Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 06:13:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/07_2023/6nyl_0545.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/07_2023/6nyl_0545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/07_2023/6nyl_0545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/07_2023/6nyl_0545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/07_2023/6nyl_0545.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyl_0545/07_2023/6nyl_0545.pdb" } resolution = 3.7 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= 0.009 sd= 0.067 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 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-1.21rc1-5013/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: 24.01, per 1000 atoms: 0.35 Number of scatterers: 68664 At special positions: 0 Unit cell: (302.1, 287.26, 117.66, 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: 21.34 Conformation dependent library (CDL) restraints added in 8.0 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: 72 helices and 216 sheets defined 5.6% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.799A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.236A pdb=" N SER A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.468A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.798A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.237A pdb=" N SER B 74 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.799A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.237A pdb=" N SER C 74 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 726 removed outlier: 3.951A pdb=" N LEU C 726 " --> pdb=" O PHE C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.468A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN C 764 " --> pdb=" O ASN C 761 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.799A pdb=" N ALA D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 4.044A 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: 4.236A pdb=" N SER D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU D 726 " --> pdb=" O PHE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.468A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN D 764 " --> pdb=" O ASN D 761 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.799A pdb=" N ALA E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.236A pdb=" N SER E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU E 726 " --> pdb=" O PHE E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN E 764 " --> pdb=" O ASN E 761 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.799A pdb=" N ALA F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.893A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.237A pdb=" N SER F 74 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU F 726 " --> pdb=" O PHE F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN F 764 " --> pdb=" O ASN F 761 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.799A pdb=" N ALA G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.235A pdb=" N SER G 74 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU G 726 " --> pdb=" O PHE G 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN G 764 " --> pdb=" O ASN G 761 " (cutoff:3.500A) removed outlier: 4.293A 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: 3.798A pdb=" N ALA H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.236A pdb=" N SER H 74 " --> pdb=" O LEU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU H 726 " --> pdb=" O PHE H 722 " (cutoff:3.500A) Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN H 764 " --> pdb=" O ASN H 761 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.798A pdb=" N ALA I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU I 59 " --> pdb=" O GLY I 56 " (cutoff:3.500A) removed outlier: 4.042A 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: 4.237A pdb=" N SER I 74 " --> pdb=" O LEU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU I 726 " --> pdb=" O PHE I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN I 764 " --> pdb=" O ASN I 761 " (cutoff:3.500A) removed outlier: 4.293A 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: 3.799A pdb=" N ALA J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU J 59 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.236A pdb=" N SER J 74 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU J 726 " --> pdb=" O PHE J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.466A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN J 764 " --> pdb=" O ASN J 761 " (cutoff:3.500A) removed outlier: 4.292A 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: 3.799A pdb=" N ALA K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU K 59 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 4.042A 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: 4.237A pdb=" N SER K 74 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 721 through 726 removed outlier: 3.952A pdb=" N LEU K 726 " --> pdb=" O PHE K 722 " (cutoff:3.500A) Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.467A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.518A pdb=" N ASN K 764 " --> pdb=" O ASN K 761 " (cutoff:3.500A) removed outlier: 4.293A 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: 3.798A pdb=" N ALA L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 3.894A pdb=" N GLU L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 4.043A 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: 4.236A pdb=" N SER L 74 " --> pdb=" O LEU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 721 through 726 removed outlier: 3.951A pdb=" N LEU L 726 " --> pdb=" O PHE L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.468A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.519A pdb=" N ASN L 764 " --> pdb=" O ASN L 761 " (cutoff:3.500A) removed outlier: 4.292A 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 156 through 157 removed outlier: 3.658A pdb=" N VAL A 125 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP A 124 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU A 99 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN A 126 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 98 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP A 49 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA A 53 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N ASP A 46 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N VAL A 48 " --> pdb=" O PRO F 341 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN F 343 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 50 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE F 345 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN A 52 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA4, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY A 278 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS A 274 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ILE A 359 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS A 276 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG A 361 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY A 278 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN A 363 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU A 211 " --> pdb=" O ASN A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.662A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 345 removed outlier: 7.373A pdb=" N VAL A 339 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 48 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG B 50 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 98 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP B 49 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA B 53 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ASP B 124 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU B 99 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN B 126 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 125 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU A 407 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 435 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS A 465 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.164A pdb=" N ILE A 413 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.714A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 502 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 531 Processing sheet with id=AB4, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB5, first strand: chain 'A' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL A 588 " --> pdb=" O THR A 614 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR A 630 " --> pdb=" O LEU A 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET A 621 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE A 642 " --> pdb=" O LYS A 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 788 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AC1, first strand: chain 'A' and resid 771 through 773 Processing sheet with id=AC2, first strand: chain 'B' and resid 109 through 111 Processing sheet with id=AC3, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.591A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY B 278 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 203 through 205 removed outlier: 6.591A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS B 274 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ILE B 359 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS B 276 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N ARG B 361 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY B 278 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN B 363 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU B 211 " --> pdb=" O ASN B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 339 through 345 removed outlier: 7.409A pdb=" N VAL B 339 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 48 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG C 50 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 98 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP C 49 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA C 53 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ASP C 124 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU C 99 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN C 126 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 125 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 377 through 378 removed outlier: 6.544A pdb=" N ALA B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU B 407 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 435 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS B 465 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE B 437 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE B 413 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 476 through 477 removed outlier: 6.714A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 502 " --> pdb=" O ILE B 518 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AD4, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AD5, first strand: chain 'B' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL B 588 " --> pdb=" O THR B 614 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR B 630 " --> pdb=" O LEU B 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET B 621 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE B 642 " --> pdb=" O LYS B 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER B 788 " --> pdb=" O THR B 781 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AE1, first strand: chain 'B' and resid 771 through 773 Processing sheet with id=AE2, first strand: chain 'C' and resid 109 through 111 Processing sheet with id=AE3, first strand: chain 'C' and resid 140 through 142 Processing sheet with id=AE4, first strand: chain 'C' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY C 278 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS C 274 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE C 359 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS C 276 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG C 361 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY C 278 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN C 363 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU C 211 " --> pdb=" O ASN C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 339 through 345 removed outlier: 7.410A pdb=" N VAL C 339 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL D 48 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ARG D 50 " --> pdb=" O PRO C 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 98 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP D 49 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA D 53 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP D 124 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU D 99 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN D 126 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL D 125 " --> pdb=" O ASP D 156 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 377 through 378 removed outlier: 6.544A pdb=" N ALA C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU C 407 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA C 435 " --> pdb=" O ASN C 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS C 465 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE C 437 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE C 413 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 502 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 530 through 531 Processing sheet with id=AF4, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AF5, first strand: chain 'C' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL C 588 " --> pdb=" O THR C 614 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR C 630 " --> pdb=" O LEU C 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'C' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET C 621 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE C 642 " --> pdb=" O LYS C 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER C 788 " --> pdb=" O THR C 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR C 781 " --> pdb=" O SER C 788 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AG1, first strand: chain 'C' and resid 771 through 773 Processing sheet with id=AG2, first strand: chain 'D' and resid 109 through 111 Processing sheet with id=AG3, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AG4, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY D 278 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS D 274 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE D 359 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS D 276 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 9.366A pdb=" N ARG D 361 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY D 278 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN D 363 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU D 211 " --> pdb=" O ASN D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 339 through 345 removed outlier: 7.347A pdb=" N VAL D 339 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL E 48 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG E 50 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS E 98 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP E 49 " --> pdb=" O LYS E 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA E 53 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP E 124 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU E 99 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN E 126 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 125 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA D 377 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU D 407 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA D 435 " --> pdb=" O ASN D 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS D 465 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE D 437 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 387 through 388 removed outlier: 6.164A pdb=" N ILE D 413 " --> pdb=" O THR D 451 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR D 502 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 530 through 531 Processing sheet with id=AH4, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AH5, first strand: chain 'D' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL D 588 " --> pdb=" O THR D 614 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR D 630 " --> pdb=" O LEU D 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'D' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET D 621 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE D 642 " --> pdb=" O LYS D 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'D' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER D 788 " --> pdb=" O THR D 781 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AI1, first strand: chain 'D' and resid 771 through 773 Processing sheet with id=AI2, first strand: chain 'E' and resid 109 through 111 Processing sheet with id=AI3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AI4, first strand: chain 'E' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY E 278 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS E 274 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE E 359 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS E 276 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG E 361 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY E 278 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN E 363 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU E 211 " --> pdb=" O ASN E 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 339 through 345 removed outlier: 7.553A pdb=" N VAL E 339 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 48 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG F 50 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 98 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP F 49 " --> pdb=" O LYS F 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA F 53 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASP F 124 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU F 99 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN F 126 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL F 125 " --> pdb=" O ASP F 156 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA E 377 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU E 407 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA E 435 " --> pdb=" O ASN E 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS E 465 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE E 437 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 387 through 388 removed outlier: 6.164A pdb=" N ILE E 413 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 476 through 477 removed outlier: 6.714A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 502 " --> pdb=" O ILE E 518 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 530 through 531 Processing sheet with id=AJ4, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AJ5, first strand: chain 'E' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL E 588 " --> pdb=" O THR E 614 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR E 630 " --> pdb=" O LEU E 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'E' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET E 621 " --> pdb=" O ASN E 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE E 642 " --> pdb=" O LYS E 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'E' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER E 788 " --> pdb=" O THR E 781 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AK1, first strand: chain 'E' and resid 771 through 773 Processing sheet with id=AK2, first strand: chain 'F' and resid 109 through 111 Processing sheet with id=AK3, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AK4, first strand: chain 'F' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY F 278 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N LYS F 274 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE F 359 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS F 276 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG F 361 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY F 278 " --> pdb=" O ARG F 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN F 363 " --> pdb=" O GLY F 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU F 211 " --> pdb=" O ASN F 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK6 Processing sheet with id=AK7, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA F 377 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU F 407 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA F 435 " --> pdb=" O ASN F 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS F 465 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE F 437 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE F 413 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 476 through 477 removed outlier: 6.714A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR F 502 " --> pdb=" O ILE F 518 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'F' and resid 530 through 531 Processing sheet with id=AL3, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AL4, first strand: chain 'F' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL F 588 " --> pdb=" O THR F 614 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'F' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR F 630 " --> pdb=" O LEU F 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'F' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET F 621 " --> pdb=" O ASN F 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE F 642 " --> pdb=" O LYS F 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'F' and resid 691 through 696 removed outlier: 7.857A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER F 788 " --> pdb=" O THR F 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR F 781 " --> pdb=" O SER F 788 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AL9, first strand: chain 'F' and resid 771 through 773 Processing sheet with id=AM1, first strand: chain 'G' and resid 156 through 157 removed outlier: 3.657A pdb=" N VAL G 125 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP G 124 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU G 99 " --> pdb=" O ASP G 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN G 126 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS G 98 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP G 49 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA G 53 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N ASP G 46 " --> pdb=" O VAL L 339 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N VAL G 48 " --> pdb=" O PRO L 341 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLN L 343 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG G 50 " --> pdb=" O GLN L 343 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE L 345 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN G 52 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'G' and resid 109 through 111 Processing sheet with id=AM3, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AM4, first strand: chain 'G' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE G 203 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL G 252 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY G 278 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'G' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE G 203 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS G 274 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE G 359 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS G 276 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG G 361 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY G 278 " --> pdb=" O ARG G 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN G 363 " --> pdb=" O GLY G 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'G' and resid 210 through 212 removed outlier: 6.731A pdb=" N LEU G 211 " --> pdb=" O ASN G 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM6 Processing sheet with id=AM7, first strand: chain 'G' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'G' and resid 339 through 345 removed outlier: 7.410A pdb=" N VAL G 339 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL H 48 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG H 50 " --> pdb=" O PRO G 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS H 98 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP H 49 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA H 53 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP H 124 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU H 99 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN H 126 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL H 125 " --> pdb=" O ASP H 156 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'G' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA G 377 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU G 407 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA G 435 " --> pdb=" O ASN G 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS G 465 " --> pdb=" O ALA G 435 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE G 437 " --> pdb=" O LYS G 465 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'G' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE G 413 " --> pdb=" O THR G 451 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'G' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR G 502 " --> pdb=" O ILE G 518 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'G' and resid 530 through 531 Processing sheet with id=AN4, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AN5, first strand: chain 'G' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL G 588 " --> pdb=" O THR G 614 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'G' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR G 630 " --> pdb=" O LEU G 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN6 Processing sheet with id=AN7, first strand: chain 'G' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET G 621 " --> pdb=" O ASN G 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE G 642 " --> pdb=" O LYS G 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN7 Processing sheet with id=AN8, first strand: chain 'G' and resid 691 through 696 removed outlier: 7.857A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER G 788 " --> pdb=" O THR G 781 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'G' and resid 729 through 730 Processing sheet with id=AO1, first strand: chain 'G' and resid 771 through 773 Processing sheet with id=AO2, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AO3, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AO4, first strand: chain 'H' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE H 203 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL H 252 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY H 278 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'H' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE H 203 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS H 274 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE H 359 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS H 276 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG H 361 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY H 278 " --> pdb=" O ARG H 361 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN H 363 " --> pdb=" O GLY H 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'H' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU H 211 " --> pdb=" O ASN H 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO6 Processing sheet with id=AO7, first strand: chain 'H' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'H' and resid 339 through 345 removed outlier: 7.409A pdb=" N VAL H 339 " --> pdb=" O ASP I 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL I 48 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG I 50 " --> pdb=" O PRO H 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 98 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP I 49 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA I 53 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ASP I 124 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU I 99 " --> pdb=" O ASP I 124 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ASN I 126 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL I 125 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'H' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA H 377 " --> pdb=" O LEU H 405 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU H 407 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA H 435 " --> pdb=" O ASN H 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS H 465 " --> pdb=" O ALA H 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE H 437 " --> pdb=" O LYS H 465 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'H' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE H 413 " --> pdb=" O THR H 451 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'H' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR H 502 " --> pdb=" O ILE H 518 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'H' and resid 530 through 531 Processing sheet with id=AP4, first strand: chain 'H' and resid 541 through 542 Processing sheet with id=AP5, first strand: chain 'H' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL H 588 " --> pdb=" O THR H 614 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'H' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR H 630 " --> pdb=" O LEU H 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP6 Processing sheet with id=AP7, first strand: chain 'H' and resid 621 through 623 removed outlier: 5.562A pdb=" N MET H 621 " --> pdb=" O ASN H 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE H 642 " --> pdb=" O LYS H 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP7 Processing sheet with id=AP8, first strand: chain 'H' and resid 691 through 696 removed outlier: 7.857A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER H 788 " --> pdb=" O THR H 781 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'H' and resid 729 through 730 Processing sheet with id=AQ1, first strand: chain 'H' and resid 771 through 773 Processing sheet with id=AQ2, first strand: chain 'I' and resid 109 through 111 Processing sheet with id=AQ3, first strand: chain 'I' and resid 140 through 142 Processing sheet with id=AQ4, first strand: chain 'I' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE I 203 " --> pdb=" O TRP I 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL I 252 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY I 278 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'I' and resid 203 through 205 removed outlier: 6.593A pdb=" N ILE I 203 " --> pdb=" O TRP I 225 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N LYS I 274 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE I 359 " --> pdb=" O LYS I 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS I 276 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG I 361 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY I 278 " --> pdb=" O ARG I 361 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ASN I 363 " --> pdb=" O GLY I 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'I' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU I 211 " --> pdb=" O ASN I 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ6 Processing sheet with id=AQ7, first strand: chain 'I' and resid 269 through 270 removed outlier: 6.662A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'I' and resid 339 through 345 removed outlier: 7.316A pdb=" N VAL I 339 " --> pdb=" O ASP J 46 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL J 48 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG J 50 " --> pdb=" O PRO I 341 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN J 52 " --> pdb=" O GLN I 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 98 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP J 49 " --> pdb=" O LYS J 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA J 53 " --> pdb=" O ASP J 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP J 124 " --> pdb=" O ASN J 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU J 99 " --> pdb=" O ASP J 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN J 126 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL J 125 " --> pdb=" O ASP J 156 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'I' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA I 377 " --> pdb=" O LEU I 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU I 407 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA I 435 " --> pdb=" O ASN I 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS I 465 " --> pdb=" O ALA I 435 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE I 437 " --> pdb=" O LYS I 465 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'I' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE I 413 " --> pdb=" O THR I 451 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'I' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR I 502 " --> pdb=" O ILE I 518 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'I' and resid 530 through 531 Processing sheet with id=AR4, first strand: chain 'I' and resid 541 through 542 Processing sheet with id=AR5, first strand: chain 'I' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL I 588 " --> pdb=" O THR I 614 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'I' and resid 608 through 609 removed outlier: 3.591A pdb=" N THR I 630 " --> pdb=" O LEU I 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR6 Processing sheet with id=AR7, first strand: chain 'I' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET I 621 " --> pdb=" O ASN I 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE I 642 " --> pdb=" O LYS I 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR7 Processing sheet with id=AR8, first strand: chain 'I' and resid 691 through 696 removed outlier: 7.857A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER I 788 " --> pdb=" O THR I 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR I 781 " --> pdb=" O SER I 788 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'I' and resid 729 through 730 Processing sheet with id=AS1, first strand: chain 'I' and resid 771 through 773 Processing sheet with id=AS2, first strand: chain 'J' and resid 109 through 111 Processing sheet with id=AS3, first strand: chain 'J' and resid 140 through 142 Processing sheet with id=AS4, first strand: chain 'J' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE J 203 " --> pdb=" O TRP J 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL J 252 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY J 278 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'J' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE J 203 " --> pdb=" O TRP J 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS J 274 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE J 359 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS J 276 " --> pdb=" O ILE J 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG J 361 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY J 278 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ASN J 363 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'J' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU J 211 " --> pdb=" O ASN J 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS6 Processing sheet with id=AS7, first strand: chain 'J' and resid 269 through 270 removed outlier: 6.662A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'J' and resid 339 through 345 removed outlier: 7.430A pdb=" N VAL J 339 " --> pdb=" O ASP K 46 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL K 48 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG K 50 " --> pdb=" O PRO J 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS K 98 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP K 49 " --> pdb=" O LYS K 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA K 53 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N ASP K 124 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU K 99 " --> pdb=" O ASP K 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN K 126 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL K 125 " --> pdb=" O ASP K 156 " (cutoff:3.500A) Processing sheet with id=AS9, first strand: chain 'J' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA J 377 " --> pdb=" O LEU J 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU J 407 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA J 435 " --> pdb=" O ASN J 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS J 465 " --> pdb=" O ALA J 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE J 437 " --> pdb=" O LYS J 465 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'J' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE J 413 " --> pdb=" O THR J 451 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'J' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR J 502 " --> pdb=" O ILE J 518 " (cutoff:3.500A) Processing sheet with id=AT3, first strand: chain 'J' and resid 530 through 531 Processing sheet with id=AT4, first strand: chain 'J' and resid 541 through 542 Processing sheet with id=AT5, first strand: chain 'J' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL J 588 " --> pdb=" O THR J 614 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'J' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR J 630 " --> pdb=" O LEU J 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT6 Processing sheet with id=AT7, first strand: chain 'J' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET J 621 " --> pdb=" O ASN J 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE J 642 " --> pdb=" O LYS J 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT7 Processing sheet with id=AT8, first strand: chain 'J' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER J 788 " --> pdb=" O THR J 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR J 781 " --> pdb=" O SER J 788 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'J' and resid 729 through 730 Processing sheet with id=AU1, first strand: chain 'J' and resid 771 through 773 Processing sheet with id=AU2, first strand: chain 'K' and resid 109 through 111 Processing sheet with id=AU3, first strand: chain 'K' and resid 140 through 142 Processing sheet with id=AU4, first strand: chain 'K' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE K 203 " --> pdb=" O TRP K 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL K 252 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY K 278 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 'K' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE K 203 " --> pdb=" O TRP K 225 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N LYS K 274 " --> pdb=" O VAL K 357 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N ILE K 359 " --> pdb=" O LYS K 274 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N HIS K 276 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG K 361 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY K 278 " --> pdb=" O ARG K 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN K 363 " --> pdb=" O GLY K 278 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'K' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU K 211 " --> pdb=" O ASN K 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU6 Processing sheet with id=AU7, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing sheet with id=AU8, first strand: chain 'K' and resid 339 through 345 removed outlier: 7.518A pdb=" N VAL K 339 " --> pdb=" O ASP L 46 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL L 48 " --> pdb=" O VAL K 339 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG L 50 " --> pdb=" O PRO K 341 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS L 98 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP L 49 " --> pdb=" O LYS L 98 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA L 53 " --> pdb=" O ASP L 102 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N ASP L 124 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU L 99 " --> pdb=" O ASP L 124 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ASN L 126 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 125 " --> pdb=" O ASP L 156 " (cutoff:3.500A) Processing sheet with id=AU9, first strand: chain 'K' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA K 377 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU K 407 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA K 435 " --> pdb=" O ASN K 463 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LYS K 465 " --> pdb=" O ALA K 435 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE K 437 " --> pdb=" O LYS K 465 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'K' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE K 413 " --> pdb=" O THR K 451 " (cutoff:3.500A) Processing sheet with id=AV2, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR K 502 " --> pdb=" O ILE K 518 " (cutoff:3.500A) Processing sheet with id=AV3, first strand: chain 'K' and resid 530 through 531 Processing sheet with id=AV4, first strand: chain 'K' and resid 541 through 542 Processing sheet with id=AV5, first strand: chain 'K' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL K 588 " --> pdb=" O THR K 614 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'K' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR K 630 " --> pdb=" O LEU K 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV6 Processing sheet with id=AV7, first strand: chain 'K' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET K 621 " --> pdb=" O ASN K 643 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE K 642 " --> pdb=" O LYS K 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV7 Processing sheet with id=AV8, first strand: chain 'K' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER K 788 " --> pdb=" O THR K 781 " (cutoff:3.500A) Processing sheet with id=AV9, first strand: chain 'K' and resid 729 through 730 Processing sheet with id=AW1, first strand: chain 'K' and resid 771 through 773 Processing sheet with id=AW2, first strand: chain 'L' and resid 109 through 111 Processing sheet with id=AW3, first strand: chain 'L' and resid 140 through 142 Processing sheet with id=AW4, first strand: chain 'L' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE L 203 " --> pdb=" O TRP L 225 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL L 252 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N GLY L 278 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'L' and resid 203 through 205 removed outlier: 6.592A pdb=" N ILE L 203 " --> pdb=" O TRP L 225 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS L 274 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ILE L 359 " --> pdb=" O LYS L 274 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N HIS L 276 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ARG L 361 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY L 278 " --> pdb=" O ARG L 361 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN L 363 " --> pdb=" O GLY L 278 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) Processing sheet with id=AW6, first strand: chain 'L' and resid 210 through 212 removed outlier: 6.732A pdb=" N LEU L 211 " --> pdb=" O ASN L 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AW6 Processing sheet with id=AW7, first strand: chain 'L' and resid 269 through 270 removed outlier: 6.663A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing sheet with id=AW8, first strand: chain 'L' and resid 377 through 378 removed outlier: 6.545A pdb=" N ALA L 377 " --> pdb=" O LEU L 405 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLU L 407 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA L 435 " --> pdb=" O ASN L 463 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LYS L 465 " --> pdb=" O ALA L 435 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE L 437 " --> pdb=" O LYS L 465 " (cutoff:3.500A) Processing sheet with id=AW9, first strand: chain 'L' and resid 387 through 388 removed outlier: 6.163A pdb=" N ILE L 413 " --> pdb=" O THR L 451 " (cutoff:3.500A) Processing sheet with id=AX1, first strand: chain 'L' and resid 476 through 477 removed outlier: 6.713A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR L 502 " --> pdb=" O ILE L 518 " (cutoff:3.500A) Processing sheet with id=AX2, first strand: chain 'L' and resid 530 through 531 Processing sheet with id=AX3, first strand: chain 'L' and resid 541 through 542 Processing sheet with id=AX4, first strand: chain 'L' and resid 588 through 590 removed outlier: 5.579A pdb=" N VAL L 588 " --> pdb=" O THR L 614 " (cutoff:3.500A) Processing sheet with id=AX5, first strand: chain 'L' and resid 608 through 609 removed outlier: 3.590A pdb=" N THR L 630 " --> pdb=" O LEU L 608 " (cutoff:3.500A) No H-bonds generated for sheet with id=AX5 Processing sheet with id=AX6, first strand: chain 'L' and resid 621 through 623 removed outlier: 5.561A pdb=" N MET L 621 " --> pdb=" O ASN L 643 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE L 642 " --> pdb=" O LYS L 680 " (cutoff:3.500A) No H-bonds generated for sheet with id=AX6 Processing sheet with id=AX7, first strand: chain 'L' and resid 691 through 696 removed outlier: 7.856A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER L 788 " --> pdb=" O THR L 781 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR L 781 " --> pdb=" O SER L 788 " (cutoff:3.500A) Processing sheet with id=AX8, first strand: chain 'L' and resid 729 through 730 Processing sheet with id=AX9, first strand: chain 'L' and resid 771 through 773 672 hydrogen bonds defined for protein. 1872 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: 36.37 Time building geometry restraints manager: 23.45 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: 21734 1.33 - 1.45: 10210 1.45 - 1.57: 37632 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" C ASP H 124 " pdb=" N VAL H 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.75e+00 bond pdb=" C ASP I 124 " pdb=" N VAL I 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.73e+00 bond pdb=" C ASP C 124 " pdb=" N VAL C 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.73e+00 bond pdb=" C ASP F 124 " pdb=" N VAL F 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.73e+00 bond pdb=" C ASP B 124 " pdb=" N VAL B 125 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.36e-02 5.41e+03 4.72e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.59: 915 105.59 - 112.73: 35907 112.73 - 119.88: 23751 119.88 - 127.03: 33342 127.03 - 134.17: 669 Bond angle restraints: 94584 Sorted by residual: angle pdb=" C GLY L 83 " pdb=" N ASN L 84 " pdb=" CA ASN L 84 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C GLY I 83 " pdb=" N ASN I 84 " pdb=" CA ASN I 84 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C GLY H 83 " pdb=" N ASN H 84 " pdb=" CA ASN H 84 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY F 83 " pdb=" N ASN F 84 " pdb=" CA ASN F 84 " ideal model delta sigma weight residual 121.54 130.90 -9.36 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 37675 15.49 - 30.97: 2946 30.97 - 46.46: 479 46.46 - 61.95: 36 61.95 - 77.43: 36 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: 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 -163.43 77.43 1 1.00e+01 1.00e-02 7.51e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual -86.00 -163.43 77.43 1 1.00e+01 1.00e-02 7.51e+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 -163.42 77.42 1 1.00e+01 1.00e-02 7.51e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6694 0.053 - 0.107: 2902 0.107 - 0.160: 834 0.160 - 0.214: 154 0.214 - 0.267: 36 Chirality restraints: 10620 Sorted by residual: 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 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE A 345 " pdb=" CA ILE A 345 " pdb=" CG1 ILE A 345 " pdb=" CG2 ILE A 345 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE K 345 " pdb=" CA ILE K 345 " pdb=" CG1 ILE K 345 " pdb=" CG2 ILE K 345 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 272 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C SER L 272 " -0.033 2.00e-02 2.50e+03 pdb=" O SER L 272 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN L 273 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 272 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C SER C 272 " 0.033 2.00e-02 2.50e+03 pdb=" O SER C 272 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN C 273 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 272 " -0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C SER B 272 " 0.033 2.00e-02 2.50e+03 pdb=" O SER B 272 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 273 " -0.011 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 13279 2.77 - 3.30: 66671 3.30 - 3.83: 122422 3.83 - 4.37: 138368 4.37 - 4.90: 242391 Nonbonded interactions: 583131 Sorted by model distance: nonbonded pdb=" O SER E 575 " pdb=" OG SER E 606 " model vdw 2.233 2.440 nonbonded pdb=" O SER I 575 " pdb=" OG SER I 606 " model vdw 2.233 2.440 nonbonded pdb=" O SER D 575 " pdb=" OG SER D 606 " model vdw 2.234 2.440 nonbonded pdb=" O SER K 575 " pdb=" OG SER K 606 " model vdw 2.234 2.440 nonbonded pdb=" O SER G 575 " pdb=" OG SER G 606 " model vdw 2.234 2.440 ... (remaining 583126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 15.710 Check model and map are aligned: 0.760 Set scattering table: 0.450 Process input model: 145.680 Find NCS groups from input model: 3.690 Set up NCS constraints: 0.400 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:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 173.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 0.070 69840 Z= 0.517 Angle : 1.139 14.227 94584 Z= 0.645 Chirality : 0.064 0.267 10620 Planarity : 0.005 0.044 12396 Dihedral : 11.102 70.590 25056 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.05 % Favored : 83.95 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -5.60 (0.07), residues: 8952 helix: -4.67 (0.08), residues: 300 sheet: -4.06 (0.09), residues: 2160 loop : -3.83 (0.06), residues: 6492 *********************** 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 326 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 254 time to evaluate : 5.884 Fit side-chains outliers start: 72 outliers final: 12 residues processed: 326 average time/residue: 0.5696 time to fit residues: 340.8022 Evaluate side-chains 151 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 5.823 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4718 time to fit residues: 18.7766 ------------------------------------------------------------------------------- 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: 1.9990 chunk 378 optimal weight: 6.9990 chunk 233 optimal weight: 6.9990 chunk 460 optimal weight: 0.9990 chunk 364 optimal weight: 0.0870 chunk 705 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 428 optimal weight: 0.9990 chunk 525 optimal weight: 10.0000 chunk 817 optimal weight: 50.0000 overall best weight: 1.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 284 GLN A 289 ASN A 387 ASN A 453 ASN A 484 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN A 655 ASN A 665 ASN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 ASN A 755 ASN B 284 GLN B 289 ASN B 387 ASN B 453 ASN B 484 ASN ** B 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN B 655 ASN B 665 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN B 755 ASN B 803 ASN C 284 GLN C 289 ASN C 387 ASN C 453 ASN C 484 ASN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN C 655 ASN C 665 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 ASN C 755 ASN C 803 ASN D 256 HIS D 284 GLN D 289 ASN D 387 ASN D 453 ASN D 484 ASN ** D 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN D 655 ASN D 665 ASN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN D 755 ASN D 803 ASN E 256 HIS E 284 GLN E 289 ASN E 387 ASN E 453 ASN E 484 ASN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN E 655 ASN E 665 ASN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 690 ASN E 755 ASN E 803 ASN F 284 GLN F 289 ASN F 387 ASN F 453 ASN F 484 ASN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 ASN F 655 ASN F 665 ASN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 690 ASN F 755 ASN G 256 HIS G 284 GLN G 289 ASN G 387 ASN G 453 ASN G 484 ASN ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 584 ASN G 655 ASN G 665 ASN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 690 ASN G 755 ASN H 284 GLN H 289 ASN H 387 ASN H 453 ASN H 484 ASN ** H 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 ASN H 655 ASN H 665 ASN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 690 ASN H 755 ASN H 803 ASN I 284 GLN I 289 ASN I 387 ASN I 453 ASN I 484 ASN ** I 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 584 ASN I 655 ASN I 665 ASN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 690 ASN I 755 ASN I 803 ASN J 256 HIS J 284 GLN J 289 ASN J 387 ASN J 453 ASN J 484 ASN ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 584 ASN J 655 ASN J 665 ASN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 690 ASN J 755 ASN K 256 HIS K 284 GLN K 289 ASN K 387 ASN K 453 ASN K 484 ASN ** K 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 584 ASN K 655 ASN K 665 ASN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 690 ASN K 755 ASN K 803 ASN L 284 GLN L 289 ASN L 387 ASN L 453 ASN L 484 ASN ** L 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 584 ASN L 655 ASN L 665 ASN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 690 ASN L 755 ASN Total number of N/Q/H flips: 133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 69840 Z= 0.140 Angle : 0.581 7.577 94584 Z= 0.306 Chirality : 0.046 0.156 10620 Planarity : 0.003 0.035 12396 Dihedral : 6.293 26.836 9516 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer Outliers : 0.80 % 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: -5.10 (0.07), residues: 8952 helix: -3.83 (0.16), residues: 360 sheet: -3.60 (0.09), residues: 2508 loop : -3.47 (0.06), residues: 6084 *********************** 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 248 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 189 time to evaluate : 5.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 31 residues processed: 244 average time/residue: 0.5715 time to fit residues: 258.8066 Evaluate side-chains 173 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 5.803 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4828 time to fit residues: 36.6606 ------------------------------------------------------------------------------- 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: 0.0270 chunk 253 optimal weight: 0.9990 chunk 680 optimal weight: 20.0000 chunk 556 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 818 optimal weight: 5.9990 chunk 884 optimal weight: 7.9990 chunk 729 optimal weight: 20.0000 chunk 811 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 656 optimal weight: 40.0000 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 GLN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 GLN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 GLN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 803 ASN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 GLN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 803 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 190 GLN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 GLN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 803 ASN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 GLN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 GLN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 803 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 69840 Z= 0.298 Angle : 0.668 13.496 94584 Z= 0.353 Chirality : 0.048 0.163 10620 Planarity : 0.003 0.025 12396 Dihedral : 6.466 26.571 9516 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.92 % Favored : 83.08 % Rotamer Outliers : 1.38 % 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: -5.00 (0.07), residues: 8952 helix: -2.80 (0.23), residues: 312 sheet: -3.51 (0.09), residues: 2256 loop : -3.53 (0.06), residues: 6384 *********************** 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 266 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 164 time to evaluate : 5.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 45 residues processed: 254 average time/residue: 0.5645 time to fit residues: 269.5320 Evaluate side-chains 200 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 155 time to evaluate : 5.815 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4820 time to fit residues: 49.3465 ------------------------------------------------------------------------------- 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: 10.0000 chunk 615 optimal weight: 20.0000 chunk 424 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 390 optimal weight: 20.0000 chunk 549 optimal weight: 9.9990 chunk 821 optimal weight: 50.0000 chunk 869 optimal weight: 7.9990 chunk 429 optimal weight: 5.9990 chunk 778 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 62 ASN ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 340 GLN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 340 GLN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 GLN J 62 ASN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 340 GLN K 658 ASN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 340 GLN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 69840 Z= 0.417 Angle : 0.765 12.462 94584 Z= 0.410 Chirality : 0.051 0.172 10620 Planarity : 0.004 0.024 12396 Dihedral : 7.126 34.146 9516 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.64 % Favored : 80.36 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -5.03 (0.07), residues: 8952 helix: -2.76 (0.24), residues: 312 sheet: -3.55 (0.09), residues: 2196 loop : -3.56 (0.06), residues: 6444 *********************** 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 346 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 161 time to evaluate : 5.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 185 outliers final: 123 residues processed: 328 average time/residue: 0.5602 time to fit residues: 340.6686 Evaluate side-chains 281 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 158 time to evaluate : 5.790 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 0 residues processed: 123 average time/residue: 0.4795 time to fit residues: 121.2633 ------------------------------------------------------------------------------- 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: 30.0000 chunk 493 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 647 optimal weight: 10.0000 chunk 358 optimal weight: 20.0000 chunk 742 optimal weight: 30.0000 chunk 601 optimal weight: 6.9990 chunk 1 optimal weight: 0.0980 chunk 444 optimal weight: 20.0000 chunk 780 optimal weight: 10.0000 chunk 219 optimal weight: 0.0170 overall best weight: 2.6224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 340 GLN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 69840 Z= 0.202 Angle : 0.618 10.856 94584 Z= 0.318 Chirality : 0.047 0.164 10620 Planarity : 0.002 0.028 12396 Dihedral : 6.170 26.780 9516 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.09 % Favored : 85.91 % Rotamer Outliers : 1.42 % 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: -4.82 (0.08), residues: 8952 helix: -3.15 (0.22), residues: 336 sheet: -3.61 (0.09), residues: 2508 loop : -3.20 (0.07), residues: 6108 *********************** 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 264 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 159 time to evaluate : 5.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 38 residues processed: 253 average time/residue: 0.6117 time to fit residues: 284.5712 Evaluate side-chains 190 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 5.911 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.5531 time to fit residues: 50.1360 ------------------------------------------------------------------------------- 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: 50.0000 chunk 783 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 510 optimal weight: 20.0000 chunk 214 optimal weight: 40.0000 chunk 870 optimal weight: 9.9990 chunk 722 optimal weight: 20.0000 chunk 403 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 288 optimal weight: 30.0000 chunk 457 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN A 128 GLN ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN B 62 ASN ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN C 62 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN D 62 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 128 GLN ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 GLN E 62 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN F 62 ASN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 756 GLN G 62 ASN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN G 128 GLN ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN H 62 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN H 128 GLN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN I 62 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 756 GLN ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 ASN J 128 GLN ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN K 62 ASN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 GLN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 GLN L 62 ASN ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 69840 Z= 0.456 Angle : 0.795 11.557 94584 Z= 0.423 Chirality : 0.052 0.187 10620 Planarity : 0.004 0.025 12396 Dihedral : 7.216 33.840 9516 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.17 % Favored : 76.83 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.07), residues: 8952 helix: -2.47 (0.25), residues: 300 sheet: -3.95 (0.09), residues: 2496 loop : -3.38 (0.07), residues: 6156 *********************** 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 277 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 146 time to evaluate : 5.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 66 residues processed: 267 average time/residue: 0.5772 time to fit residues: 286.3216 Evaluate side-chains 214 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 148 time to evaluate : 7.231 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.4965 time to fit residues: 70.6214 ------------------------------------------------------------------------------- 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: 10.0000 chunk 496 optimal weight: 6.9990 chunk 635 optimal weight: 5.9990 chunk 492 optimal weight: 9.9990 chunk 733 optimal weight: 4.9990 chunk 486 optimal weight: 10.0000 chunk 867 optimal weight: 9.9990 chunk 542 optimal weight: 10.0000 chunk 528 optimal weight: 0.9990 chunk 400 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 128 GLN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN F 128 GLN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 513 ASN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN I 128 GLN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 ASN L 128 GLN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 69840 Z= 0.302 Angle : 0.691 9.346 94584 Z= 0.363 Chirality : 0.049 0.178 10620 Planarity : 0.003 0.029 12396 Dihedral : 6.690 27.374 9516 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.12 % Favored : 82.88 % Rotamer Outliers : 1.15 % 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: -4.89 (0.07), residues: 8952 helix: -2.36 (0.29), residues: 264 sheet: -3.86 (0.09), residues: 2244 loop : -3.28 (0.07), residues: 6444 *********************** 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 236 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 151 time to evaluate : 5.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 37 residues processed: 232 average time/residue: 0.5926 time to fit residues: 254.1188 Evaluate side-chains 190 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 5.825 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.5341 time to fit residues: 44.6695 ------------------------------------------------------------------------------- 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: 8.9990 chunk 346 optimal weight: 6.9990 chunk 518 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 170 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 551 optimal weight: 2.9990 chunk 590 optimal weight: 20.0000 chunk 428 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 681 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 513 ASN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 ASN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 ASN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 513 ASN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 513 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 69840 Z= 0.289 Angle : 0.683 10.288 94584 Z= 0.357 Chirality : 0.049 0.197 10620 Planarity : 0.003 0.030 12396 Dihedral : 6.497 27.083 9516 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Rotamer Outliers : 1.22 % 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: -4.80 (0.08), residues: 8952 helix: -2.16 (0.30), residues: 264 sheet: -3.83 (0.09), residues: 2316 loop : -3.19 (0.07), residues: 6372 *********************** 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 243 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 153 time to evaluate : 5.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 41 residues processed: 233 average time/residue: 0.6266 time to fit residues: 264.7397 Evaluate side-chains 191 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 5.893 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.5203 time to fit residues: 48.1073 ------------------------------------------------------------------------------- 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: 10.0000 chunk 831 optimal weight: 6.9990 chunk 758 optimal weight: 5.9990 chunk 808 optimal weight: 20.0000 chunk 830 optimal weight: 20.0000 chunk 486 optimal weight: 20.0000 chunk 352 optimal weight: 30.0000 chunk 634 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 730 optimal weight: 5.9990 chunk 764 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN C 531 HIS ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 GLN ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN F 531 HIS ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 GLN ** G 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN I 531 HIS ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** J 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 GLN ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 GLN L 531 HIS ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 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 : 0.007 0.061 69840 Z= 0.448 Angle : 0.807 10.952 94584 Z= 0.425 Chirality : 0.052 0.204 10620 Planarity : 0.004 0.025 12396 Dihedral : 7.242 32.794 9516 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 27.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.33 % Favored : 77.67 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.07), residues: 8952 helix: -2.34 (0.24), residues: 372 sheet: -4.00 (0.09), residues: 2268 loop : -3.29 (0.07), residues: 6312 *********************** 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 215 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 143 time to evaluate : 5.926 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 32 residues processed: 208 average time/residue: 0.6030 time to fit residues: 232.8918 Evaluate side-chains 172 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 5.850 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.5073 time to fit residues: 38.7594 ------------------------------------------------------------------------------- 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: 40.0000 chunk 530 optimal weight: 20.0000 chunk 854 optimal weight: 2.9990 chunk 521 optimal weight: 40.0000 chunk 405 optimal weight: 6.9990 chunk 594 optimal weight: 7.9990 chunk 896 optimal weight: 30.0000 chunk 825 optimal weight: 5.9990 chunk 713 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 551 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 69840 Z= 0.290 Angle : 0.703 11.388 94584 Z= 0.361 Chirality : 0.049 0.186 10620 Planarity : 0.003 0.025 12396 Dihedral : 6.597 26.983 9516 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.71 % Favored : 83.29 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.08), residues: 8952 helix: -2.09 (0.30), residues: 264 sheet: -3.84 (0.09), residues: 2316 loop : -3.15 (0.07), residues: 6372 ********************** 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 177 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 5.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 175 average time/residue: 0.6162 time to fit residues: 202.6633 Evaluate side-chains 157 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 5.922 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5190 time to fit residues: 20.7553 ------------------------------------------------------------------------------- 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: 20.0000 chunk 567 optimal weight: 10.0000 chunk 760 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 658 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 198 optimal weight: 0.0010 chunk 715 optimal weight: 20.0000 chunk 299 optimal weight: 5.9990 chunk 734 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 ASN ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 513 ASN ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 513 ASN ** L 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.079204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.044161 restraints weight = 219120.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.045510 restraints weight = 131429.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.046399 restraints weight = 97910.776| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 69840 Z= 0.345 Angle : 0.739 12.863 94584 Z= 0.382 Chirality : 0.050 0.180 10620 Planarity : 0.003 0.023 12396 Dihedral : 6.785 30.026 9516 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.06 % Favored : 79.94 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -4.78 (0.08), residues: 8952 helix: -2.20 (0.27), residues: 336 sheet: -3.89 (0.09), residues: 2388 loop : -3.11 (0.07), residues: 6228 =============================================================================== Job complete usr+sys time: 8918.43 seconds wall clock time: 163 minutes 33.44 seconds (9813.44 seconds total)