50 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE E 345 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN D 52 " --> pdb=" O ILE E 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS D 88 " --> pdb=" O GLY D 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN D 140 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU D 168 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL D 224 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU D 257 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL D 155 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU D 187 " --> pdb=" O ASN D 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'D' and resid 252 through 253 removed outlier: 6.296A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 381 " --> pdb=" O GLU D 407 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU D 517 " --> pdb=" O ARG D 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS D 562 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU D 534 " --> pdb=" O LYS D 562 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU D 567 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 589 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL D 588 " --> pdb=" O THR D 614 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE D 572 " --> pdb=" O ALA D 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'D' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU D 645 " --> pdb=" O TYR D 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE D 642 " --> pdb=" O LYS D 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN D 682 " --> pdb=" O ILE D 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR D 644 " --> pdb=" O ASN D 682 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 662 through 664 Processing sheet with id=AG5, first strand: chain 'D' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR D 691 " --> pdb=" O TYR D 791 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR D 791 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AG7, first strand: chain 'D' and resid 737 through 740 removed outlier: 3.683A pdb=" N TRP D 773 " --> pdb=" O CYS D 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 771 " --> pdb=" O VAL D 740 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN E 126 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP E 49 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP E 102 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE E 51 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG E 50 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE F 345 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN E 52 " --> pdb=" O ILE F 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'E' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS E 88 " --> pdb=" O GLY E 79 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN E 140 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU E 168 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 224 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU E 257 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'E' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL E 155 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU E 187 " --> pdb=" O ASN E 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.296A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR E 381 " --> pdb=" O GLU E 407 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU E 517 " --> pdb=" O ARG E 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'E' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS E 562 " --> pdb=" O PHE E 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU E 534 " --> pdb=" O LYS E 562 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU E 567 " --> pdb=" O ASN E 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 589 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL E 588 " --> pdb=" O THR E 614 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE E 572 " --> pdb=" O ALA E 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU E 645 " --> pdb=" O TYR E 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE E 642 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN E 682 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 644 " --> pdb=" O ASN E 682 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 662 through 664 Processing sheet with id=AI2, first strand: chain 'E' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR E 691 " --> pdb=" O TYR E 791 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR E 791 " --> pdb=" O THR E 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AI4, first strand: chain 'E' and resid 737 through 740 removed outlier: 3.683A pdb=" N TRP E 773 " --> pdb=" O CYS E 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS E 771 " --> pdb=" O VAL E 740 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS F 88 " --> pdb=" O GLY F 79 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN F 140 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU F 168 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL F 224 " --> pdb=" O THR F 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU F 257 " --> pdb=" O ASP F 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'F' and resid 155 through 157 removed outlier: 6.631A pdb=" N VAL F 155 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU F 187 " --> pdb=" O ASN F 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'F' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR F 381 " --> pdb=" O GLU F 407 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU F 517 " --> pdb=" O ARG F 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'F' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS F 562 " --> pdb=" O PHE F 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU F 534 " --> pdb=" O LYS F 562 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU F 567 " --> pdb=" O ASN F 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU F 589 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL F 588 " --> pdb=" O THR F 614 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE F 572 " --> pdb=" O ALA F 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'F' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU F 645 " --> pdb=" O TYR F 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE F 642 " --> pdb=" O LYS F 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN F 682 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR F 644 " --> pdb=" O ASN F 682 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 662 through 664 Processing sheet with id=AJ7, first strand: chain 'F' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR F 691 " --> pdb=" O TYR F 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR F 791 " --> pdb=" O THR F 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AJ9, first strand: chain 'F' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP F 773 " --> pdb=" O CYS F 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS F 771 " --> pdb=" O VAL F 740 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'G' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN G 126 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP G 49 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP G 102 " --> pdb=" O TRP G 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE G 51 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ARG G 50 " --> pdb=" O GLN H 343 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE H 345 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN G 52 " --> pdb=" O ILE H 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'G' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS G 88 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN G 140 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU G 168 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE G 203 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL G 224 " --> pdb=" O THR G 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU G 257 " --> pdb=" O ASP G 281 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'G' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL G 155 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU G 187 " --> pdb=" O ASN G 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 Processing sheet with id=AK5, first strand: chain 'G' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL G 252 " --> pdb=" O HIS G 276 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 381 " --> pdb=" O GLU G 407 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 343 through 345 removed outlier: 6.368A pdb=" N TRP L 49 " --> pdb=" O GLU L 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP L 102 " --> pdb=" O TRP L 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE L 51 " --> pdb=" O ASP L 102 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN L 126 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 476 through 477 removed outlier: 6.456A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU G 500 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU G 517 " --> pdb=" O ARG G 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'G' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS G 562 " --> pdb=" O PHE G 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU G 534 " --> pdb=" O LYS G 562 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU G 567 " --> pdb=" O ASN G 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 589 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL G 588 " --> pdb=" O THR G 614 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE G 572 " --> pdb=" O ALA G 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'G' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU G 645 " --> pdb=" O TYR G 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE G 642 " --> pdb=" O LYS G 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN G 682 " --> pdb=" O ILE G 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR G 644 " --> pdb=" O ASN G 682 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 662 through 664 Processing sheet with id=AL5, first strand: chain 'G' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR G 691 " --> pdb=" O TYR G 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR G 791 " --> pdb=" O THR G 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'G' and resid 729 through 730 Processing sheet with id=AL7, first strand: chain 'G' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP G 773 " --> pdb=" O CYS G 738 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 771 " --> pdb=" O VAL G 740 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'H' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN H 126 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP H 49 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP H 102 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE H 51 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ARG H 50 " --> pdb=" O GLN I 343 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE I 345 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN H 52 " --> pdb=" O ILE I 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 Processing sheet with id=AL9, first strand: chain 'H' and resid 78 through 79 removed outlier: 3.540A pdb=" N HIS H 88 " --> pdb=" O GLY H 79 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN H 140 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU H 168 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE H 203 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL H 224 " --> pdb=" O THR H 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU H 257 " --> pdb=" O ASP H 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM1 Processing sheet with id=AM2, first strand: chain 'H' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL H 155 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU H 187 " --> pdb=" O ASN H 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM2 Processing sheet with id=AM3, first strand: chain 'H' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL H 252 " --> pdb=" O HIS H 276 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'H' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR H 381 " --> pdb=" O GLU H 407 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'H' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU H 500 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU H 517 " --> pdb=" O ARG H 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM5 Processing sheet with id=AM6, first strand: chain 'H' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS H 562 " --> pdb=" O PHE H 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU H 534 " --> pdb=" O LYS H 562 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'H' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU H 567 " --> pdb=" O ASN H 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU H 589 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 588 " --> pdb=" O THR H 614 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'H' and resid 572 through 573 removed outlier: 6.282A pdb=" N PHE H 572 " --> pdb=" O ALA H 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM8 Processing sheet with id=AM9, first strand: chain 'H' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU H 645 " --> pdb=" O TYR H 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE H 642 " --> pdb=" O LYS H 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN H 682 " --> pdb=" O ILE H 642 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR H 644 " --> pdb=" O ASN H 682 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'H' and resid 662 through 664 Processing sheet with id=AN2, first strand: chain 'H' and resid 691 through 697 removed outlier: 4.068A pdb=" N THR H 691 " --> pdb=" O TYR H 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR H 791 " --> pdb=" O THR H 691 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'H' and resid 729 through 730 Processing sheet with id=AN4, first strand: chain 'H' and resid 737 through 740 removed outlier: 3.683A pdb=" N TRP H 773 " --> pdb=" O CYS H 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 771 " --> pdb=" O VAL H 740 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'I' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN I 126 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP I 49 " --> pdb=" O GLU I 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP I 102 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE I 51 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ARG I 50 " --> pdb=" O GLN J 343 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE J 345 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN I 52 " --> pdb=" O ILE J 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'I' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS I 88 " --> pdb=" O GLY I 79 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'I' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN I 140 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU I 168 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE I 203 " --> pdb=" O TRP I 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL I 224 " --> pdb=" O THR I 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU I 257 " --> pdb=" O ASP I 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN7 Processing sheet with id=AN8, first strand: chain 'I' and resid 155 through 157 removed outlier: 6.631A pdb=" N VAL I 155 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU I 187 " --> pdb=" O ASN I 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN8 Processing sheet with id=AN9, first strand: chain 'I' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL I 252 " --> pdb=" O HIS I 276 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'I' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR I 381 " --> pdb=" O GLU I 407 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'I' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU I 500 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU I 517 " --> pdb=" O ARG I 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'I' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS I 562 " --> pdb=" O PHE I 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU I 534 " --> pdb=" O LYS I 562 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'I' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU I 567 " --> pdb=" O ASN I 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU I 589 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL I 588 " --> pdb=" O THR I 614 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'I' and resid 572 through 573 removed outlier: 6.284A pdb=" N PHE I 572 " --> pdb=" O ALA I 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO5 Processing sheet with id=AO6, first strand: chain 'I' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU I 645 " --> pdb=" O TYR I 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE I 642 " --> pdb=" O LYS I 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN I 682 " --> pdb=" O ILE I 642 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR I 644 " --> pdb=" O ASN I 682 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'I' and resid 662 through 664 Processing sheet with id=AO8, first strand: chain 'I' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR I 691 " --> pdb=" O TYR I 791 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR I 791 " --> pdb=" O THR I 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'I' and resid 729 through 730 Processing sheet with id=AP1, first strand: chain 'I' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP I 773 " --> pdb=" O CYS I 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS I 771 " --> pdb=" O VAL I 740 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'J' and resid 125 through 126 removed outlier: 8.278A pdb=" N ASN J 126 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP J 49 " --> pdb=" O GLU J 100 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP J 102 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE J 51 " --> pdb=" O ASP J 102 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ARG J 50 " --> pdb=" O GLN K 343 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE K 345 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN J 52 " --> pdb=" O ILE K 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP2 Processing sheet with id=AP3, first strand: chain 'J' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS J 88 " --> pdb=" O GLY J 79 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'J' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN J 140 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU J 168 " --> pdb=" O SER J 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE J 203 " --> pdb=" O TRP J 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL J 224 " --> pdb=" O THR J 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU J 257 " --> pdb=" O ASP J 281 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP4 Processing sheet with id=AP5, first strand: chain 'J' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL J 155 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU J 187 " --> pdb=" O ASN J 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP5 Processing sheet with id=AP6, first strand: chain 'J' and resid 252 through 253 removed outlier: 6.298A pdb=" N VAL J 252 " --> pdb=" O HIS J 276 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'J' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR J 381 " --> pdb=" O GLU J 407 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'J' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU J 500 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU J 517 " --> pdb=" O ARG J 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP8 Processing sheet with id=AP9, first strand: chain 'J' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS J 562 " --> pdb=" O PHE J 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU J 534 " --> pdb=" O LYS J 562 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'J' and resid 541 through 542 removed outlier: 3.833A pdb=" N LEU J 567 " --> pdb=" O ASN J 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU J 589 " --> pdb=" O LEU J 567 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL J 588 " --> pdb=" O THR J 614 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'J' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE J 572 " --> pdb=" O ALA J 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ2 Processing sheet with id=AQ3, first strand: chain 'J' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU J 645 " --> pdb=" O TYR J 623 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE J 642 " --> pdb=" O LYS J 680 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN J 682 " --> pdb=" O ILE J 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR J 644 " --> pdb=" O ASN J 682 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'J' and resid 662 through 664 Processing sheet with id=AQ5, first strand: chain 'J' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR J 691 " --> pdb=" O TYR J 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR J 791 " --> pdb=" O THR J 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'J' and resid 729 through 730 Processing sheet with id=AQ7, first strand: chain 'J' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP J 773 " --> pdb=" O CYS J 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS J 771 " --> pdb=" O VAL J 740 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'K' and resid 125 through 126 removed outlier: 8.279A pdb=" N ASN K 126 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N TRP K 49 " --> pdb=" O GLU K 100 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP K 102 " --> pdb=" O TRP K 49 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE K 51 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ARG K 50 " --> pdb=" O GLN L 343 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE L 345 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN K 52 " --> pdb=" O ILE L 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ8 Processing sheet with id=AQ9, first strand: chain 'K' and resid 78 through 79 removed outlier: 3.539A pdb=" N HIS K 88 " --> pdb=" O GLY K 79 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'K' and resid 140 through 142 removed outlier: 6.456A pdb=" N ASN K 140 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU K 168 " --> pdb=" O SER K 204 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE K 203 " --> pdb=" O TRP K 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL K 224 " --> pdb=" O THR K 258 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU K 257 " --> pdb=" O ASP K 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR1 Processing sheet with id=AR2, first strand: chain 'K' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL K 155 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU K 187 " --> pdb=" O ASN K 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR2 Processing sheet with id=AR3, first strand: chain 'K' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL K 252 " --> pdb=" O HIS K 276 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.730A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR K 381 " --> pdb=" O GLU K 407 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU K 500 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU K 517 " --> pdb=" O ARG K 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR5 Processing sheet with id=AR6, first strand: chain 'K' and resid 530 through 535 removed outlier: 3.586A pdb=" N LYS K 562 " --> pdb=" O PHE K 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU K 534 " --> pdb=" O LYS K 562 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'K' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU K 567 " --> pdb=" O ASN K 587 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU K 589 " --> pdb=" O LEU K 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL K 588 " --> pdb=" O THR K 614 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'K' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE K 572 " --> pdb=" O ALA K 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR8 Processing sheet with id=AR9, first strand: chain 'K' and resid 621 through 623 removed outlier: 3.625A pdb=" N LEU K 645 " --> pdb=" O TYR K 623 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE K 642 " --> pdb=" O LYS K 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN K 682 " --> pdb=" O ILE K 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR K 644 " --> pdb=" O ASN K 682 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'K' and resid 662 through 664 Processing sheet with id=AS2, first strand: chain 'K' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR K 691 " --> pdb=" O TYR K 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR K 791 " --> pdb=" O THR K 691 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'K' and resid 729 through 730 Processing sheet with id=AS4, first strand: chain 'K' and resid 737 through 740 removed outlier: 3.683A pdb=" N TRP K 773 " --> pdb=" O CYS K 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS K 771 " --> pdb=" O VAL K 740 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'L' and resid 78 through 79 removed outlier: 3.538A pdb=" N HIS L 88 " --> pdb=" O GLY L 79 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'L' and resid 140 through 142 removed outlier: 6.455A pdb=" N ASN L 140 " --> pdb=" O GLU L 169 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU L 168 " --> pdb=" O SER L 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE L 203 " --> pdb=" O TRP L 225 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL L 224 " --> pdb=" O THR L 258 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU L 257 " --> pdb=" O ASP L 281 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS6 Processing sheet with id=AS7, first strand: chain 'L' and resid 155 through 157 removed outlier: 6.630A pdb=" N VAL L 155 " --> pdb=" O THR L 188 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU L 187 " --> pdb=" O ASN L 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS7 Processing sheet with id=AS8, first strand: chain 'L' and resid 252 through 253 removed outlier: 6.297A pdb=" N VAL L 252 " --> pdb=" O HIS L 276 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'L' and resid 269 through 270 removed outlier: 6.729A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR L 381 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'L' and resid 476 through 477 removed outlier: 6.457A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU L 500 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU L 517 " --> pdb=" O ARG L 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT1 Processing sheet with id=AT2, first strand: chain 'L' and resid 530 through 535 removed outlier: 3.587A pdb=" N LYS L 562 " --> pdb=" O PHE L 532 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLU L 534 " --> pdb=" O LYS L 562 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'L' and resid 541 through 542 removed outlier: 3.834A pdb=" N LEU L 567 " --> pdb=" O ASN L 587 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU L 589 " --> pdb=" O LEU L 567 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL L 588 " --> pdb=" O THR L 614 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'L' and resid 572 through 573 removed outlier: 6.283A pdb=" N PHE L 572 " --> pdb=" O ALA L 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT4 Processing sheet with id=AT5, first strand: chain 'L' and resid 621 through 623 removed outlier: 3.626A pdb=" N LEU L 645 " --> pdb=" O TYR L 623 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE L 642 " --> pdb=" O LYS L 680 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASN L 682 " --> pdb=" O ILE L 642 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR L 644 " --> pdb=" O ASN L 682 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'L' and resid 662 through 664 Processing sheet with id=AT7, first strand: chain 'L' and resid 691 through 697 removed outlier: 4.067A pdb=" N THR L 691 " --> pdb=" O TYR L 791 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR L 791 " --> pdb=" O THR L 691 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'L' and resid 729 through 730 Processing sheet with id=AT9, first strand: chain 'L' and resid 737 through 740 removed outlier: 3.684A pdb=" N TRP L 773 " --> pdb=" O CYS L 738 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS L 771 " --> pdb=" O VAL L 740 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1884 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: 40.67 Time building geometry restraints manager: 22.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 22096 1.33 - 1.45: 10105 1.45 - 1.57: 37375 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" C ASN C 358 " pdb=" N ILE C 359 " ideal model delta sigma weight residual 1.334 1.302 0.032 1.29e-02 6.01e+03 5.99e+00 bond pdb=" C ASN L 358 " pdb=" N ILE L 359 " ideal model delta sigma weight residual 1.334 1.302 0.032 1.29e-02 6.01e+03 5.99e+00 bond pdb=" C ASN K 358 " pdb=" N ILE K 359 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.92e+00 bond pdb=" C ASN E 358 " pdb=" N ILE E 359 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.92e+00 bond pdb=" C ASN B 358 " pdb=" N ILE B 359 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.92e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.60: 891 105.60 - 112.71: 35795 112.71 - 119.82: 23467 119.82 - 126.92: 33764 126.92 - 134.03: 667 Bond angle restraints: 94584 Sorted by residual: angle pdb=" CA ASN I 273 " pdb=" CB ASN I 273 " pdb=" CG ASN I 273 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" CA ASN C 273 " pdb=" CB ASN C 273 " pdb=" CG ASN C 273 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.91e+01 angle pdb=" CA ASN E 273 " pdb=" CB ASN E 273 " pdb=" CG ASN E 273 " ideal model delta sigma weight residual 112.60 116.97 -4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" CA ASN A 273 " pdb=" CB ASN A 273 " pdb=" CG ASN A 273 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CA ASN H 273 " pdb=" CB ASN H 273 " pdb=" CG ASN H 273 " ideal model delta sigma weight residual 112.60 116.95 -4.35 1.00e+00 1.00e+00 1.89e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.22: 37804 14.22 - 28.43: 2673 28.43 - 42.65: 587 42.65 - 56.87: 60 56.87 - 71.08: 48 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: 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 -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 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 -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 749 " pdb=" CB CYS E 749 " ideal model delta sinusoidal sigma weight residual -86.00 -157.08 71.08 1 1.00e+01 1.00e-02 6.49e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6784 0.055 - 0.110: 2984 0.110 - 0.165: 703 0.165 - 0.220: 114 0.220 - 0.275: 35 Chirality restraints: 10620 Sorted by residual: chirality pdb=" CB ILE J 345 " pdb=" CA ILE J 345 " pdb=" CG1 ILE J 345 " pdb=" CG2 ILE J 345 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE C 345 " pdb=" CA ILE C 345 " pdb=" CG1 ILE C 345 " pdb=" CG2 ILE C 345 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE B 345 " pdb=" CA ILE B 345 " pdb=" CG1 ILE B 345 " pdb=" CG2 ILE B 345 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 225 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP H 225 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP H 225 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP H 225 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP H 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 225 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 225 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 225 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.67e+00 pdb=" CG TRP I 225 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP I 225 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP I 225 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 225 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP I 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 225 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP I 225 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 225 " 0.014 2.00e-02 2.50e+03 1.50e-02 5.66e+00 pdb=" CG TRP J 225 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP J 225 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP J 225 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP J 225 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 225 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP J 225 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 225 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 225 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP J 225 " 0.001 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 15150 2.78 - 3.31: 63322 3.31 - 3.84: 114468 3.84 - 4.37: 135260 4.37 - 4.90: 238125 Nonbonded interactions: 566325 Sorted by model distance: nonbonded pdb=" O SER A 575 " pdb=" OG SER A 606 " model vdw 2.247 2.440 nonbonded pdb=" O SER J 575 " pdb=" OG SER J 606 " model vdw 2.247 2.440 nonbonded pdb=" O SER L 575 " pdb=" OG SER L 606 " model vdw 2.247 2.440 nonbonded pdb=" O SER B 575 " pdb=" OG SER B 606 " model vdw 2.247 2.440 nonbonded pdb=" O SER K 575 " pdb=" OG SER K 606 " model vdw 2.247 2.440 ... (remaining 566320 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.050 Extract box with map and model: 15.650 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 149.730 Find NCS groups from input model: 4.130 Set up NCS constraints: 0.430 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.072 69840 Z= 0.536 Angle : 1.058 11.173 94584 Z= 0.595 Chirality : 0.064 0.275 10620 Planarity : 0.005 0.051 12396 Dihedral : 10.596 70.311 25056 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.07), residues: 8952 helix: -4.59 (0.11), residues: 360 sheet: -3.42 (0.09), residues: 2556 loop : -3.70 (0.06), residues: 6036 *********************** 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 552 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 512 time to evaluate : 5.866 Fit side-chains outliers start: 40 outliers final: 6 residues processed: 543 average time/residue: 0.6531 time to fit residues: 611.9002 Evaluate side-chains 241 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 5.849 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4976 time to fit residues: 13.7227 ------------------------------------------------------------------------------- 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: 0.9990 chunk 682 optimal weight: 0.7980 chunk 378 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 460 optimal weight: 0.8980 chunk 364 optimal weight: 7.9990 chunk 705 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 428 optimal weight: 4.9990 chunk 525 optimal weight: 2.9990 chunk 817 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS A 387 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS B 387 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN C 140 ASN C 256 HIS C 387 ASN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 665 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN ** D 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 HIS D 387 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 ASN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 HIS E 387 ASN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 715 ASN ** E 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 755 ASN F 140 ASN F 256 HIS F 387 ASN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 715 ASN ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 755 ASN ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 HIS G 387 ASN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 715 ASN ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 755 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 HIS H 387 ASN ** H 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 715 ASN ** H 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 755 ASN I 140 ASN I 256 HIS I 387 ASN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 ASN I 665 ASN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 715 ASN ** I 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 755 ASN ** J 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 HIS J 387 ASN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 715 ASN ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 755 ASN ** K 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 256 HIS K 387 ASN ** K 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 715 ASN ** K 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 755 ASN L 140 ASN L 256 HIS L 387 ASN ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 665 ASN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 715 ASN ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 755 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 69840 Z= 0.213 Angle : 0.599 7.219 94584 Z= 0.319 Chirality : 0.047 0.161 10620 Planarity : 0.003 0.041 12396 Dihedral : 5.933 22.258 9516 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.07), residues: 8952 helix: -3.38 (0.18), residues: 384 sheet: -3.55 (0.09), residues: 2868 loop : -3.26 (0.07), residues: 5700 *********************** 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 376 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 314 time to evaluate : 5.892 Fit side-chains outliers start: 62 outliers final: 26 residues processed: 360 average time/residue: 0.6660 time to fit residues: 426.9605 Evaluate side-chains 275 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 249 time to evaluate : 5.970 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5698 time to fit residues: 35.8654 ------------------------------------------------------------------------------- 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: 0.9980 chunk 253 optimal weight: 5.9990 chunk 680 optimal weight: 8.9990 chunk 556 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 818 optimal weight: 7.9990 chunk 884 optimal weight: 20.0000 chunk 729 optimal weight: 2.9990 chunk 811 optimal weight: 20.0000 chunk 279 optimal weight: 0.9980 chunk 656 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN A 543 ASN A 685 GLN A 731 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 340 GLN C 543 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 340 GLN D 543 ASN D 685 GLN D 731 ASN ** E 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN E 685 GLN E 731 ASN F 140 ASN F 340 GLN F 543 ASN F 665 ASN F 685 GLN F 731 ASN ** G 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN G 543 ASN G 685 GLN G 731 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 543 ASN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 ASN I 340 GLN I 543 ASN I 685 GLN I 731 ASN J 140 ASN J 340 GLN J 543 ASN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 543 ASN K 685 GLN K 731 ASN L 140 ASN L 543 ASN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 69840 Z= 0.235 Angle : 0.585 7.971 94584 Z= 0.312 Chirality : 0.047 0.156 10620 Planarity : 0.003 0.032 12396 Dihedral : 5.637 21.241 9516 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer Outliers : 1.30 % 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: -4.54 (0.08), residues: 8952 helix: -2.35 (0.23), residues: 384 sheet: -3.37 (0.09), residues: 2652 loop : -3.04 (0.07), residues: 5916 *********************** 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 359 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 263 time to evaluate : 5.905 Fit side-chains outliers start: 96 outliers final: 47 residues processed: 338 average time/residue: 0.6297 time to fit residues: 382.8037 Evaluate side-chains 273 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 226 time to evaluate : 5.891 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.5499 time to fit residues: 55.4880 ------------------------------------------------------------------------------- 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: 6.9990 chunk 615 optimal weight: 6.9990 chunk 424 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 390 optimal weight: 6.9990 chunk 549 optimal weight: 5.9990 chunk 821 optimal weight: 40.0000 chunk 869 optimal weight: 9.9990 chunk 429 optimal weight: 4.9990 chunk 778 optimal weight: 3.9990 chunk 234 optimal weight: 6.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN A 498 ASN B 340 GLN B 469 HIS ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN C 498 ASN C 685 GLN C 731 ASN D 140 ASN D 284 GLN D 617 GLN E 340 GLN E 469 HIS G 284 GLN G 498 ASN G 617 GLN H 340 GLN H 469 HIS ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 GLN I 498 ASN J 140 ASN J 284 GLN J 685 GLN J 731 ASN K 340 GLN K 469 HIS L 340 GLN L 498 ASN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 69840 Z= 0.466 Angle : 0.734 11.068 94584 Z= 0.394 Chirality : 0.052 0.176 10620 Planarity : 0.004 0.039 12396 Dihedral : 6.276 24.101 9516 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.91 % Favored : 82.09 % Rotamer Outliers : 1.80 % 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: -4.52 (0.08), residues: 8952 helix: -1.69 (0.25), residues: 384 sheet: -3.47 (0.10), residues: 2232 loop : -3.11 (0.07), residues: 6336 *********************** 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 376 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 243 time to evaluate : 6.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 73 residues processed: 361 average time/residue: 0.6674 time to fit residues: 432.4699 Evaluate side-chains 284 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 211 time to evaluate : 5.917 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.5272 time to fit residues: 81.6614 ------------------------------------------------------------------------------- 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: 10.0000 chunk 493 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 647 optimal weight: 10.0000 chunk 358 optimal weight: 3.9990 chunk 742 optimal weight: 10.0000 chunk 601 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 444 optimal weight: 4.9990 chunk 780 optimal weight: 4.9990 chunk 219 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 685 GLN H 731 ASN ** K 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 685 GLN L 731 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 69840 Z= 0.377 Angle : 0.677 9.790 94584 Z= 0.362 Chirality : 0.050 0.168 10620 Planarity : 0.003 0.037 12396 Dihedral : 6.020 22.954 9516 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.76 % Favored : 84.24 % Rotamer Outliers : 1.19 % 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: -4.51 (0.08), residues: 8952 helix: -1.56 (0.25), residues: 384 sheet: -3.46 (0.10), residues: 2352 loop : -3.09 (0.07), residues: 6216 *********************** 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 322 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 234 time to evaluate : 5.762 Fit side-chains outliers start: 88 outliers final: 44 residues processed: 302 average time/residue: 0.6222 time to fit residues: 340.4577 Evaluate side-chains 255 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 5.901 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5366 time to fit residues: 52.7655 ------------------------------------------------------------------------------- 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: 20.0000 chunk 783 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 chunk 510 optimal weight: 0.8980 chunk 214 optimal weight: 8.9990 chunk 870 optimal weight: 7.9990 chunk 722 optimal weight: 4.9990 chunk 403 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 288 optimal weight: 30.0000 chunk 457 optimal weight: 0.7980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 GLN B 731 ASN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 628 ASN ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 69840 Z= 0.274 Angle : 0.613 9.825 94584 Z= 0.326 Chirality : 0.048 0.157 10620 Planarity : 0.003 0.034 12396 Dihedral : 5.683 21.897 9516 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Rotamer Outliers : 0.90 % 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: -4.33 (0.08), residues: 8952 helix: -1.40 (0.25), residues: 384 sheet: -3.25 (0.10), residues: 2532 loop : -2.96 (0.07), residues: 6036 *********************** 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 313 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 246 time to evaluate : 5.929 Fit side-chains outliers start: 67 outliers final: 35 residues processed: 300 average time/residue: 0.6363 time to fit residues: 341.6754 Evaluate side-chains 251 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 216 time to evaluate : 5.870 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.5232 time to fit residues: 42.7089 ------------------------------------------------------------------------------- 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: 6.9990 chunk 98 optimal weight: 5.9990 chunk 496 optimal weight: 20.0000 chunk 635 optimal weight: 6.9990 chunk 492 optimal weight: 9.9990 chunk 733 optimal weight: 0.2980 chunk 486 optimal weight: 8.9990 chunk 867 optimal weight: 6.9990 chunk 542 optimal weight: 0.6980 chunk 528 optimal weight: 5.9990 chunk 400 optimal weight: 0.9980 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 69840 Z= 0.304 Angle : 0.635 9.051 94584 Z= 0.334 Chirality : 0.048 0.162 10620 Planarity : 0.003 0.034 12396 Dihedral : 5.707 21.901 9516 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.33 % Favored : 84.67 % Rotamer Outliers : 0.72 % 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: -4.23 (0.08), residues: 8952 helix: -1.23 (0.26), residues: 384 sheet: -3.20 (0.10), residues: 2592 loop : -2.87 (0.07), residues: 5976 *********************** 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 298 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 245 time to evaluate : 5.941 Fit side-chains outliers start: 53 outliers final: 29 residues processed: 289 average time/residue: 0.6577 time to fit residues: 340.7973 Evaluate side-chains 245 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 5.906 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5382 time to fit residues: 37.8074 ------------------------------------------------------------------------------- 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: 2.9990 chunk 346 optimal weight: 0.6980 chunk 518 optimal weight: 30.0000 chunk 261 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 551 optimal weight: 1.9990 chunk 590 optimal weight: 5.9990 chunk 428 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 681 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2988 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= 0.242 Angle : 0.601 8.228 94584 Z= 0.314 Chirality : 0.047 0.154 10620 Planarity : 0.003 0.036 12396 Dihedral : 5.449 20.926 9516 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer Outliers : 0.38 % 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: -4.07 (0.08), residues: 8952 helix: -1.10 (0.26), residues: 384 sheet: -3.12 (0.09), residues: 2724 loop : -2.71 (0.07), residues: 5844 *********************** 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 274 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 246 time to evaluate : 5.956 Fit side-chains outliers start: 28 outliers final: 19 residues processed: 262 average time/residue: 0.6452 time to fit residues: 302.6821 Evaluate side-chains 236 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 5.812 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.5534 time to fit residues: 27.4913 ------------------------------------------------------------------------------- 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: 9.9990 chunk 831 optimal weight: 6.9990 chunk 758 optimal weight: 4.9990 chunk 808 optimal weight: 0.8980 chunk 830 optimal weight: 5.9990 chunk 486 optimal weight: 5.9990 chunk 352 optimal weight: 9.9990 chunk 634 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 730 optimal weight: 20.0000 chunk 764 optimal weight: 0.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 69840 Z= 0.394 Angle : 0.689 9.618 94584 Z= 0.363 Chirality : 0.050 0.171 10620 Planarity : 0.003 0.033 12396 Dihedral : 5.892 22.929 9516 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.26 % Favored : 82.74 % Rotamer Outliers : 0.26 % 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: -4.27 (0.08), residues: 8952 helix: -1.09 (0.26), residues: 384 sheet: -3.33 (0.09), residues: 2796 loop : -2.82 (0.07), residues: 5772 *********************** 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 251 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 232 time to evaluate : 5.848 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 248 average time/residue: 0.6588 time to fit residues: 291.9112 Evaluate side-chains 224 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 216 time to evaluate : 6.037 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.5514 time to fit residues: 16.3078 ------------------------------------------------------------------------------- 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: 20.0000 chunk 530 optimal weight: 10.0000 chunk 854 optimal weight: 2.9990 chunk 521 optimal weight: 5.9990 chunk 405 optimal weight: 6.9990 chunk 594 optimal weight: 2.9990 chunk 896 optimal weight: 3.9990 chunk 825 optimal weight: 0.9980 chunk 713 optimal weight: 0.0970 chunk 74 optimal weight: 40.0000 chunk 551 optimal weight: 0.9980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 69840 Z= 0.201 Angle : 0.594 7.737 94584 Z= 0.309 Chirality : 0.047 0.152 10620 Planarity : 0.003 0.038 12396 Dihedral : 5.356 20.693 9516 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer Outliers : 0.20 % 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: -4.02 (0.08), residues: 8952 helix: -1.06 (0.27), residues: 384 sheet: -3.10 (0.09), residues: 2940 loop : -2.62 (0.07), residues: 5628 ********************** 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 248 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 6.032 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 245 average time/residue: 0.6621 time to fit residues: 289.8414 Evaluate side-chains 223 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 5.906 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5361 time to fit residues: 15.2344 ------------------------------------------------------------------------------- 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: 5.9990 chunk 567 optimal weight: 4.9990 chunk 760 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 658 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 715 optimal weight: 9.9990 chunk 299 optimal weight: 0.6980 chunk 734 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN ** G 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.133466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.078612 restraints weight = 117273.708| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.57 r_work: 0.3289 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.060 69840 Z= 0.443 Angle : 0.721 10.035 94584 Z= 0.380 Chirality : 0.051 0.176 10620 Planarity : 0.004 0.034 12396 Dihedral : 6.002 24.325 9516 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.09 % Favored : 81.91 % 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: -4.31 (0.08), residues: 8952 helix: -1.12 (0.26), residues: 384 sheet: -3.34 (0.09), residues: 2808 loop : -2.84 (0.07), residues: 5760 =============================================================================== Job complete usr+sys time: 11677.44 seconds wall clock time: 209 minutes 43.33 seconds (12583.33 seconds total)