Starting phenix.real_space_refine (version: dev) on Wed Dec 14 03:35:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/12_2022/6nyg_0543.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/12_2022/6nyg_0543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/12_2022/6nyg_0543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/12_2022/6nyg_0543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/12_2022/6nyg_0543.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nyg_0543/12_2022/6nyg_0543.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A 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-dev-4807/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: 28.32, per 1000 atoms: 0.41 Number of scatterers: 68664 At special positions: 0 Unit cell: (297.86, 297.86, 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=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.02 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 749 " distance=2.02 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 749 " distance=2.02 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 749 " distance=2.03 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: 19.65 Conformation dependent library (CDL) restraints added in 7.8 seconds 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16080 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 192 sheets defined 5.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA A 38 " --> pdb=" O ALA A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.873A pdb=" N ARG A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 721 through 725' Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.038A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN A 764 " --> pdb=" O ASN A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 38 removed outlier: 3.601A pdb=" N ALA B 38 " --> pdb=" O ALA B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.872A pdb=" N ARG B 725 " --> pdb=" O GLN B 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 721 through 725' Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.040A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 752 " --> pdb=" O ALA B 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 3.753A pdb=" N MET B 758 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 38 removed outlier: 3.601A pdb=" N ALA C 38 " --> pdb=" O ALA C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.873A pdb=" N ARG C 725 " --> pdb=" O GLN C 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 721 through 725' Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 752 " --> pdb=" O ALA C 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE C 753 " --> pdb=" O CYS C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET C 758 " --> pdb=" O ASN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN C 764 " --> pdb=" O ASN C 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA D 38 " --> pdb=" O ALA D 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 35 through 38' Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.872A pdb=" N ARG D 725 " --> pdb=" O GLN D 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 721 through 725' Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA D 752 " --> pdb=" O ALA D 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE D 753 " --> pdb=" O CYS D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET D 758 " --> pdb=" O ASN D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN D 764 " --> pdb=" O ASN D 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 35 through 38' Processing helix chain 'E' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.872A pdb=" N ARG E 725 " --> pdb=" O GLN E 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 721 through 725' Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA E 752 " --> pdb=" O ALA E 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE E 753 " --> pdb=" O CYS E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET E 758 " --> pdb=" O ASN E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.513A pdb=" N ASN E 764 " --> pdb=" O ASN E 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA F 38 " --> pdb=" O ALA F 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 35 through 38' Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.873A pdb=" N ARG F 725 " --> pdb=" O GLN F 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 721 through 725' Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA F 752 " --> pdb=" O ALA F 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE F 753 " --> pdb=" O CYS F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET F 758 " --> pdb=" O ASN F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN F 764 " --> pdb=" O ASN F 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 38 removed outlier: 3.601A pdb=" N ALA G 38 " --> pdb=" O ALA G 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 35 through 38' Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 4.138A 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 721 through 725 removed outlier: 3.873A pdb=" N ARG G 725 " --> pdb=" O GLN G 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 721 through 725' Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.040A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA G 752 " --> pdb=" O ALA G 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE G 753 " --> pdb=" O CYS G 749 " (cutoff:3.500A) Processing helix chain 'G' and resid 755 through 759 removed outlier: 3.753A pdb=" N MET G 758 " --> pdb=" O ASN G 755 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN G 764 " --> pdb=" O ASN G 761 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA H 38 " --> pdb=" O ALA H 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 35 through 38' Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.872A pdb=" N ARG H 725 " --> pdb=" O GLN H 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 721 through 725' Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.040A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA H 752 " --> pdb=" O ALA H 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE H 753 " --> pdb=" O CYS H 749 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET H 758 " --> pdb=" O ASN H 755 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN H 764 " --> pdb=" O ASN H 761 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'I' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA I 38 " --> pdb=" O ALA I 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU I 59 " --> pdb=" O GLY I 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.873A pdb=" N ARG I 725 " --> pdb=" O GLN I 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 721 through 725' Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.040A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA I 752 " --> pdb=" O ALA I 748 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE I 753 " --> pdb=" O CYS I 749 " (cutoff:3.500A) Processing helix chain 'I' and resid 755 through 759 removed outlier: 3.751A pdb=" N MET I 758 " --> pdb=" O ASN I 755 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN I 764 " --> pdb=" O ASN I 761 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA J 38 " --> pdb=" O ALA J 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 35 through 38' Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU J 59 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.872A pdb=" N ARG J 725 " --> pdb=" O GLN J 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 721 through 725' Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA J 752 " --> pdb=" O ALA J 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE J 753 " --> pdb=" O CYS J 749 " (cutoff:3.500A) Processing helix chain 'J' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET J 758 " --> pdb=" O ASN J 755 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.513A pdb=" N ASN J 764 " --> pdb=" O ASN J 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 34 Processing helix chain 'K' and resid 35 through 38 removed outlier: 3.600A pdb=" N ALA K 38 " --> pdb=" O ALA K 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 35 through 38' Processing helix chain 'K' and resid 56 through 60 removed outlier: 3.788A pdb=" N GLU K 59 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.872A pdb=" N ARG K 725 " --> pdb=" O GLN K 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 721 through 725' Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA K 752 " --> pdb=" O ALA K 748 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE K 753 " --> pdb=" O CYS K 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 755 through 759 removed outlier: 3.752A pdb=" N MET K 758 " --> pdb=" O ASN K 755 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.513A pdb=" N ASN K 764 " --> pdb=" O ASN K 761 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 35 through 38 removed outlier: 3.601A pdb=" N ALA L 38 " --> pdb=" O ALA L 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 35 through 38' Processing helix chain 'L' and resid 56 through 60 removed outlier: 3.789A pdb=" N GLU L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 4.137A 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 721 through 725 removed outlier: 3.873A pdb=" N ARG L 725 " --> pdb=" O GLN L 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 721 through 725' Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.039A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA L 752 " --> pdb=" O ALA L 748 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE L 753 " --> pdb=" O CYS L 749 " (cutoff:3.500A) Processing helix chain 'L' and resid 755 through 759 removed outlier: 3.753A pdb=" N MET L 758 " --> pdb=" O ASN L 755 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.512A pdb=" N ASN L 764 " --> pdb=" O ASN L 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 212 removed outlier: 7.003A pdb=" N LEU A 187 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 155 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 125 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP A 124 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU A 99 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN A 126 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS A 47 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU A 100 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP A 49 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP A 102 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 51 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL F 339 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL A 48 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 50 " --> pdb=" O PRO F 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY A 108 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG A 133 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR A 110 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU A 169 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL A 252 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 220 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE A 254 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY A 222 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS A 256 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN A 253 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 277 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN A 255 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS A 276 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG A 361 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY A 278 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN A 363 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.305A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 345 removed outlier: 5.466A pdb=" N VAL A 339 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ARG B 50 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN B 52 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN A 343 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS B 47 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU B 100 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N TRP B 49 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP B 102 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 51 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP B 124 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU B 99 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN B 126 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 125 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 155 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 187 " --> pdb=" O ASN B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU A 407 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 435 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS A 465 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE A 437 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'A' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE A 456 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A 517 " --> pdb=" O ARG A 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 530 through 532 Processing sheet with id=AB3, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB4, first strand: chain 'A' and resid 572 through 574 removed outlier: 5.444A pdb=" N PHE A 572 " --> pdb=" O ALA A 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE A 636 " --> pdb=" O LEU A 613 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET A 621 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE A 679 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AB9, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY B 108 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG B 133 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR B 110 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.573A pdb=" N GLU B 169 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL B 252 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU B 220 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE B 254 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY B 222 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS B 256 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN B 253 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 277 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS B 276 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG B 361 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B 278 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN B 363 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 339 through 345 removed outlier: 5.471A pdb=" N VAL B 339 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ARG C 50 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN C 52 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLN B 343 " --> pdb=" O GLN C 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS C 47 " --> pdb=" O LYS C 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU C 100 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP C 49 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP C 102 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE C 51 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP C 124 " --> pdb=" O ASN C 97 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU C 99 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN C 126 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 125 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 155 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU C 187 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 377 through 379 removed outlier: 3.709A pdb=" N GLU B 407 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA B 435 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS B 465 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 437 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AC7, first strand: chain 'B' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE B 456 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 517 " --> pdb=" O ARG B 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 470 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 530 through 532 Processing sheet with id=AD1, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AD2, first strand: chain 'B' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE B 572 " --> pdb=" O ALA B 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE B 636 " --> pdb=" O LEU B 613 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET B 621 " --> pdb=" O ASN B 643 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE B 679 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 693 through 697 removed outlier: 7.700A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD7, first strand: chain 'C' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY C 108 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG C 133 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR C 110 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU C 169 " --> pdb=" O ASN C 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 218 through 224 removed outlier: 4.058A pdb=" N VAL C 252 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU C 220 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE C 254 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY C 222 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS C 256 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN C 253 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE C 277 " --> pdb=" O ASN C 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN C 255 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N HIS C 276 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG C 361 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY C 278 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN C 363 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 339 through 345 removed outlier: 5.652A pdb=" N VAL C 339 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ARG D 50 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN D 52 " --> pdb=" O PRO C 341 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N GLN C 343 " --> pdb=" O GLN D 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS D 47 " --> pdb=" O LYS D 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU D 100 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TRP D 49 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP D 102 " --> pdb=" O TRP D 49 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE D 51 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP D 124 " --> pdb=" O ASN D 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU D 99 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN D 126 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL D 125 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL D 155 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU D 187 " --> pdb=" O ASN D 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 377 through 379 removed outlier: 3.707A pdb=" N GLU C 407 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA C 435 " --> pdb=" O ASN C 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS C 465 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE C 437 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 387 through 388 Processing sheet with id=AE5, first strand: chain 'C' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE C 456 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 517 " --> pdb=" O ARG C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 470 through 472 Processing sheet with id=AE7, first strand: chain 'C' and resid 530 through 532 Processing sheet with id=AE8, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AE9, first strand: chain 'C' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE C 572 " --> pdb=" O ALA C 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE C 636 " --> pdb=" O LEU C 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET C 621 " --> pdb=" O ASN C 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE C 679 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AF5, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY D 108 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARG D 133 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR D 110 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU D 169 " --> pdb=" O ASN D 140 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL D 252 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU D 220 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE D 254 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY D 222 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS D 256 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN D 253 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE D 277 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN D 255 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS D 276 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG D 361 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY D 278 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN D 363 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'D' and resid 339 through 345 removed outlier: 5.608A pdb=" N VAL D 339 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ARG E 50 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLN E 52 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLN D 343 " --> pdb=" O GLN E 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS E 47 " --> pdb=" O LYS E 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU E 100 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP E 49 " --> pdb=" O GLU E 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP E 102 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE E 51 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP E 124 " --> pdb=" O ASN E 97 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU E 99 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN E 126 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 125 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL E 155 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU E 187 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 377 through 379 removed outlier: 3.707A pdb=" N GLU D 407 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA D 435 " --> pdb=" O ASN D 463 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LYS D 465 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE D 437 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AG3, first strand: chain 'D' and resid 456 through 457 removed outlier: 7.158A pdb=" N ILE D 456 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU D 517 " --> pdb=" O ARG D 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'D' and resid 470 through 472 Processing sheet with id=AG5, first strand: chain 'D' and resid 530 through 532 Processing sheet with id=AG6, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AG7, first strand: chain 'D' and resid 572 through 574 removed outlier: 5.446A pdb=" N PHE D 572 " --> pdb=" O ALA D 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'D' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE D 636 " --> pdb=" O LEU D 613 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET D 621 " --> pdb=" O ASN D 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE D 679 " --> pdb=" O ALA D 727 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AH3, first strand: chain 'E' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ARG E 133 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR E 110 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU E 169 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL E 252 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU E 220 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE E 254 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY E 222 " --> pdb=" O PHE E 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS E 256 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN E 253 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE E 277 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN E 255 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS E 276 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG E 361 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY E 278 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN E 363 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'E' and resid 339 through 345 removed outlier: 5.408A pdb=" N VAL E 339 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ARG F 50 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN F 52 " --> pdb=" O PRO E 341 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN E 343 " --> pdb=" O GLN F 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS F 47 " --> pdb=" O LYS F 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU F 100 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TRP F 49 " --> pdb=" O GLU F 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP F 102 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 51 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ASP F 124 " --> pdb=" O ASN F 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU F 99 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN F 126 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 125 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL F 155 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU F 187 " --> pdb=" O ASN F 212 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU E 407 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA E 435 " --> pdb=" O ASN E 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS E 465 " --> pdb=" O ALA E 435 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE E 437 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AI1, first strand: chain 'E' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE E 456 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU E 517 " --> pdb=" O ARG E 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'E' and resid 470 through 472 Processing sheet with id=AI3, first strand: chain 'E' and resid 530 through 532 Processing sheet with id=AI4, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AI5, first strand: chain 'E' and resid 572 through 574 removed outlier: 5.444A pdb=" N PHE E 572 " --> pdb=" O ALA E 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'E' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE E 636 " --> pdb=" O LEU E 613 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'E' and resid 621 through 622 removed outlier: 6.496A pdb=" N MET E 621 " --> pdb=" O ASN E 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE E 679 " --> pdb=" O ALA E 727 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AJ1, first strand: chain 'F' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY F 108 " --> pdb=" O THR F 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG F 133 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR F 110 " --> pdb=" O ARG F 133 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU F 169 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 218 through 224 removed outlier: 4.058A pdb=" N VAL F 252 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU F 220 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE F 254 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY F 222 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS F 256 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN F 253 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE F 277 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN F 255 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS F 276 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG F 361 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY F 278 " --> pdb=" O ARG F 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN F 363 " --> pdb=" O GLY F 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'F' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU F 407 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA F 435 " --> pdb=" O ASN F 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS F 465 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE F 437 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AJ7, first strand: chain 'F' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE F 456 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU F 517 " --> pdb=" O ARG F 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'F' and resid 470 through 472 Processing sheet with id=AJ9, first strand: chain 'F' and resid 530 through 532 Processing sheet with id=AK1, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AK2, first strand: chain 'F' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE F 572 " --> pdb=" O ALA F 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'F' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE F 636 " --> pdb=" O LEU F 613 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET F 621 " --> pdb=" O ASN F 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE F 679 " --> pdb=" O ALA F 727 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 693 through 697 removed outlier: 7.700A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AK7, first strand: chain 'G' and resid 210 through 212 removed outlier: 7.003A pdb=" N LEU G 187 " --> pdb=" O ASN G 212 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 155 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 125 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP G 124 " --> pdb=" O ASN G 97 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU G 99 " --> pdb=" O ASP G 124 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN G 126 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS G 47 " --> pdb=" O LYS G 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU G 100 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP G 49 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP G 102 " --> pdb=" O TRP G 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE G 51 " --> pdb=" O ASP G 102 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL L 339 " --> pdb=" O ASP G 46 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL G 48 " --> pdb=" O VAL L 339 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ARG G 50 " --> pdb=" O PRO L 341 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY G 108 " --> pdb=" O THR G 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG G 133 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR G 110 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU G 169 " --> pdb=" O ASN G 140 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL G 252 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU G 220 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE G 254 " --> pdb=" O LEU G 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY G 222 " --> pdb=" O PHE G 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS G 256 " --> pdb=" O GLY G 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN G 253 " --> pdb=" O THR G 275 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE G 277 " --> pdb=" O ASN G 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN G 255 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N HIS G 276 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG G 361 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY G 278 " --> pdb=" O ARG G 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN G 363 " --> pdb=" O GLY G 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'G' and resid 339 through 345 removed outlier: 5.535A pdb=" N VAL G 339 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ARG H 50 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN H 52 " --> pdb=" O PRO G 341 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN G 343 " --> pdb=" O GLN H 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS H 47 " --> pdb=" O LYS H 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU H 100 " --> pdb=" O LYS H 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP H 49 " --> pdb=" O GLU H 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP H 102 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE H 51 " --> pdb=" O ASP H 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP H 124 " --> pdb=" O ASN H 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU H 99 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN H 126 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 125 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL H 155 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU H 187 " --> pdb=" O ASN H 212 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU G 407 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA G 435 " --> pdb=" O ASN G 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS G 465 " --> pdb=" O ALA G 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE G 437 " --> pdb=" O LYS G 465 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AL6, first strand: chain 'G' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE G 456 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU G 500 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU G 517 " --> pdb=" O ARG G 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'G' and resid 470 through 472 Processing sheet with id=AL8, first strand: chain 'G' and resid 530 through 532 Processing sheet with id=AL9, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AM1, first strand: chain 'G' and resid 572 through 574 removed outlier: 5.444A pdb=" N PHE G 572 " --> pdb=" O ALA G 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM1 Processing sheet with id=AM2, first strand: chain 'G' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE G 636 " --> pdb=" O LEU G 613 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'G' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET G 621 " --> pdb=" O ASN G 643 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE G 679 " --> pdb=" O ALA G 727 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'G' and resid 693 through 697 removed outlier: 7.702A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'G' and resid 729 through 730 Processing sheet with id=AM6, first strand: chain 'H' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY H 108 " --> pdb=" O THR H 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG H 133 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR H 110 " --> pdb=" O ARG H 133 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU H 169 " --> pdb=" O ASN H 140 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'H' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL H 252 " --> pdb=" O VAL H 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU H 220 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE H 254 " --> pdb=" O LEU H 220 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY H 222 " --> pdb=" O PHE H 254 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS H 256 " --> pdb=" O GLY H 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN H 253 " --> pdb=" O THR H 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE H 277 " --> pdb=" O ASN H 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN H 255 " --> pdb=" O ILE H 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS H 276 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG H 361 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY H 278 " --> pdb=" O ARG H 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN H 363 " --> pdb=" O GLY H 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'H' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM9 Processing sheet with id=AN1, first strand: chain 'H' and resid 339 through 345 removed outlier: 5.445A pdb=" N VAL H 339 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ARG I 50 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN I 52 " --> pdb=" O PRO H 341 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN H 343 " --> pdb=" O GLN I 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS I 47 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU I 100 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP I 49 " --> pdb=" O GLU I 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP I 102 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE I 51 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ASP I 124 " --> pdb=" O ASN I 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU I 99 " --> pdb=" O ASP I 124 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN I 126 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL I 125 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL I 155 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU I 187 " --> pdb=" O ASN I 212 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'H' and resid 377 through 379 removed outlier: 3.707A pdb=" N GLU H 407 " --> pdb=" O LEU H 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA H 435 " --> pdb=" O ASN H 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS H 465 " --> pdb=" O ALA H 435 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE H 437 " --> pdb=" O LYS H 465 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'H' and resid 387 through 388 Processing sheet with id=AN4, first strand: chain 'H' and resid 456 through 457 removed outlier: 7.160A pdb=" N ILE H 456 " --> pdb=" O ASP H 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU H 500 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU H 517 " --> pdb=" O ARG H 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN4 Processing sheet with id=AN5, first strand: chain 'H' and resid 470 through 472 Processing sheet with id=AN6, first strand: chain 'H' and resid 530 through 532 Processing sheet with id=AN7, first strand: chain 'H' and resid 541 through 542 Processing sheet with id=AN8, first strand: chain 'H' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE H 572 " --> pdb=" O ALA H 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN8 Processing sheet with id=AN9, first strand: chain 'H' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE H 636 " --> pdb=" O LEU H 613 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'H' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET H 621 " --> pdb=" O ASN H 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE H 679 " --> pdb=" O ALA H 727 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'H' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'H' and resid 729 through 730 Processing sheet with id=AO4, first strand: chain 'I' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY I 108 " --> pdb=" O THR I 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG I 133 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR I 110 " --> pdb=" O ARG I 133 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'I' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU I 169 " --> pdb=" O ASN I 140 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'I' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL I 252 " --> pdb=" O VAL I 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU I 220 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE I 254 " --> pdb=" O LEU I 220 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY I 222 " --> pdb=" O PHE I 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS I 256 " --> pdb=" O GLY I 222 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASN I 253 " --> pdb=" O THR I 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE I 277 " --> pdb=" O ASN I 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN I 255 " --> pdb=" O ILE I 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS I 276 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG I 361 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY I 278 " --> pdb=" O ARG I 361 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN I 363 " --> pdb=" O GLY I 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'I' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO7 Processing sheet with id=AO8, first strand: chain 'I' and resid 339 through 345 removed outlier: 5.542A pdb=" N VAL I 339 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ARG J 50 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLN J 52 " --> pdb=" O PRO I 341 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLN I 343 " --> pdb=" O GLN J 52 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS J 47 " --> pdb=" O LYS J 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU J 100 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP J 49 " --> pdb=" O GLU J 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP J 102 " --> pdb=" O TRP J 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE J 51 " --> pdb=" O ASP J 102 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N ASP J 124 " --> pdb=" O ASN J 97 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU J 99 " --> pdb=" O ASP J 124 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN J 126 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL J 125 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL J 155 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU J 187 " --> pdb=" O ASN J 212 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'I' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU I 407 " --> pdb=" O LEU I 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA I 435 " --> pdb=" O ASN I 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS I 465 " --> pdb=" O ALA I 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE I 437 " --> pdb=" O LYS I 465 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'I' and resid 387 through 388 Processing sheet with id=AP2, first strand: chain 'I' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE I 456 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU I 500 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU I 517 " --> pdb=" O ARG I 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP2 Processing sheet with id=AP3, first strand: chain 'I' and resid 470 through 472 Processing sheet with id=AP4, first strand: chain 'I' and resid 530 through 532 Processing sheet with id=AP5, first strand: chain 'I' and resid 541 through 542 Processing sheet with id=AP6, first strand: chain 'I' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE I 572 " --> pdb=" O ALA I 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP6 Processing sheet with id=AP7, first strand: chain 'I' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE I 636 " --> pdb=" O LEU I 613 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'I' and resid 621 through 622 removed outlier: 6.495A pdb=" N MET I 621 " --> pdb=" O ASN I 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE I 679 " --> pdb=" O ALA I 727 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'I' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'I' and resid 729 through 730 Processing sheet with id=AQ2, first strand: chain 'J' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY J 108 " --> pdb=" O THR J 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG J 133 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR J 110 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'J' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU J 169 " --> pdb=" O ASN J 140 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'J' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL J 252 " --> pdb=" O VAL J 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU J 220 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE J 254 " --> pdb=" O LEU J 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY J 222 " --> pdb=" O PHE J 254 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS J 256 " --> pdb=" O GLY J 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN J 253 " --> pdb=" O THR J 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE J 277 " --> pdb=" O ASN J 253 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASN J 255 " --> pdb=" O ILE J 277 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N HIS J 276 " --> pdb=" O ILE J 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG J 361 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY J 278 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN J 363 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'J' and resid 269 through 270 removed outlier: 6.307A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ5 Processing sheet with id=AQ6, first strand: chain 'J' and resid 339 through 345 removed outlier: 5.560A pdb=" N VAL J 339 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ARG K 50 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLN K 52 " --> pdb=" O PRO J 341 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN J 343 " --> pdb=" O GLN K 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS K 47 " --> pdb=" O LYS K 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU K 100 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP K 49 " --> pdb=" O GLU K 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP K 102 " --> pdb=" O TRP K 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE K 51 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP K 124 " --> pdb=" O ASN K 97 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU K 99 " --> pdb=" O ASP K 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN K 126 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL K 125 " --> pdb=" O ASP K 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL K 155 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU K 187 " --> pdb=" O ASN K 212 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'J' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU J 407 " --> pdb=" O LEU J 379 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA J 435 " --> pdb=" O ASN J 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS J 465 " --> pdb=" O ALA J 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE J 437 " --> pdb=" O LYS J 465 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AQ9, first strand: chain 'J' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE J 456 " --> pdb=" O ASP J 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU J 500 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU J 517 " --> pdb=" O ARG J 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ9 Processing sheet with id=AR1, first strand: chain 'J' and resid 470 through 472 Processing sheet with id=AR2, first strand: chain 'J' and resid 530 through 532 Processing sheet with id=AR3, first strand: chain 'J' and resid 541 through 542 Processing sheet with id=AR4, first strand: chain 'J' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE J 572 " --> pdb=" O ALA J 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR4 Processing sheet with id=AR5, first strand: chain 'J' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE J 636 " --> pdb=" O LEU J 613 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'J' and resid 621 through 622 removed outlier: 6.496A pdb=" N MET J 621 " --> pdb=" O ASN J 643 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE J 679 " --> pdb=" O ALA J 727 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'J' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'J' and resid 729 through 730 Processing sheet with id=AR9, first strand: chain 'K' and resid 65 through 66 removed outlier: 6.096A pdb=" N GLY K 108 " --> pdb=" O THR K 131 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ARG K 133 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR K 110 " --> pdb=" O ARG K 133 " (cutoff:3.500A) Processing sheet with id=AS1, first strand: chain 'K' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU K 169 " --> pdb=" O ASN K 140 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'K' and resid 218 through 224 removed outlier: 4.059A pdb=" N VAL K 252 " --> pdb=" O VAL K 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU K 220 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE K 254 " --> pdb=" O LEU K 220 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY K 222 " --> pdb=" O PHE K 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS K 256 " --> pdb=" O GLY K 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN K 253 " --> pdb=" O THR K 275 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE K 277 " --> pdb=" O ASN K 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN K 255 " --> pdb=" O ILE K 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS K 276 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ARG K 361 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY K 278 " --> pdb=" O ARG K 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN K 363 " --> pdb=" O GLY K 278 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS3 Processing sheet with id=AS4, first strand: chain 'K' and resid 339 through 345 removed outlier: 5.385A pdb=" N VAL K 339 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG L 50 " --> pdb=" O VAL K 339 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLN L 52 " --> pdb=" O PRO K 341 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN K 343 " --> pdb=" O GLN L 52 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS L 47 " --> pdb=" O LYS L 98 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU L 100 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TRP L 49 " --> pdb=" O GLU L 100 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP L 102 " --> pdb=" O TRP L 49 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE L 51 " --> pdb=" O ASP L 102 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP L 124 " --> pdb=" O ASN L 97 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU L 99 " --> pdb=" O ASP L 124 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN L 126 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL L 125 " --> pdb=" O ASP L 156 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL L 155 " --> pdb=" O THR L 188 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU L 187 " --> pdb=" O ASN L 212 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'K' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU K 407 " --> pdb=" O LEU K 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA K 435 " --> pdb=" O ASN K 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS K 465 " --> pdb=" O ALA K 435 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE K 437 " --> pdb=" O LYS K 465 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'K' and resid 387 through 388 Processing sheet with id=AS7, first strand: chain 'K' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE K 456 " --> pdb=" O ASP K 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU K 500 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU K 517 " --> pdb=" O ARG K 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS7 Processing sheet with id=AS8, first strand: chain 'K' and resid 470 through 472 Processing sheet with id=AS9, first strand: chain 'K' and resid 530 through 532 Processing sheet with id=AT1, first strand: chain 'K' and resid 541 through 542 Processing sheet with id=AT2, first strand: chain 'K' and resid 572 through 574 removed outlier: 5.444A pdb=" N PHE K 572 " --> pdb=" O ALA K 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT2 Processing sheet with id=AT3, first strand: chain 'K' and resid 589 through 590 removed outlier: 3.826A pdb=" N ILE K 636 " --> pdb=" O LEU K 613 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'K' and resid 621 through 622 removed outlier: 6.496A pdb=" N MET K 621 " --> pdb=" O ASN K 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE K 679 " --> pdb=" O ALA K 727 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'K' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'K' and resid 729 through 730 Processing sheet with id=AT7, first strand: chain 'L' and resid 65 through 66 removed outlier: 6.095A pdb=" N GLY L 108 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N ARG L 133 " --> pdb=" O GLY L 108 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR L 110 " --> pdb=" O ARG L 133 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'L' and resid 140 through 142 removed outlier: 3.572A pdb=" N GLU L 169 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AT9, first strand: chain 'L' and resid 218 through 224 removed outlier: 4.058A pdb=" N VAL L 252 " --> pdb=" O VAL L 218 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LEU L 220 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE L 254 " --> pdb=" O LEU L 220 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY L 222 " --> pdb=" O PHE L 254 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS L 256 " --> pdb=" O GLY L 222 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASN L 253 " --> pdb=" O THR L 275 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE L 277 " --> pdb=" O ASN L 253 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN L 255 " --> pdb=" O ILE L 277 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N HIS L 276 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ARG L 361 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY L 278 " --> pdb=" O ARG L 361 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN L 363 " --> pdb=" O GLY L 278 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) Processing sheet with id=AU1, first strand: chain 'L' and resid 269 through 270 removed outlier: 6.306A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU1 Processing sheet with id=AU2, first strand: chain 'L' and resid 377 through 379 removed outlier: 3.708A pdb=" N GLU L 407 " --> pdb=" O LEU L 379 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA L 435 " --> pdb=" O ASN L 463 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LYS L 465 " --> pdb=" O ALA L 435 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE L 437 " --> pdb=" O LYS L 465 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'L' and resid 387 through 388 Processing sheet with id=AU4, first strand: chain 'L' and resid 456 through 457 removed outlier: 7.159A pdb=" N ILE L 456 " --> pdb=" O ASP L 477 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU L 500 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU L 517 " --> pdb=" O ARG L 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU4 Processing sheet with id=AU5, first strand: chain 'L' and resid 470 through 472 Processing sheet with id=AU6, first strand: chain 'L' and resid 530 through 532 Processing sheet with id=AU7, first strand: chain 'L' and resid 541 through 542 Processing sheet with id=AU8, first strand: chain 'L' and resid 572 through 574 removed outlier: 5.445A pdb=" N PHE L 572 " --> pdb=" O ALA L 595 " (cutoff:3.500A) No H-bonds generated for sheet with id=AU8 Processing sheet with id=AU9, first strand: chain 'L' and resid 589 through 590 removed outlier: 3.827A pdb=" N ILE L 636 " --> pdb=" O LEU L 613 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'L' and resid 621 through 622 removed outlier: 6.496A pdb=" N MET L 621 " --> pdb=" O ASN L 643 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE L 679 " --> pdb=" O ALA L 727 " (cutoff:3.500A) Processing sheet with id=AV2, first strand: chain 'L' and resid 693 through 697 removed outlier: 7.701A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) Processing sheet with id=AV3, first strand: chain 'L' and resid 729 through 730 522 hydrogen bonds defined for protein. 1350 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: 27.47 Time building geometry restraints manager: 21.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22846 1.34 - 1.46: 13485 1.46 - 1.58: 33245 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" CB ASN C 273 " pdb=" CG ASN C 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" CB ASN H 273 " pdb=" CG ASN H 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.80e+00 bond pdb=" CB ASN E 273 " pdb=" CG ASN E 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.78e+00 bond pdb=" CB ASN K 273 " pdb=" CG ASN K 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.78e+00 bond pdb=" CB ASN B 273 " pdb=" CG ASN B 273 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.78e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 1574 106.74 - 113.57: 38399 113.57 - 120.40: 24107 120.40 - 127.23: 29899 127.23 - 134.06: 605 Bond angle restraints: 94584 Sorted by residual: angle pdb=" C GLY F 83 " pdb=" N ASN F 84 " pdb=" CA ASN F 84 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" C GLY I 83 " pdb=" N ASN I 84 " pdb=" CA ASN I 84 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C GLY A 83 " pdb=" N ASN A 84 " pdb=" CA ASN A 84 " ideal model delta sigma weight residual 121.54 130.61 -9.07 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C GLY B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta sigma weight residual 121.54 130.60 -9.06 1.91e+00 2.74e-01 2.25e+01 angle pdb=" C GLY E 83 " pdb=" N ASN E 84 " pdb=" CA ASN E 84 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 38733 16.32 - 32.64: 2077 32.64 - 48.96: 302 48.96 - 65.28: 24 65.28 - 81.60: 36 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: dihedral pdb=" CB CYS H 738 " pdb=" SG CYS H 738 " pdb=" SG CYS H 749 " pdb=" CB CYS H 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS F 738 " pdb=" SG CYS F 738 " pdb=" SG CYS F 749 " pdb=" CB CYS F 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.60 81.60 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 749 " pdb=" CB CYS E 749 " ideal model delta sinusoidal sigma weight residual -86.00 -167.57 81.57 1 1.00e+01 1.00e-02 8.19e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 6591 0.047 - 0.094: 2758 0.094 - 0.141: 1116 0.141 - 0.188: 119 0.188 - 0.235: 36 Chirality restraints: 10620 Sorted by residual: chirality pdb=" CA ASN L 84 " pdb=" N ASN L 84 " pdb=" C ASN L 84 " pdb=" CB ASN L 84 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN G 84 " pdb=" N ASN G 84 " pdb=" C ASN G 84 " pdb=" CB ASN G 84 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASN H 84 " pdb=" N ASN H 84 " pdb=" C ASN H 84 " pdb=" CB ASN H 84 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU K 163 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LEU K 163 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU K 163 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE K 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 163 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LEU E 163 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU E 163 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE E 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 163 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C LEU B 163 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 163 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 164 " -0.012 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 13030 2.77 - 3.31: 65906 3.31 - 3.84: 119118 3.84 - 4.37: 138948 4.37 - 4.90: 237978 Nonbonded interactions: 574980 Sorted by model distance: nonbonded pdb=" OG1 THR D 153 " pdb=" OG1 THR D 185 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR A 153 " pdb=" OG1 THR A 185 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR B 153 " pdb=" OG1 THR B 185 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR C 153 " pdb=" OG1 THR C 185 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR F 153 " pdb=" OG1 THR F 185 " model vdw 2.242 2.440 ... (remaining 574975 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 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. 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: 5.070 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: 0.070 Extract box with map and model: 15.960 Check model and map are aligned: 0.740 Convert atoms to be neutral: 0.450 Process input model: 134.120 Find NCS groups from input model: 3.530 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 69840 Z= 0.344 Angle : 0.972 9.413 94584 Z= 0.547 Chirality : 0.058 0.235 10620 Planarity : 0.005 0.041 12396 Dihedral : 10.451 69.840 25056 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer Outliers : 0.16 % 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: -4.66 (0.07), residues: 8952 helix: -3.66 (0.25), residues: 144 sheet: -3.25 (0.12), residues: 1476 loop : -3.38 (0.06), residues: 7332 *********************** 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 564 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 552 time to evaluate : 5.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 564 average time/residue: 0.6736 time to fit residues: 645.7867 Evaluate side-chains 225 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 6.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.6826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 5.9990 chunk 682 optimal weight: 7.9990 chunk 378 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 460 optimal weight: 10.0000 chunk 364 optimal weight: 50.0000 chunk 705 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 chunk 525 optimal weight: 10.0000 chunk 817 optimal weight: 50.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 ASN ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 463 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 ASN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 617 GLN ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 422 ASN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 755 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 755 ASN ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 ASN ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 755 ASN ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 422 ASN ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 755 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 ASN H 463 ASN ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 755 ASN ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 422 ASN I 617 GLN ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 755 ASN ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 422 ASN ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 755 ASN ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 422 ASN ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 755 ASN ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 422 ASN ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 755 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 69840 Z= 0.435 Angle : 0.808 9.331 94584 Z= 0.427 Chirality : 0.052 0.213 10620 Planarity : 0.004 0.032 12396 Dihedral : 7.530 29.966 9516 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.18 % Favored : 82.82 % Rotamer Outliers : 2.61 % 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: -4.63 (0.07), residues: 8952 helix: -3.54 (0.21), residues: 168 sheet: -3.21 (0.12), residues: 1404 loop : -3.37 (0.06), residues: 7380 *********************** 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 413 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 220 time to evaluate : 6.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 193 outliers final: 81 residues processed: 398 average time/residue: 0.6247 time to fit residues: 430.3641 Evaluate side-chains 259 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 178 time to evaluate : 5.909 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.5261 time to fit residues: 85.6396 ------------------------------------------------------------------------------- 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: 10.0000 chunk 253 optimal weight: 8.9990 chunk 680 optimal weight: 9.9990 chunk 556 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 818 optimal weight: 7.9990 chunk 884 optimal weight: 4.9990 chunk 729 optimal weight: 9.9990 chunk 811 optimal weight: 30.0000 chunk 279 optimal weight: 6.9990 chunk 656 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 584 ASN ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN E 584 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 463 ASN ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 584 ASN ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 ASN I 584 ASN ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 463 ASN ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 ASN K 584 ASN ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** 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 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 69840 Z= 0.344 Angle : 0.750 10.807 94584 Z= 0.395 Chirality : 0.051 0.250 10620 Planarity : 0.004 0.027 12396 Dihedral : 7.268 30.539 9516 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.64 % Favored : 82.36 % Rotamer Outliers : 2.61 % 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: -4.69 (0.07), residues: 8952 helix: -3.33 (0.23), residues: 168 sheet: -3.50 (0.11), residues: 1656 loop : -3.31 (0.06), residues: 7128 *********************** 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 377 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 184 time to evaluate : 6.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 193 outliers final: 145 residues processed: 361 average time/residue: 0.6047 time to fit residues: 390.3238 Evaluate side-chains 317 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 172 time to evaluate : 5.991 Switching outliers to nearest non-outliers outliers start: 145 outliers final: 0 residues processed: 145 average time/residue: 0.4888 time to fit residues: 142.4600 ------------------------------------------------------------------------------- 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: 5.9990 chunk 615 optimal weight: 20.0000 chunk 424 optimal weight: 30.0000 chunk 90 optimal weight: 20.0000 chunk 390 optimal weight: 30.0000 chunk 549 optimal weight: 8.9990 chunk 821 optimal weight: 50.0000 chunk 869 optimal weight: 3.9990 chunk 429 optimal weight: 0.5980 chunk 778 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 ASN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 584 ASN ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 584 ASN ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 412 ASN ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 584 ASN ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 584 ASN ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3021 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= 0.277 Angle : 0.680 10.422 94584 Z= 0.356 Chirality : 0.049 0.172 10620 Planarity : 0.003 0.026 12396 Dihedral : 6.852 29.211 9516 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.39 % Favored : 82.61 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.08), residues: 8952 helix: -2.64 (0.28), residues: 168 sheet: -3.44 (0.11), residues: 1656 loop : -3.17 (0.07), residues: 7128 *********************** 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 328 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 174 time to evaluate : 7.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 57 residues processed: 304 average time/residue: 0.6210 time to fit residues: 343.0373 Evaluate side-chains 213 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 156 time to evaluate : 5.968 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.4909 time to fit residues: 61.6421 ------------------------------------------------------------------------------- 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: 3.9990 chunk 12 optimal weight: 9.9990 chunk 647 optimal weight: 6.9990 chunk 358 optimal weight: 40.0000 chunk 742 optimal weight: 1.9990 chunk 601 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 444 optimal weight: 20.0000 chunk 780 optimal weight: 20.0000 chunk 219 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 412 ASN ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 412 ASN ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 412 ASN ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 463 ASN ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 69840 Z= 0.246 Angle : 0.664 11.366 94584 Z= 0.344 Chirality : 0.049 0.170 10620 Planarity : 0.003 0.029 12396 Dihedral : 6.573 28.570 9516 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.47 % Favored : 84.53 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.08), residues: 8952 helix: -2.06 (0.31), residues: 168 sheet: -3.15 (0.12), residues: 1596 loop : -3.12 (0.07), residues: 7188 *********************** 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 314 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 181 time to evaluate : 6.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 73 residues processed: 304 average time/residue: 0.5810 time to fit residues: 319.6511 Evaluate side-chains 226 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 153 time to evaluate : 5.992 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.4811 time to fit residues: 74.9179 ------------------------------------------------------------------------------- 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: 10.0000 chunk 783 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 510 optimal weight: 30.0000 chunk 214 optimal weight: 9.9990 chunk 870 optimal weight: 9.9990 chunk 722 optimal weight: 20.0000 chunk 403 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 288 optimal weight: 0.0970 chunk 457 optimal weight: 8.9990 overall best weight: 7.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 ASN A 412 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 ASN ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 ASN ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 ASN ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 387 ASN ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 387 ASN ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 ASN ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 387 ASN ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 775 ASN ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 387 ASN ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 387 ASN ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 387 ASN ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3828 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= 0.362 Angle : 0.750 10.182 94584 Z= 0.390 Chirality : 0.051 0.255 10620 Planarity : 0.004 0.030 12396 Dihedral : 6.988 28.741 9516 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 28.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.66 % Favored : 80.34 % Rotamer Outliers : 2.11 % 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: -4.42 (0.08), residues: 8952 helix: -1.57 (0.36), residues: 168 sheet: -3.22 (0.12), residues: 1572 loop : -3.20 (0.07), residues: 7212 *********************** 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 333 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 177 time to evaluate : 7.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 56 residues processed: 319 average time/residue: 0.5970 time to fit residues: 345.4826 Evaluate side-chains 215 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 159 time to evaluate : 6.014 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.5092 time to fit residues: 62.4890 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 10.0000 chunk 496 optimal weight: 10.0000 chunk 635 optimal weight: 7.9990 chunk 492 optimal weight: 10.0000 chunk 733 optimal weight: 0.8980 chunk 486 optimal weight: 30.0000 chunk 867 optimal weight: 3.9990 chunk 542 optimal weight: 10.0000 chunk 528 optimal weight: 0.9990 chunk 400 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 775 ASN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 775 ASN ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 69840 Z= 0.218 Angle : 0.657 9.572 94584 Z= 0.339 Chirality : 0.048 0.171 10620 Planarity : 0.003 0.030 12396 Dihedral : 6.456 29.665 9516 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.01 % Favored : 85.99 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.08), residues: 8952 helix: -2.13 (0.28), residues: 240 sheet: -2.93 (0.13), residues: 1512 loop : -3.10 (0.07), residues: 7200 *********************** 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 240 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 165 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 39 residues processed: 232 average time/residue: 0.5946 time to fit residues: 251.3111 Evaluate side-chains 194 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 6.055 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4878 time to fit residues: 44.4024 ------------------------------------------------------------------------------- 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: 5.9990 chunk 346 optimal weight: 7.9990 chunk 518 optimal weight: 8.9990 chunk 261 optimal weight: 30.0000 chunk 170 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 551 optimal weight: 2.9990 chunk 590 optimal weight: 0.1980 chunk 428 optimal weight: 7.9990 chunk 80 optimal weight: 50.0000 chunk 681 optimal weight: 20.0000 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 ASN ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 764 ASN G 775 ASN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 775 ASN ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 69840 Z= 0.272 Angle : 0.690 9.984 94584 Z= 0.356 Chirality : 0.049 0.189 10620 Planarity : 0.003 0.032 12396 Dihedral : 6.523 28.323 9516 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.96 % Favored : 82.04 % Rotamer Outliers : 0.68 % 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: -4.25 (0.08), residues: 8952 helix: -1.83 (0.30), residues: 240 sheet: -3.00 (0.13), residues: 1548 loop : -3.10 (0.07), residues: 7164 *********************** 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 216 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 166 time to evaluate : 6.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 21 residues processed: 210 average time/residue: 0.6033 time to fit residues: 230.8801 Evaluate side-chains 181 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 5.985 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4965 time to fit residues: 27.8830 ------------------------------------------------------------------------------- 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: 0.5980 chunk 831 optimal weight: 20.0000 chunk 758 optimal weight: 0.0040 chunk 808 optimal weight: 1.9990 chunk 830 optimal weight: 9.9990 chunk 486 optimal weight: 30.0000 chunk 352 optimal weight: 20.0000 chunk 634 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 730 optimal weight: 50.0000 chunk 764 optimal weight: 3.9990 overall best weight: 2.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 775 ASN ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.4167 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= 0.194 Angle : 0.644 12.050 94584 Z= 0.329 Chirality : 0.048 0.204 10620 Planarity : 0.003 0.032 12396 Dihedral : 6.110 29.390 9516 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.08), residues: 8952 helix: -1.66 (0.30), residues: 240 sheet: -2.56 (0.14), residues: 1356 loop : -3.07 (0.06), residues: 7356 *********************** 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 200 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 6.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 196 average time/residue: 0.6258 time to fit residues: 222.0139 Evaluate side-chains 169 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 6.028 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5213 time to fit residues: 18.9172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 20.0000 chunk 530 optimal weight: 50.0000 chunk 854 optimal weight: 0.9990 chunk 521 optimal weight: 9.9990 chunk 405 optimal weight: 7.9990 chunk 594 optimal weight: 0.0470 chunk 896 optimal weight: 0.9980 chunk 825 optimal weight: 10.0000 chunk 713 optimal weight: 0.0470 chunk 74 optimal weight: 50.0000 chunk 551 optimal weight: 6.9990 overall best weight: 1.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 775 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 453 ASN ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 775 ASN ** I 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 69840 Z= 0.156 Angle : 0.615 11.012 94584 Z= 0.311 Chirality : 0.047 0.171 10620 Planarity : 0.003 0.031 12396 Dihedral : 5.655 29.077 9516 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.08), residues: 8952 helix: -1.02 (0.33), residues: 240 sheet: -2.71 (0.14), residues: 1356 loop : -2.97 (0.06), residues: 7356 ********************** 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 215 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 205 time to evaluate : 6.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 214 average time/residue: 0.6383 time to fit residues: 247.3521 Evaluate side-chains 178 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 6.132 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4916 time to fit residues: 10.0360 ------------------------------------------------------------------------------- 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: 9.9990 chunk 567 optimal weight: 8.9990 chunk 760 optimal weight: 9.9990 chunk 218 optimal weight: 30.0000 chunk 658 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 715 optimal weight: 6.9990 chunk 299 optimal weight: 20.0000 chunk 734 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 overall best weight: 6.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 HIS C 84 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 775 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 618 ASN ** H 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 775 ASN I 84 ASN ** I 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 ASN ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.070852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.052672 restraints weight = 386821.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.053630 restraints weight = 240842.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.054318 restraints weight = 175932.954| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 69840 Z= 0.336 Angle : 0.735 10.830 94584 Z= 0.378 Chirality : 0.050 0.222 10620 Planarity : 0.004 0.042 12396 Dihedral : 6.502 28.242 9516 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 28.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 18.77 % Favored : 81.21 % Rotamer Outliers : 0.46 % 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: -4.18 (0.08), residues: 8952 helix: -1.00 (0.34), residues: 240 sheet: -2.87 (0.13), residues: 1524 loop : -3.11 (0.06), residues: 7188 =============================================================================== Job complete usr+sys time: 9512.30 seconds wall clock time: 173 minutes 46.15 seconds (10426.15 seconds total)