Starting phenix.real_space_refine on Fri Mar 15 11:55:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/03_2024/6nym_0546.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/03_2024/6nym_0546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/03_2024/6nym_0546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/03_2024/6nym_0546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/03_2024/6nym_0546.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nym_0546/03_2024/6nym_0546.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 42948 2.51 5 N 12060 2.21 5 O 13512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 27.29, per 1000 atoms: 0.40 Number of scatterers: 68664 At special positions: 0 Unit cell: (306.34, 276.66, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 13512 8.00 N 12060 7.00 C 42948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 749 " distance=2.02 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 749 " distance=2.02 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 749 " distance=2.02 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 749 " distance=2.02 Simple disulfide: pdb=" SG CYS H 738 " - pdb=" SG CYS H 749 " distance=2.02 Simple disulfide: pdb=" SG CYS I 738 " - pdb=" SG CYS I 749 " distance=2.02 Simple disulfide: pdb=" SG CYS J 738 " - pdb=" SG CYS J 749 " distance=2.02 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 749 " distance=2.02 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 749 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.87 Conformation dependent library (CDL) restraints added in 9.4 seconds 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16080 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 204 sheets defined 6.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.10 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU A 59 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 60 " --> pdb=" O PHE A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU A 720 " --> pdb=" O ASN A 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 720' Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET A 758 " --> pdb=" O ASN A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU B 59 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE B 60 " --> pdb=" O PHE B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU B 720 " --> pdb=" O ASN B 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 717 through 720' Processing helix chain 'B' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA B 748 " --> pdb=" O ASP B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET B 758 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 37 removed outlier: 3.805A pdb=" N ALA C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU C 59 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 60 " --> pdb=" O PHE C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU C 720 " --> pdb=" O ASN C 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 717 through 720' Processing helix chain 'C' and resid 721 through 726 removed outlier: 3.617A pdb=" N LEU C 726 " --> pdb=" O PHE C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA C 748 " --> pdb=" O ASP C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET C 758 " --> pdb=" O ASN C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 4.129A pdb=" N GLU D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE D 60 " --> pdb=" O PHE D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU D 720 " --> pdb=" O ASN D 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 717 through 720' Processing helix chain 'D' and resid 721 through 726 removed outlier: 3.617A pdb=" N LEU D 726 " --> pdb=" O PHE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA D 748 " --> pdb=" O ASP D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 759 removed outlier: 3.661A pdb=" N MET D 758 " --> pdb=" O ASN D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU E 59 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE E 60 " --> pdb=" O PHE E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 60' Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU E 720 " --> pdb=" O ASN E 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 717 through 720' Processing helix chain 'E' and resid 721 through 726 removed outlier: 3.619A pdb=" N LEU E 726 " --> pdb=" O PHE E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA E 748 " --> pdb=" O ASP E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET E 758 " --> pdb=" O ASN E 755 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR E 765 " --> pdb=" O PRO E 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 37 removed outlier: 3.805A pdb=" N ALA F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU F 59 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE F 60 " --> pdb=" O PHE F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 71 through 75 Processing helix chain 'F' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU F 720 " --> pdb=" O ASN F 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 717 through 720' Processing helix chain 'F' and resid 721 through 726 removed outlier: 3.619A pdb=" N LEU F 726 " --> pdb=" O PHE F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA F 748 " --> pdb=" O ASP F 744 " (cutoff:3.500A) Processing helix chain 'F' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET F 758 " --> pdb=" O ASN F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR F 765 " --> pdb=" O PRO F 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE G 60 " --> pdb=" O PHE G 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 60' Processing helix chain 'G' and resid 71 through 75 Processing helix chain 'G' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU G 720 " --> pdb=" O ASN G 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 717 through 720' Processing helix chain 'G' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU G 726 " --> pdb=" O PHE G 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA G 748 " --> pdb=" O ASP G 744 " (cutoff:3.500A) Processing helix chain 'G' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET G 758 " --> pdb=" O ASN G 755 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR G 765 " --> pdb=" O PRO G 762 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU H 59 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE H 60 " --> pdb=" O PHE H 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 71 through 75 Processing helix chain 'H' and resid 717 through 720 removed outlier: 3.842A pdb=" N GLU H 720 " --> pdb=" O ASN H 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 717 through 720' Processing helix chain 'H' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU H 726 " --> pdb=" O PHE H 722 " (cutoff:3.500A) Processing helix chain 'H' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA H 748 " --> pdb=" O ASP H 744 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 759 removed outlier: 3.661A pdb=" N MET H 758 " --> pdb=" O ASN H 755 " (cutoff:3.500A) Processing helix chain 'H' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR H 765 " --> pdb=" O PRO H 762 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 37 removed outlier: 3.805A pdb=" N ALA I 35 " --> pdb=" O GLY I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 4.129A pdb=" N GLU I 59 " --> pdb=" O GLY I 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE I 60 " --> pdb=" O PHE I 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 71 through 75 Processing helix chain 'I' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU I 720 " --> pdb=" O ASN I 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 717 through 720' Processing helix chain 'I' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU I 726 " --> pdb=" O PHE I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA I 748 " --> pdb=" O ASP I 744 " (cutoff:3.500A) Processing helix chain 'I' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET I 758 " --> pdb=" O ASN I 755 " (cutoff:3.500A) Processing helix chain 'I' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR I 765 " --> pdb=" O PRO I 762 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA J 35 " --> pdb=" O GLY J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU J 59 " --> pdb=" O GLY J 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE J 60 " --> pdb=" O PHE J 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU J 720 " --> pdb=" O ASN J 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 717 through 720' Processing helix chain 'J' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU J 726 " --> pdb=" O PHE J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA J 748 " --> pdb=" O ASP J 744 " (cutoff:3.500A) Processing helix chain 'J' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET J 758 " --> pdb=" O ASN J 755 " (cutoff:3.500A) Processing helix chain 'J' and resid 761 through 765 removed outlier: 3.898A pdb=" N TYR J 765 " --> pdb=" O PRO J 762 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA K 35 " --> pdb=" O GLY K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU K 59 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE K 60 " --> pdb=" O PHE K 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 71 through 75 Processing helix chain 'K' and resid 717 through 720 removed outlier: 3.840A pdb=" N GLU K 720 " --> pdb=" O ASN K 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 717 through 720' Processing helix chain 'K' and resid 721 through 726 removed outlier: 3.618A pdb=" N LEU K 726 " --> pdb=" O PHE K 722 " (cutoff:3.500A) Processing helix chain 'K' and resid 744 through 754 removed outlier: 4.215A pdb=" N ALA K 748 " --> pdb=" O ASP K 744 " (cutoff:3.500A) Processing helix chain 'K' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET K 758 " --> pdb=" O ASN K 755 " (cutoff:3.500A) Processing helix chain 'K' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR K 765 " --> pdb=" O PRO K 762 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 37 removed outlier: 3.806A pdb=" N ALA L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 4.130A pdb=" N GLU L 59 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE L 60 " --> pdb=" O PHE L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 60' Processing helix chain 'L' and resid 71 through 75 Processing helix chain 'L' and resid 717 through 720 removed outlier: 3.841A pdb=" N GLU L 720 " --> pdb=" O ASN L 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 717 through 720' Processing helix chain 'L' and resid 721 through 726 removed outlier: 3.619A pdb=" N LEU L 726 " --> pdb=" O PHE L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 744 through 754 removed outlier: 4.214A pdb=" N ALA L 748 " --> pdb=" O ASP L 744 " (cutoff:3.500A) Processing helix chain 'L' and resid 755 through 759 removed outlier: 3.662A pdb=" N MET L 758 " --> pdb=" O ASN L 755 " (cutoff:3.500A) Processing helix chain 'L' and resid 761 through 765 removed outlier: 3.897A pdb=" N TYR L 765 " --> pdb=" O PRO L 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 8.840A pdb=" N VAL A 48 " --> pdb=" O PRO F 341 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLN F 343 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ARG A 50 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE F 345 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN A 52 " --> pdb=" O ILE F 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL A 101 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 155 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 211 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY A 108 " --> pdb=" O THR A 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN A 140 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 168 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 203 " --> pdb=" O TRP A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY A 278 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL A 252 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY A 278 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LYS A 274 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE A 359 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N HIS A 276 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG A 361 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY A 278 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN A 363 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 280 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 357 " --> pdb=" O HIS A 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 413 " --> pdb=" O THR A 451 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE A 269 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 288 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU A 407 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU A 379 " --> pdb=" O GLU A 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 339 through 345 removed outlier: 6.539A pdb=" N VAL B 48 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG B 50 " --> pdb=" O PRO A 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA A 435 " --> pdb=" O ASN A 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 519 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG A 541 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 569 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 543 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 547 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE A 476 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 500 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 519 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG A 541 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE A 569 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 543 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 547 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 567 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 589 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL A 588 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY A 704 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET A 662 " --> pdb=" O GLY A 704 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR A 505 " --> pdb=" O HIS A 531 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 608 through 609 Processing sheet with id=AB6, first strand: chain 'A' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN A 643 " --> pdb=" O MET A 621 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 691 through 697 removed outlier: 3.649A pdb=" N THR A 691 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 791 " --> pdb=" O THR A 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE A 787 " --> pdb=" O LEU A 695 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AB9, first strand: chain 'A' and resid 771 through 773 Processing sheet with id=AC1, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL B 101 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL B 155 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU B 211 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY B 108 " --> pdb=" O THR B 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN B 140 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU B 168 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 203 " --> pdb=" O TRP B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.815A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY B 278 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 252 through 253 removed outlier: 6.815A pdb=" N VAL B 252 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY B 278 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS B 274 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE B 359 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS B 276 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG B 361 " --> pdb=" O HIS B 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY B 278 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B 363 " --> pdb=" O GLY B 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU B 280 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 357 " --> pdb=" O HIS B 385 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 413 " --> pdb=" O THR B 451 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE B 269 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 288 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU B 407 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU B 379 " --> pdb=" O GLU B 407 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 339 through 345 removed outlier: 6.207A pdb=" N VAL C 48 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG C 50 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA B 435 " --> pdb=" O ASN B 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 470 through 472 Processing sheet with id=AD1, first strand: chain 'B' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 519 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG B 541 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 569 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 543 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 547 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE B 476 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU B 500 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 519 " --> pdb=" O ARG B 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG B 541 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE B 569 " --> pdb=" O ARG B 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN B 543 " --> pdb=" O ILE B 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 547 " --> pdb=" O TYR B 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 567 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU B 589 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL B 588 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY B 704 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET B 662 " --> pdb=" O GLY B 704 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR B 505 " --> pdb=" O HIS B 531 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD5, first strand: chain 'B' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN B 643 " --> pdb=" O MET B 621 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 691 through 697 removed outlier: 3.649A pdb=" N THR B 691 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR B 791 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE B 787 " --> pdb=" O LEU B 695 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AD8, first strand: chain 'B' and resid 771 through 773 Processing sheet with id=AD9, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL C 101 " --> pdb=" O ASN C 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 155 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU C 211 " --> pdb=" O ASN C 244 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY C 108 " --> pdb=" O THR C 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN C 140 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 168 " --> pdb=" O SER C 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 203 " --> pdb=" O TRP C 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY C 278 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL C 252 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY C 278 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS C 274 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ILE C 359 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS C 276 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG C 361 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY C 278 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN C 363 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU C 280 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 357 " --> pdb=" O HIS C 385 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE C 413 " --> pdb=" O THR C 451 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 269 through 270 removed outlier: 6.782A pdb=" N ILE C 269 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 288 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU C 407 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU C 379 " --> pdb=" O GLU C 407 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 339 through 345 removed outlier: 6.214A pdb=" N VAL D 48 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG D 50 " --> pdb=" O PRO C 341 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA C 435 " --> pdb=" O ASN C 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 470 through 472 Processing sheet with id=AE9, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 519 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 541 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 569 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN C 543 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 547 " --> pdb=" O TYR C 573 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE C 476 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU C 500 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 519 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG C 541 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 569 " --> pdb=" O ARG C 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN C 543 " --> pdb=" O ILE C 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 547 " --> pdb=" O TYR C 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 567 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C 589 " --> pdb=" O LEU C 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL C 588 " --> pdb=" O THR C 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY C 704 " --> pdb=" O ALA C 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET C 662 " --> pdb=" O GLY C 704 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR C 505 " --> pdb=" O HIS C 531 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AF4, first strand: chain 'C' and resid 621 through 623 removed outlier: 3.501A pdb=" N ASN C 643 " --> pdb=" O MET C 621 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR C 691 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR C 791 " --> pdb=" O THR C 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE C 787 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 729 through 730 Processing sheet with id=AF7, first strand: chain 'C' and resid 771 through 773 Processing sheet with id=AF8, first strand: chain 'D' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL D 101 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 155 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU D 211 " --> pdb=" O ASN D 244 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY D 108 " --> pdb=" O THR D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'D' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN D 140 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU D 168 " --> pdb=" O SER D 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE D 203 " --> pdb=" O TRP D 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY D 278 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL D 252 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY D 278 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LYS D 274 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE D 359 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N HIS D 276 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG D 361 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY D 278 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN D 363 " --> pdb=" O GLY D 278 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU D 280 " --> pdb=" O ASN D 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 357 " --> pdb=" O HIS D 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 413 " --> pdb=" O THR D 451 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 269 through 270 removed outlier: 6.782A pdb=" N ILE D 269 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU D 288 " --> pdb=" O THR D 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 377 " --> pdb=" O LEU D 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU D 407 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU D 379 " --> pdb=" O GLU D 407 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 339 through 345 removed outlier: 6.175A pdb=" N VAL E 48 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG E 50 " --> pdb=" O PRO D 341 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA D 435 " --> pdb=" O ASN D 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'D' and resid 470 through 472 Processing sheet with id=AG8, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 519 " --> pdb=" O ARG D 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG D 541 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 569 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN D 543 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 547 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE D 476 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU D 500 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL D 519 " --> pdb=" O ARG D 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG D 541 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE D 569 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN D 543 " --> pdb=" O ILE D 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 547 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU D 567 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU D 589 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL D 588 " --> pdb=" O THR D 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY D 704 " --> pdb=" O ALA D 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET D 662 " --> pdb=" O GLY D 704 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.090A pdb=" N THR D 505 " --> pdb=" O HIS D 531 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 608 through 609 Processing sheet with id=AH3, first strand: chain 'D' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN D 643 " --> pdb=" O MET D 621 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR D 691 " --> pdb=" O TYR D 791 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N TYR D 791 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE D 787 " --> pdb=" O LEU D 695 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AH6, first strand: chain 'D' and resid 771 through 773 Processing sheet with id=AH7, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.354A pdb=" N VAL E 101 " --> pdb=" O ASN E 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL E 155 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU E 211 " --> pdb=" O ASN E 244 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY E 108 " --> pdb=" O THR E 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 140 through 142 removed outlier: 6.384A pdb=" N ASN E 140 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU E 168 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE E 203 " --> pdb=" O TRP E 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY E 278 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL E 252 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY E 278 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS E 274 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE E 359 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N HIS E 276 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG E 361 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY E 278 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN E 363 " --> pdb=" O GLY E 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU E 280 " --> pdb=" O ASN E 363 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 357 " --> pdb=" O HIS E 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE E 413 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE E 269 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU E 288 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA E 377 " --> pdb=" O LEU E 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU E 407 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU E 379 " --> pdb=" O GLU E 407 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 343 through 345 Processing sheet with id=AI5, first strand: chain 'E' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA E 435 " --> pdb=" O ASN E 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'E' and resid 470 through 472 Processing sheet with id=AI7, first strand: chain 'E' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL E 519 " --> pdb=" O ARG E 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG E 541 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 569 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN E 543 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 547 " --> pdb=" O TYR E 573 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE E 476 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU E 500 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL E 519 " --> pdb=" O ARG E 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG E 541 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 569 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN E 543 " --> pdb=" O ILE E 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 547 " --> pdb=" O TYR E 573 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU E 567 " --> pdb=" O ASN E 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 589 " --> pdb=" O LEU E 567 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL E 588 " --> pdb=" O THR E 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY E 704 " --> pdb=" O ALA E 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET E 662 " --> pdb=" O GLY E 704 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR E 505 " --> pdb=" O HIS E 531 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 608 through 609 Processing sheet with id=AJ2, first strand: chain 'E' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN E 643 " --> pdb=" O MET E 621 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR E 691 " --> pdb=" O TYR E 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR E 791 " --> pdb=" O THR E 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE E 787 " --> pdb=" O LEU E 695 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 729 through 730 Processing sheet with id=AJ5, first strand: chain 'E' and resid 771 through 773 Processing sheet with id=AJ6, first strand: chain 'F' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL F 101 " --> pdb=" O ASN F 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL F 155 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU F 211 " --> pdb=" O ASN F 244 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY F 108 " --> pdb=" O THR F 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'F' and resid 140 through 142 removed outlier: 6.382A pdb=" N ASN F 140 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU F 168 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 203 " --> pdb=" O TRP F 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ8 Processing sheet with id=AJ9, first strand: chain 'F' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY F 278 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL F 252 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY F 278 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LYS F 274 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE F 359 " --> pdb=" O LYS F 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS F 276 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG F 361 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY F 278 " --> pdb=" O ARG F 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN F 363 " --> pdb=" O GLY F 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU F 280 " --> pdb=" O ASN F 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 357 " --> pdb=" O HIS F 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE F 413 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'F' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE F 269 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU F 288 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA F 377 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU F 407 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU F 379 " --> pdb=" O GLU F 407 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 435 through 436 removed outlier: 7.017A pdb=" N ALA F 435 " --> pdb=" O ASN F 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK3 Processing sheet with id=AK4, first strand: chain 'F' and resid 470 through 472 Processing sheet with id=AK5, first strand: chain 'F' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 519 " --> pdb=" O ARG F 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG F 541 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE F 569 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN F 543 " --> pdb=" O ILE F 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 547 " --> pdb=" O TYR F 573 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'F' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE F 476 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU F 500 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 519 " --> pdb=" O ARG F 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG F 541 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE F 569 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN F 543 " --> pdb=" O ILE F 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 547 " --> pdb=" O TYR F 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 567 " --> pdb=" O ASN F 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU F 589 " --> pdb=" O LEU F 567 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL F 588 " --> pdb=" O THR F 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY F 704 " --> pdb=" O ALA F 660 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET F 662 " --> pdb=" O GLY F 704 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'F' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR F 505 " --> pdb=" O HIS F 531 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 608 through 609 Processing sheet with id=AK9, first strand: chain 'F' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN F 643 " --> pdb=" O MET F 621 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR F 691 " --> pdb=" O TYR F 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR F 791 " --> pdb=" O THR F 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE F 787 " --> pdb=" O LEU F 695 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'F' and resid 729 through 730 Processing sheet with id=AL3, first strand: chain 'F' and resid 771 through 773 Processing sheet with id=AL4, first strand: chain 'G' and resid 48 through 53 removed outlier: 8.861A pdb=" N VAL G 48 " --> pdb=" O PRO L 341 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLN L 343 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG G 50 " --> pdb=" O GLN L 343 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE L 345 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN G 52 " --> pdb=" O ILE L 345 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'G' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL G 101 " --> pdb=" O ASN G 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL G 155 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU G 211 " --> pdb=" O ASN G 244 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'G' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY G 108 " --> pdb=" O THR G 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL6 Processing sheet with id=AL7, first strand: chain 'G' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN G 140 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU G 168 " --> pdb=" O SER G 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE G 203 " --> pdb=" O TRP G 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 Processing sheet with id=AL8, first strand: chain 'G' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL G 252 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY G 278 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'G' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL G 252 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY G 278 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS G 274 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE G 359 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS G 276 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG G 361 " --> pdb=" O HIS G 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY G 278 " --> pdb=" O ARG G 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN G 363 " --> pdb=" O GLY G 278 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU G 280 " --> pdb=" O ASN G 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL G 357 " --> pdb=" O HIS G 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE G 413 " --> pdb=" O THR G 451 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'G' and resid 269 through 270 removed outlier: 6.782A pdb=" N ILE G 269 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU G 288 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA G 377 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU G 407 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU G 379 " --> pdb=" O GLU G 407 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'G' and resid 339 through 345 removed outlier: 6.267A pdb=" N VAL H 48 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG H 50 " --> pdb=" O PRO G 341 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'G' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA G 435 " --> pdb=" O ASN G 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM3 Processing sheet with id=AM4, first strand: chain 'G' and resid 470 through 472 Processing sheet with id=AM5, first strand: chain 'G' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU G 500 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 519 " --> pdb=" O ARG G 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG G 541 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE G 569 " --> pdb=" O ARG G 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN G 543 " --> pdb=" O ILE G 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU G 547 " --> pdb=" O TYR G 573 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'G' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE G 476 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU G 500 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 519 " --> pdb=" O ARG G 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG G 541 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE G 569 " --> pdb=" O ARG G 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN G 543 " --> pdb=" O ILE G 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU G 547 " --> pdb=" O TYR G 573 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU G 567 " --> pdb=" O ASN G 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 589 " --> pdb=" O LEU G 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL G 588 " --> pdb=" O THR G 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY G 704 " --> pdb=" O ALA G 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET G 662 " --> pdb=" O GLY G 704 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'G' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR G 505 " --> pdb=" O HIS G 531 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'G' and resid 608 through 609 Processing sheet with id=AM9, first strand: chain 'G' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN G 643 " --> pdb=" O MET G 621 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'G' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR G 691 " --> pdb=" O TYR G 791 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR G 791 " --> pdb=" O THR G 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE G 787 " --> pdb=" O LEU G 695 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'G' and resid 729 through 730 Processing sheet with id=AN3, first strand: chain 'G' and resid 771 through 773 Processing sheet with id=AN4, first strand: chain 'H' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL H 101 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL H 155 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU H 211 " --> pdb=" O ASN H 244 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'H' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY H 108 " --> pdb=" O THR H 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'H' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN H 140 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU H 168 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE H 203 " --> pdb=" O TRP H 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN6 Processing sheet with id=AN7, first strand: chain 'H' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL H 252 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY H 278 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'H' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL H 252 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY H 278 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LYS H 274 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE H 359 " --> pdb=" O LYS H 274 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N HIS H 276 " --> pdb=" O ILE H 359 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N ARG H 361 " --> pdb=" O HIS H 276 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY H 278 " --> pdb=" O ARG H 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN H 363 " --> pdb=" O GLY H 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU H 280 " --> pdb=" O ASN H 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL H 357 " --> pdb=" O HIS H 385 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE H 413 " --> pdb=" O THR H 451 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'H' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE H 269 " --> pdb=" O ILE H 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU H 288 " --> pdb=" O THR H 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA H 377 " --> pdb=" O LEU H 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU H 407 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU H 379 " --> pdb=" O GLU H 407 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'H' and resid 339 through 345 removed outlier: 6.417A pdb=" N VAL I 48 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG I 50 " --> pdb=" O PRO H 341 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'H' and resid 435 through 436 removed outlier: 7.017A pdb=" N ALA H 435 " --> pdb=" O ASN H 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'H' and resid 470 through 472 Processing sheet with id=AO4, first strand: chain 'H' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU H 500 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H 519 " --> pdb=" O ARG H 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG H 541 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 569 " --> pdb=" O ARG H 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN H 543 " --> pdb=" O ILE H 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU H 547 " --> pdb=" O TYR H 573 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'H' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE H 476 " --> pdb=" O ILE H 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU H 500 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL H 519 " --> pdb=" O ARG H 546 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG H 541 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE H 569 " --> pdb=" O ARG H 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN H 543 " --> pdb=" O ILE H 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU H 547 " --> pdb=" O TYR H 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU H 567 " --> pdb=" O ASN H 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU H 589 " --> pdb=" O LEU H 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL H 588 " --> pdb=" O THR H 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY H 704 " --> pdb=" O ALA H 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET H 662 " --> pdb=" O GLY H 704 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'H' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR H 505 " --> pdb=" O HIS H 531 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'H' and resid 608 through 609 Processing sheet with id=AO8, first strand: chain 'H' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN H 643 " --> pdb=" O MET H 621 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'H' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR H 691 " --> pdb=" O TYR H 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR H 791 " --> pdb=" O THR H 691 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE H 787 " --> pdb=" O LEU H 695 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'H' and resid 729 through 730 Processing sheet with id=AP2, first strand: chain 'H' and resid 771 through 773 Processing sheet with id=AP3, first strand: chain 'I' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL I 101 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL I 155 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU I 211 " --> pdb=" O ASN I 244 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'I' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY I 108 " --> pdb=" O THR I 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP4 Processing sheet with id=AP5, first strand: chain 'I' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN I 140 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU I 168 " --> pdb=" O SER I 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE I 203 " --> pdb=" O TRP I 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP5 Processing sheet with id=AP6, first strand: chain 'I' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL I 252 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY I 278 " --> pdb=" O VAL I 252 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'I' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL I 252 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY I 278 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS I 274 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE I 359 " --> pdb=" O LYS I 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS I 276 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG I 361 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY I 278 " --> pdb=" O ARG I 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN I 363 " --> pdb=" O GLY I 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU I 280 " --> pdb=" O ASN I 363 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL I 357 " --> pdb=" O HIS I 385 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE I 413 " --> pdb=" O THR I 451 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'I' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE I 269 " --> pdb=" O ILE I 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU I 288 " --> pdb=" O THR I 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA I 377 " --> pdb=" O LEU I 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU I 407 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU I 379 " --> pdb=" O GLU I 407 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'I' and resid 339 through 345 removed outlier: 6.225A pdb=" N VAL J 48 " --> pdb=" O VAL I 339 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG J 50 " --> pdb=" O PRO I 341 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'I' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA I 435 " --> pdb=" O ASN I 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ1 Processing sheet with id=AQ2, first strand: chain 'I' and resid 470 through 472 Processing sheet with id=AQ3, first strand: chain 'I' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU I 500 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL I 519 " --> pdb=" O ARG I 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG I 541 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE I 569 " --> pdb=" O ARG I 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN I 543 " --> pdb=" O ILE I 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU I 547 " --> pdb=" O TYR I 573 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'I' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE I 476 " --> pdb=" O ILE I 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU I 500 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL I 519 " --> pdb=" O ARG I 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG I 541 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE I 569 " --> pdb=" O ARG I 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN I 543 " --> pdb=" O ILE I 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU I 547 " --> pdb=" O TYR I 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU I 567 " --> pdb=" O ASN I 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU I 589 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL I 588 " --> pdb=" O THR I 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY I 704 " --> pdb=" O ALA I 660 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET I 662 " --> pdb=" O GLY I 704 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'I' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR I 505 " --> pdb=" O HIS I 531 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'I' and resid 608 through 609 Processing sheet with id=AQ7, first strand: chain 'I' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN I 643 " --> pdb=" O MET I 621 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'I' and resid 691 through 697 removed outlier: 3.647A pdb=" N THR I 691 " --> pdb=" O TYR I 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR I 791 " --> pdb=" O THR I 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE I 787 " --> pdb=" O LEU I 695 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'I' and resid 729 through 730 Processing sheet with id=AR1, first strand: chain 'I' and resid 771 through 773 Processing sheet with id=AR2, first strand: chain 'J' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL J 101 " --> pdb=" O ASN J 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL J 155 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU J 211 " --> pdb=" O ASN J 244 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'J' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY J 108 " --> pdb=" O THR J 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR3 Processing sheet with id=AR4, first strand: chain 'J' and resid 140 through 142 removed outlier: 6.384A pdb=" N ASN J 140 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU J 168 " --> pdb=" O SER J 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE J 203 " --> pdb=" O TRP J 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR4 Processing sheet with id=AR5, first strand: chain 'J' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL J 252 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY J 278 " --> pdb=" O VAL J 252 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'J' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL J 252 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY J 278 " --> pdb=" O VAL J 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS J 274 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ILE J 359 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N HIS J 276 " --> pdb=" O ILE J 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG J 361 " --> pdb=" O HIS J 276 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY J 278 " --> pdb=" O ARG J 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN J 363 " --> pdb=" O GLY J 278 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU J 280 " --> pdb=" O ASN J 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL J 357 " --> pdb=" O HIS J 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE J 413 " --> pdb=" O THR J 451 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'J' and resid 269 through 270 removed outlier: 6.782A pdb=" N ILE J 269 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU J 288 " --> pdb=" O THR J 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA J 377 " --> pdb=" O LEU J 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU J 407 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU J 379 " --> pdb=" O GLU J 407 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'J' and resid 339 through 345 removed outlier: 6.481A pdb=" N VAL K 48 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG K 50 " --> pdb=" O PRO J 341 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'J' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA J 435 " --> pdb=" O ASN J 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR9 Processing sheet with id=AS1, first strand: chain 'J' and resid 470 through 472 Processing sheet with id=AS2, first strand: chain 'J' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU J 500 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL J 519 " --> pdb=" O ARG J 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG J 541 " --> pdb=" O LEU J 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE J 569 " --> pdb=" O ARG J 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN J 543 " --> pdb=" O ILE J 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU J 547 " --> pdb=" O TYR J 573 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'J' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE J 476 " --> pdb=" O ILE J 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU J 500 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL J 519 " --> pdb=" O ARG J 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG J 541 " --> pdb=" O LEU J 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE J 569 " --> pdb=" O ARG J 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN J 543 " --> pdb=" O ILE J 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU J 547 " --> pdb=" O TYR J 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU J 567 " --> pdb=" O ASN J 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU J 589 " --> pdb=" O LEU J 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL J 588 " --> pdb=" O THR J 614 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLY J 704 " --> pdb=" O ALA J 660 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET J 662 " --> pdb=" O GLY J 704 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'J' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR J 505 " --> pdb=" O HIS J 531 " (cutoff:3.500A) Processing sheet with id=AS5, first strand: chain 'J' and resid 608 through 609 Processing sheet with id=AS6, first strand: chain 'J' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN J 643 " --> pdb=" O MET J 621 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'J' and resid 691 through 697 removed outlier: 3.647A pdb=" N THR J 691 " --> pdb=" O TYR J 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR J 791 " --> pdb=" O THR J 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE J 787 " --> pdb=" O LEU J 695 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'J' and resid 729 through 730 Processing sheet with id=AS9, first strand: chain 'J' and resid 771 through 773 Processing sheet with id=AT1, first strand: chain 'K' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL K 101 " --> pdb=" O ASN K 126 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL K 155 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU K 211 " --> pdb=" O ASN K 244 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.168A pdb=" N GLY K 108 " --> pdb=" O THR K 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT2 Processing sheet with id=AT3, first strand: chain 'K' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN K 140 " --> pdb=" O GLU K 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU K 168 " --> pdb=" O SER K 204 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE K 203 " --> pdb=" O TRP K 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT3 Processing sheet with id=AT4, first strand: chain 'K' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL K 252 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY K 278 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'K' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL K 252 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY K 278 " --> pdb=" O VAL K 252 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LYS K 274 " --> pdb=" O VAL K 357 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N ILE K 359 " --> pdb=" O LYS K 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS K 276 " --> pdb=" O ILE K 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG K 361 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY K 278 " --> pdb=" O ARG K 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN K 363 " --> pdb=" O GLY K 278 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU K 280 " --> pdb=" O ASN K 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL K 357 " --> pdb=" O HIS K 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE K 413 " --> pdb=" O THR K 451 " (cutoff:3.500A) Processing sheet with id=AT6, first strand: chain 'K' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE K 269 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU K 288 " --> pdb=" O THR K 380 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA K 377 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLU K 407 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU K 379 " --> pdb=" O GLU K 407 " (cutoff:3.500A) Processing sheet with id=AT7, first strand: chain 'K' and resid 339 through 345 removed outlier: 6.339A pdb=" N VAL L 48 " --> pdb=" O VAL K 339 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG L 50 " --> pdb=" O PRO K 341 " (cutoff:3.500A) Processing sheet with id=AT8, first strand: chain 'K' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA K 435 " --> pdb=" O ASN K 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AT8 Processing sheet with id=AT9, first strand: chain 'K' and resid 470 through 472 Processing sheet with id=AU1, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU K 500 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL K 519 " --> pdb=" O ARG K 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG K 541 " --> pdb=" O LEU K 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE K 569 " --> pdb=" O ARG K 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN K 543 " --> pdb=" O ILE K 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU K 547 " --> pdb=" O TYR K 573 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.682A pdb=" N ILE K 476 " --> pdb=" O ILE K 501 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU K 500 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL K 519 " --> pdb=" O ARG K 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG K 541 " --> pdb=" O LEU K 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE K 569 " --> pdb=" O ARG K 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN K 543 " --> pdb=" O ILE K 569 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU K 547 " --> pdb=" O TYR K 573 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU K 567 " --> pdb=" O ASN K 587 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU K 589 " --> pdb=" O LEU K 567 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL K 588 " --> pdb=" O THR K 614 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY K 704 " --> pdb=" O ALA K 660 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET K 662 " --> pdb=" O GLY K 704 " (cutoff:3.500A) Processing sheet with id=AU3, first strand: chain 'K' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR K 505 " --> pdb=" O HIS K 531 " (cutoff:3.500A) Processing sheet with id=AU4, first strand: chain 'K' and resid 608 through 609 Processing sheet with id=AU5, first strand: chain 'K' and resid 621 through 623 removed outlier: 3.503A pdb=" N ASN K 643 " --> pdb=" O MET K 621 " (cutoff:3.500A) Processing sheet with id=AU6, first strand: chain 'K' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR K 691 " --> pdb=" O TYR K 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR K 791 " --> pdb=" O THR K 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE K 787 " --> pdb=" O LEU K 695 " (cutoff:3.500A) Processing sheet with id=AU7, first strand: chain 'K' and resid 729 through 730 Processing sheet with id=AU8, first strand: chain 'K' and resid 771 through 773 Processing sheet with id=AU9, first strand: chain 'L' and resid 101 through 102 removed outlier: 6.353A pdb=" N VAL L 101 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL L 155 " --> pdb=" O THR L 188 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU L 211 " --> pdb=" O ASN L 244 " (cutoff:3.500A) Processing sheet with id=AV1, first strand: chain 'L' and resid 108 through 109 removed outlier: 6.167A pdb=" N GLY L 108 " --> pdb=" O THR L 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV1 Processing sheet with id=AV2, first strand: chain 'L' and resid 140 through 142 removed outlier: 6.383A pdb=" N ASN L 140 " --> pdb=" O GLU L 169 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU L 168 " --> pdb=" O SER L 204 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE L 203 " --> pdb=" O TRP L 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV2 Processing sheet with id=AV3, first strand: chain 'L' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL L 252 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY L 278 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AV4, first strand: chain 'L' and resid 252 through 253 removed outlier: 6.814A pdb=" N VAL L 252 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY L 278 " --> pdb=" O VAL L 252 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LYS L 274 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ILE L 359 " --> pdb=" O LYS L 274 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS L 276 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N ARG L 361 " --> pdb=" O HIS L 276 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLY L 278 " --> pdb=" O ARG L 361 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN L 363 " --> pdb=" O GLY L 278 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU L 280 " --> pdb=" O ASN L 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 357 " --> pdb=" O HIS L 385 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE L 413 " --> pdb=" O THR L 451 " (cutoff:3.500A) Processing sheet with id=AV5, first strand: chain 'L' and resid 269 through 270 removed outlier: 6.781A pdb=" N ILE L 269 " --> pdb=" O ILE L 291 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU L 288 " --> pdb=" O THR L 380 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA L 377 " --> pdb=" O LEU L 405 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU L 407 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU L 379 " --> pdb=" O GLU L 407 " (cutoff:3.500A) Processing sheet with id=AV6, first strand: chain 'L' and resid 435 through 436 removed outlier: 7.016A pdb=" N ALA L 435 " --> pdb=" O ASN L 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AV6 Processing sheet with id=AV7, first strand: chain 'L' and resid 470 through 472 Processing sheet with id=AV8, first strand: chain 'L' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU L 500 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL L 519 " --> pdb=" O ARG L 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG L 541 " --> pdb=" O LEU L 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE L 569 " --> pdb=" O ARG L 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN L 543 " --> pdb=" O ILE L 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU L 547 " --> pdb=" O TYR L 573 " (cutoff:3.500A) Processing sheet with id=AV9, first strand: chain 'L' and resid 476 through 477 removed outlier: 6.681A pdb=" N ILE L 476 " --> pdb=" O ILE L 501 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU L 500 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL L 519 " --> pdb=" O ARG L 546 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG L 541 " --> pdb=" O LEU L 567 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE L 569 " --> pdb=" O ARG L 541 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN L 543 " --> pdb=" O ILE L 569 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU L 547 " --> pdb=" O TYR L 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU L 567 " --> pdb=" O ASN L 587 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU L 589 " --> pdb=" O LEU L 567 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL L 588 " --> pdb=" O THR L 614 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N GLY L 704 " --> pdb=" O ALA L 660 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N MET L 662 " --> pdb=" O GLY L 704 " (cutoff:3.500A) Processing sheet with id=AW1, first strand: chain 'L' and resid 505 through 507 removed outlier: 6.091A pdb=" N THR L 505 " --> pdb=" O HIS L 531 " (cutoff:3.500A) Processing sheet with id=AW2, first strand: chain 'L' and resid 608 through 609 Processing sheet with id=AW3, first strand: chain 'L' and resid 621 through 623 removed outlier: 3.502A pdb=" N ASN L 643 " --> pdb=" O MET L 621 " (cutoff:3.500A) Processing sheet with id=AW4, first strand: chain 'L' and resid 691 through 697 removed outlier: 3.648A pdb=" N THR L 691 " --> pdb=" O TYR L 791 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR L 791 " --> pdb=" O THR L 691 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE L 787 " --> pdb=" O LEU L 695 " (cutoff:3.500A) Processing sheet with id=AW5, first strand: chain 'L' and resid 729 through 730 Processing sheet with id=AW6, first strand: chain 'L' and resid 771 through 773 809 hydrogen bonds defined for protein. 2103 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 34.16 Time building geometry restraints manager: 22.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22641 1.34 - 1.45: 10887 1.45 - 1.57: 36048 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 69840 Sorted by residual: bond pdb=" N LYS F 129 " pdb=" CA LYS F 129 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.88e+00 bond pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.85e+00 bond pdb=" N LYS D 129 " pdb=" CA LYS D 129 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.81e+00 bond pdb=" N LYS E 129 " pdb=" CA LYS E 129 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.75e+00 bond pdb=" N LYS K 129 " pdb=" CA LYS K 129 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.75e+00 ... (remaining 69835 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.55: 804 105.55 - 112.68: 35766 112.68 - 119.80: 22965 119.80 - 126.92: 34322 126.92 - 134.04: 727 Bond angle restraints: 94584 Sorted by residual: angle pdb=" C GLY E 83 " pdb=" N ASN E 84 " pdb=" CA ASN E 84 " ideal model delta sigma weight residual 122.46 130.70 -8.24 1.41e+00 5.03e-01 3.41e+01 angle pdb=" C GLY D 83 " pdb=" N ASN D 84 " pdb=" CA ASN D 84 " ideal model delta sigma weight residual 122.46 130.69 -8.23 1.41e+00 5.03e-01 3.41e+01 angle pdb=" C GLY A 83 " pdb=" N ASN A 84 " pdb=" CA ASN A 84 " ideal model delta sigma weight residual 122.46 130.68 -8.22 1.41e+00 5.03e-01 3.40e+01 angle pdb=" C GLY L 83 " pdb=" N ASN L 84 " pdb=" CA ASN L 84 " ideal model delta sigma weight residual 122.46 130.67 -8.21 1.41e+00 5.03e-01 3.39e+01 angle pdb=" C GLY H 83 " pdb=" N ASN H 84 " pdb=" CA ASN H 84 " ideal model delta sigma weight residual 122.46 130.67 -8.21 1.41e+00 5.03e-01 3.39e+01 ... (remaining 94579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 38618 15.99 - 31.99: 2131 31.99 - 47.98: 363 47.98 - 63.97: 24 63.97 - 79.96: 36 Dihedral angle restraints: 41172 sinusoidal: 15828 harmonic: 25344 Sorted by residual: dihedral pdb=" CB CYS G 738 " pdb=" SG CYS G 738 " pdb=" SG CYS G 749 " pdb=" CB CYS G 749 " ideal model delta sinusoidal sigma weight residual 93.00 172.96 -79.96 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS I 738 " pdb=" SG CYS I 738 " pdb=" SG CYS I 749 " pdb=" CB CYS I 749 " ideal model delta sinusoidal sigma weight residual 93.00 172.94 -79.94 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS J 738 " pdb=" SG CYS J 738 " pdb=" SG CYS J 749 " pdb=" CB CYS J 749 " ideal model delta sinusoidal sigma weight residual 93.00 172.94 -79.94 1 1.00e+01 1.00e-02 7.92e+01 ... (remaining 41169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 6261 0.043 - 0.086: 2845 0.086 - 0.129: 1192 0.129 - 0.172: 274 0.172 - 0.215: 48 Chirality restraints: 10620 Sorted by residual: chirality pdb=" CA ASN C 273 " pdb=" N ASN C 273 " pdb=" C ASN C 273 " pdb=" CB ASN C 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN L 273 " pdb=" N ASN L 273 " pdb=" C ASN L 273 " pdb=" CB ASN L 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN K 273 " pdb=" N ASN K 273 " pdb=" C ASN K 273 " pdb=" CB ASN K 273 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 10617 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 574 " 0.018 2.00e-02 2.50e+03 1.46e-02 4.24e+00 pdb=" CG TYR I 574 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR I 574 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR I 574 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR I 574 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I 574 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR I 574 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 574 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 574 " -0.018 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR A 574 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 574 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 574 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 574 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 574 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 574 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 574 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 574 " 0.018 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR G 574 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR G 574 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR G 574 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 574 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR G 574 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR G 574 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 574 " 0.006 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 16111 2.79 - 3.32: 63105 3.32 - 3.84: 117525 3.84 - 4.37: 134784 4.37 - 4.90: 234226 Nonbonded interactions: 565751 Sorted by model distance: nonbonded pdb=" OG1 THR L 153 " pdb=" OG1 THR L 185 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR G 153 " pdb=" OG1 THR G 185 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR C 153 " pdb=" OG1 THR C 185 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR I 153 " pdb=" OG1 THR I 185 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR H 153 " pdb=" OG1 THR H 185 " model vdw 2.261 2.440 ... (remaining 565746 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 13.700 Check model and map are aligned: 0.770 Set scattering table: 0.480 Process input model: 147.660 Find NCS groups from input model: 3.460 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 69840 Z= 0.333 Angle : 0.935 11.187 94584 Z= 0.534 Chirality : 0.057 0.215 10620 Planarity : 0.005 0.049 12396 Dihedral : 10.432 70.751 25056 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 0.32 % Allowed : 2.92 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.07), residues: 8952 helix: -4.39 (0.13), residues: 288 sheet: -3.69 (0.09), residues: 2076 loop : -3.50 (0.06), residues: 6588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 225 HIS 0.005 0.001 HIS K 385 PHE 0.018 0.002 PHE L 167 TYR 0.035 0.003 TYR I 574 ARG 0.005 0.001 ARG D 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17904 Ramachandran restraints generated. 8952 Oldfield, 0 Emsley, 8952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 383 time to evaluate : 5.937 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: A 48 VAL cc_start: 0.8102 (t) cc_final: 0.7873 (p) REVERT: A 226 MET cc_start: 0.8365 (mtm) cc_final: 0.8072 (mtp) REVERT: A 662 MET cc_start: 0.7543 (mtm) cc_final: 0.6700 (mtt) REVERT: A 758 MET cc_start: 0.7029 (mpt) cc_final: 0.5240 (ttm) REVERT: B 226 MET cc_start: 0.8117 (mtm) cc_final: 0.7844 (mtp) REVERT: B 629 LEU cc_start: 0.8666 (tt) cc_final: 0.8182 (tt) REVERT: B 662 MET cc_start: 0.7762 (mtm) cc_final: 0.7007 (mtt) REVERT: B 735 MET cc_start: 0.8442 (mtp) cc_final: 0.7766 (ttm) REVERT: B 758 MET cc_start: 0.7071 (mpt) cc_final: 0.5372 (ttm) REVERT: C 718 LEU cc_start: 0.8686 (mm) cc_final: 0.8336 (mm) REVERT: C 758 MET cc_start: 0.7225 (mpt) cc_final: 0.6865 (mpt) REVERT: D 226 MET cc_start: 0.8369 (mtm) cc_final: 0.8062 (mtp) REVERT: D 629 LEU cc_start: 0.8385 (tt) cc_final: 0.8109 (tt) REVERT: D 662 MET cc_start: 0.7542 (mtm) cc_final: 0.6666 (mtm) REVERT: D 758 MET cc_start: 0.7118 (mpt) cc_final: 0.5515 (ttm) REVERT: E 226 MET cc_start: 0.8270 (mtm) cc_final: 0.7901 (mtp) REVERT: E 662 MET cc_start: 0.7867 (mtm) cc_final: 0.7164 (mtt) REVERT: E 758 MET cc_start: 0.6479 (mpt) cc_final: 0.4569 (ttm) REVERT: F 243 ILE cc_start: 0.9155 (mt) cc_final: 0.8863 (mt) REVERT: F 758 MET cc_start: 0.6961 (mpt) cc_final: 0.6502 (mpt) REVERT: G 662 MET cc_start: 0.7611 (mtm) cc_final: 0.6749 (ttm) REVERT: G 758 MET cc_start: 0.7028 (mpt) cc_final: 0.5279 (ttm) REVERT: H 48 VAL cc_start: 0.8177 (t) cc_final: 0.7955 (p) REVERT: H 662 MET cc_start: 0.7702 (mtm) cc_final: 0.6914 (mpp) REVERT: H 758 MET cc_start: 0.6754 (mpt) cc_final: 0.4826 (ttm) REVERT: I 243 ILE cc_start: 0.9206 (mt) cc_final: 0.8962 (mt) REVERT: I 662 MET cc_start: 0.7112 (mtm) cc_final: 0.6486 (mpp) REVERT: I 718 LEU cc_start: 0.8703 (mm) cc_final: 0.8404 (mm) REVERT: I 751 MET cc_start: 0.9333 (mmt) cc_final: 0.9096 (tmm) REVERT: I 758 MET cc_start: 0.6917 (mpt) cc_final: 0.6430 (mpt) REVERT: J 226 MET cc_start: 0.8303 (mtm) cc_final: 0.8010 (mtp) REVERT: J 662 MET cc_start: 0.6957 (mtm) cc_final: 0.6371 (mpp) REVERT: J 718 LEU cc_start: 0.8681 (mm) cc_final: 0.8346 (mm) REVERT: J 735 MET cc_start: 0.8161 (mtp) cc_final: 0.7905 (mtt) REVERT: J 758 MET cc_start: 0.7137 (mpt) cc_final: 0.6818 (mpt) REVERT: K 226 MET cc_start: 0.8101 (mtm) cc_final: 0.7869 (mtp) REVERT: K 629 LEU cc_start: 0.8579 (tt) cc_final: 0.8107 (tt) REVERT: K 662 MET cc_start: 0.7764 (mtm) cc_final: 0.6904 (mtt) REVERT: K 735 MET cc_start: 0.8309 (mtp) cc_final: 0.7676 (ttm) REVERT: K 758 MET cc_start: 0.7074 (mpt) cc_final: 0.5421 (ttm) REVERT: L 243 ILE cc_start: 0.9099 (mt) cc_final: 0.8815 (mt) REVERT: L 758 MET cc_start: 0.7222 (mpt) cc_final: 0.6960 (mpt) outliers start: 24 outliers final: 8 residues processed: 403 average time/residue: 0.6179 time to fit residues: 442.4212 Evaluate side-chains 195 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 5.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain K residue 613 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 6.9990 chunk 682 optimal weight: 3.9990 chunk 378 optimal weight: 9.9990 chunk 233 optimal weight: 0.1980 chunk 460 optimal weight: 4.9990 chunk 364 optimal weight: 40.0000 chunk 705 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 428 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 817 optimal weight: 7.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 543 ASN A 685 GLN A 730 ASN A 755 ASN B 289 ASN B 543 ASN B 618 ASN B 685 GLN B 730 ASN B 755 ASN C 289 ASN C 469 HIS C 543 ASN C 685 GLN C 730 ASN C 755 ASN D 289 ASN D 543 ASN D 685 GLN D 730 ASN D 755 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 543 ASN E 618 ASN E 685 GLN E 730 ASN E 755 ASN F 289 ASN F 543 ASN F 685 GLN F 730 ASN F 755 ASN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 289 ASN G 543 ASN G 685 GLN G 730 ASN G 755 ASN H 289 ASN H 543 ASN H 665 ASN H 685 GLN H 730 ASN H 755 ASN I 289 ASN I 340 GLN I 469 HIS I 543 ASN I 685 GLN ** I 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 730 ASN I 755 ASN J 289 ASN J 469 HIS J 543 ASN J 685 GLN J 730 ASN J 755 ASN K 289 ASN K 543 ASN K 618 ASN K 685 GLN K 730 ASN K 755 ASN L 289 ASN L 543 ASN L 685 GLN L 730 ASN L 755 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 69840 Z= 0.368 Angle : 0.690 8.411 94584 Z= 0.371 Chirality : 0.049 0.156 10620 Planarity : 0.004 0.043 12396 Dihedral : 6.546 54.941 9532 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.74 % Favored : 84.26 % Rotamer: Outliers : 1.61 % Allowed : 6.21 % Favored : 92.18 % 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: -4.86 (0.07), residues: 8952 helix: -3.24 (0.17), residues: 384 sheet: -3.48 (0.10), residues: 1932 loop : -3.41 (0.06), residues: 6636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 30 HIS 0.008 0.002 HIS I 385 PHE 0.018 0.002 PHE G 57 TYR 0.017 0.002 TYR L 574 ARG 0.004 0.001 ARG H 228 *********************** 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 357 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 238 time to evaluate : 5.896 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: A 634 ASP cc_start: 0.8390 (p0) cc_final: 0.8048 (p0) REVERT: A 662 MET cc_start: 0.7510 (mtm) cc_final: 0.7047 (mpp) REVERT: A 663 MET cc_start: 0.8335 (mmm) cc_final: 0.7850 (mmm) REVERT: A 758 MET cc_start: 0.7031 (mpt) cc_final: 0.6459 (mpt) REVERT: B 580 PHE cc_start: 0.8459 (t80) cc_final: 0.8143 (t80) REVERT: B 662 MET cc_start: 0.7599 (mtm) cc_final: 0.6854 (mpp) REVERT: B 735 MET cc_start: 0.8326 (mtp) cc_final: 0.7549 (ttm) REVERT: B 758 MET cc_start: 0.7044 (mpt) cc_final: 0.5315 (ttm) REVERT: C 124 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7091 (p0) REVERT: C 662 MET cc_start: 0.7792 (mtt) cc_final: 0.7028 (mpp) REVERT: C 663 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7378 (tmm) REVERT: C 758 MET cc_start: 0.7199 (mpt) cc_final: 0.6726 (mpt) REVERT: D 539 GLN cc_start: 0.7863 (mm110) cc_final: 0.7449 (mm110) REVERT: D 662 MET cc_start: 0.7419 (mtm) cc_final: 0.6951 (mpp) REVERT: D 663 MET cc_start: 0.8268 (mmm) cc_final: 0.7812 (mmm) REVERT: D 758 MET cc_start: 0.7074 (mpt) cc_final: 0.6522 (mpt) REVERT: E 662 MET cc_start: 0.7786 (mtm) cc_final: 0.6957 (mpp) REVERT: E 758 MET cc_start: 0.6689 (mpt) cc_final: 0.4647 (ttm) REVERT: F 662 MET cc_start: 0.8287 (mtt) cc_final: 0.7108 (mpp) REVERT: F 758 MET cc_start: 0.7344 (mpt) cc_final: 0.6836 (mpt) REVERT: G 109 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8727 (p) REVERT: G 609 MET cc_start: 0.8230 (mtp) cc_final: 0.7734 (ttt) REVERT: G 662 MET cc_start: 0.7547 (mtm) cc_final: 0.6999 (mpp) REVERT: G 663 MET cc_start: 0.8096 (mmm) cc_final: 0.7522 (mmm) REVERT: G 758 MET cc_start: 0.7019 (mpt) cc_final: 0.5074 (ttm) REVERT: H 109 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8713 (p) REVERT: H 124 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7148 (p0) REVERT: H 580 PHE cc_start: 0.8478 (t80) cc_final: 0.8192 (t80) REVERT: H 662 MET cc_start: 0.8091 (mtm) cc_final: 0.7306 (mpp) REVERT: H 663 MET cc_start: 0.8550 (mtp) cc_final: 0.7594 (tmm) REVERT: I 124 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7222 (p0) REVERT: I 662 MET cc_start: 0.7509 (mtm) cc_final: 0.6788 (mpp) REVERT: I 663 MET cc_start: 0.8403 (mtp) cc_final: 0.7543 (tmm) REVERT: I 718 LEU cc_start: 0.8586 (mm) cc_final: 0.8250 (mm) REVERT: J 662 MET cc_start: 0.7706 (mtm) cc_final: 0.7030 (mpp) REVERT: J 758 MET cc_start: 0.7209 (mpt) cc_final: 0.6801 (mpt) REVERT: K 735 MET cc_start: 0.8347 (mtp) cc_final: 0.7651 (ttm) REVERT: K 758 MET cc_start: 0.7168 (mpt) cc_final: 0.5490 (ttm) REVERT: L 109 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8638 (p) REVERT: L 124 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7151 (p0) REVERT: L 539 GLN cc_start: 0.8145 (mm110) cc_final: 0.7831 (mm110) REVERT: L 662 MET cc_start: 0.8178 (mtt) cc_final: 0.7235 (mpp) REVERT: L 758 MET cc_start: 0.7085 (mpt) cc_final: 0.6688 (mpt) outliers start: 119 outliers final: 74 residues processed: 322 average time/residue: 0.5514 time to fit residues: 330.2272 Evaluate side-chains 272 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 190 time to evaluate : 5.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 124 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain C residue 663 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 591 THR Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 654 LEU Chi-restraints excluded: chain L residue 776 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 680 optimal weight: 2.9990 chunk 556 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 818 optimal weight: 10.0000 chunk 884 optimal weight: 7.9990 chunk 729 optimal weight: 9.9990 chunk 811 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 656 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 256 HIS A 340 GLN A 385 HIS B 62 ASN B 256 HIS B 340 GLN B 385 HIS ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 256 HIS C 340 GLN C 385 HIS D 62 ASN D 256 HIS D 340 GLN D 385 HIS E 62 ASN E 256 HIS E 340 GLN E 385 HIS ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN F 256 HIS F 340 GLN F 385 HIS G 62 ASN G 256 HIS G 340 GLN G 385 HIS H 62 ASN H 256 HIS H 340 GLN H 385 HIS I 62 ASN I 256 HIS I 385 HIS J 62 ASN ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 256 HIS J 340 GLN J 385 HIS K 62 ASN K 256 HIS K 340 GLN K 385 HIS ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN L 256 HIS L 340 GLN L 385 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 69840 Z= 0.441 Angle : 0.746 8.080 94584 Z= 0.402 Chirality : 0.051 0.158 10620 Planarity : 0.004 0.037 12396 Dihedral : 6.675 59.623 9532 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.31 % Favored : 80.69 % Rotamer: Outliers : 2.96 % Allowed : 8.21 % Favored : 88.83 % 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: -4.78 (0.07), residues: 8952 helix: -2.31 (0.22), residues: 384 sheet: -3.64 (0.09), residues: 1872 loop : -3.35 (0.06), residues: 6696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 82 HIS 0.008 0.002 HIS H 385 PHE 0.023 0.003 PHE G 57 TYR 0.015 0.002 TYR G 574 ARG 0.006 0.001 ARG E 154 *********************** 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 437 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 218 time to evaluate : 6.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 MET cc_start: 0.8040 (mtp) cc_final: 0.7762 (ttm) REVERT: A 634 ASP cc_start: 0.8476 (p0) cc_final: 0.7995 (p0) REVERT: A 662 MET cc_start: 0.7641 (mtm) cc_final: 0.7023 (mpp) REVERT: A 663 MET cc_start: 0.8174 (mmm) cc_final: 0.7597 (mmm) REVERT: A 718 LEU cc_start: 0.8681 (mm) cc_final: 0.8276 (mm) REVERT: B 662 MET cc_start: 0.7818 (mtm) cc_final: 0.6985 (mpp) REVERT: B 758 MET cc_start: 0.7169 (mpt) cc_final: 0.6702 (mpt) REVERT: C 452 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: C 662 MET cc_start: 0.7844 (mtt) cc_final: 0.7124 (mpp) REVERT: C 758 MET cc_start: 0.7348 (mpt) cc_final: 0.6778 (mpt) REVERT: D 109 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8826 (p) REVERT: D 662 MET cc_start: 0.7688 (mtm) cc_final: 0.7118 (mpp) REVERT: D 663 MET cc_start: 0.8163 (mmm) cc_final: 0.7605 (mmm) REVERT: D 735 MET cc_start: 0.7875 (mtp) cc_final: 0.7437 (ptp) REVERT: E 634 ASP cc_start: 0.8311 (p0) cc_final: 0.8013 (p0) REVERT: E 662 MET cc_start: 0.7860 (mtm) cc_final: 0.7060 (mpp) REVERT: E 758 MET cc_start: 0.7006 (mpt) cc_final: 0.5030 (ttm) REVERT: F 430 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7735 (pp) REVERT: F 452 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: F 662 MET cc_start: 0.8104 (mtt) cc_final: 0.7254 (mpp) REVERT: G 539 GLN cc_start: 0.7938 (mm110) cc_final: 0.7526 (mm110) REVERT: G 621 MET cc_start: 0.7989 (mtp) cc_final: 0.7711 (ttm) REVERT: G 662 MET cc_start: 0.7723 (mtm) cc_final: 0.7096 (mpp) REVERT: G 663 MET cc_start: 0.8101 (mmm) cc_final: 0.7534 (mmm) REVERT: G 718 LEU cc_start: 0.8607 (mm) cc_final: 0.8189 (mm) REVERT: H 109 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8910 (p) REVERT: H 124 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7333 (p0) REVERT: H 662 MET cc_start: 0.8061 (mtm) cc_final: 0.7238 (mpp) REVERT: H 663 MET cc_start: 0.8502 (mtp) cc_final: 0.8260 (tpp) REVERT: I 124 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7384 (p0) REVERT: I 452 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: I 662 MET cc_start: 0.7596 (mtm) cc_final: 0.6794 (mpp) REVERT: I 718 LEU cc_start: 0.8785 (mm) cc_final: 0.8422 (mm) REVERT: J 109 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8802 (p) REVERT: J 594 PHE cc_start: 0.8364 (t80) cc_final: 0.8067 (t80) REVERT: J 662 MET cc_start: 0.7887 (mtm) cc_final: 0.7242 (mpp) REVERT: J 735 MET cc_start: 0.7555 (mtp) cc_final: 0.7321 (mtt) REVERT: K 662 MET cc_start: 0.7586 (mtt) cc_final: 0.7346 (mtt) REVERT: K 735 MET cc_start: 0.8289 (mtp) cc_final: 0.7578 (ttm) REVERT: K 758 MET cc_start: 0.7261 (mpt) cc_final: 0.5660 (ttm) REVERT: L 124 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7218 (p0) REVERT: L 430 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7802 (pp) REVERT: L 452 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: L 662 MET cc_start: 0.8204 (mtt) cc_final: 0.7396 (mpp) REVERT: L 718 LEU cc_start: 0.8647 (mm) cc_final: 0.8279 (mm) REVERT: L 758 MET cc_start: 0.7233 (mpt) cc_final: 0.6722 (mpt) outliers start: 219 outliers final: 141 residues processed: 383 average time/residue: 0.5541 time to fit residues: 392.0625 Evaluate side-chains 342 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 189 time to evaluate : 6.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 621 MET Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 654 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 591 THR Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 613 LEU Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 452 PHE Chi-restraints excluded: chain F residue 621 MET Chi-restraints excluded: chain F residue 654 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 404 LEU Chi-restraints excluded: chain G residue 452 PHE Chi-restraints excluded: chain G residue 613 LEU Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain G residue 654 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 452 PHE Chi-restraints excluded: chain H residue 621 MET Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 654 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 452 PHE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 621 MET Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 452 PHE Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 591 THR Chi-restraints excluded: chain J residue 613 LEU Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 654 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 100 GLU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 404 LEU Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 613 LEU Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 718 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 452 PHE Chi-restraints excluded: chain L residue 654 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 9.9990 chunk 615 optimal weight: 0.0970 chunk 424 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 390 optimal weight: 20.0000 chunk 549 optimal weight: 0.0010 chunk 821 optimal weight: 0.1980 chunk 869 optimal weight: 10.0000 chunk 429 optimal weight: 9.9990 chunk 778 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 618 ASN ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 618 ASN ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 618 ASN H 618 ASN I 618 ASN ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 69840 Z= 0.212 Angle : 0.587 8.107 94584 Z= 0.309 Chirality : 0.046 0.148 10620 Planarity : 0.003 0.030 12396 Dihedral : 5.807 58.678 9532 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % Rotamer: Outliers : 2.22 % Allowed : 9.86 % Favored : 87.93 % 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: -4.36 (0.08), residues: 8952 helix: -2.02 (0.24), residues: 384 sheet: -3.20 (0.11), residues: 1692 loop : -3.13 (0.07), residues: 6876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 577 HIS 0.003 0.001 HIS B 531 PHE 0.019 0.001 PHE B 580 TYR 0.021 0.001 TYR I 574 ARG 0.003 0.000 ARG J 133 *********************** 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 409 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 245 time to evaluate : 6.021 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: A 539 GLN cc_start: 0.7780 (mm110) cc_final: 0.7414 (mm110) REVERT: A 634 ASP cc_start: 0.8479 (p0) cc_final: 0.8007 (p0) REVERT: A 662 MET cc_start: 0.7706 (mtm) cc_final: 0.7184 (mpp) REVERT: A 663 MET cc_start: 0.8212 (mmm) cc_final: 0.7609 (mmm) REVERT: A 718 LEU cc_start: 0.8668 (mm) cc_final: 0.8287 (mm) REVERT: B 226 MET cc_start: 0.7993 (mtp) cc_final: 0.7254 (mtp) REVERT: B 662 MET cc_start: 0.7845 (mtm) cc_final: 0.7019 (mpp) REVERT: C 662 MET cc_start: 0.7912 (mtt) cc_final: 0.7089 (mpp) REVERT: C 663 MET cc_start: 0.8311 (mtp) cc_final: 0.7780 (mmm) REVERT: C 758 MET cc_start: 0.7158 (mpt) cc_final: 0.6639 (mpt) REVERT: D 539 GLN cc_start: 0.7794 (mm110) cc_final: 0.7423 (mm110) REVERT: D 662 MET cc_start: 0.7745 (mtm) cc_final: 0.7087 (mpp) REVERT: D 663 MET cc_start: 0.8238 (mmm) cc_final: 0.7934 (mpp) REVERT: D 735 MET cc_start: 0.7926 (mtp) cc_final: 0.7709 (mtt) REVERT: E 125 VAL cc_start: 0.8651 (t) cc_final: 0.8438 (t) REVERT: E 634 ASP cc_start: 0.8261 (p0) cc_final: 0.7898 (p0) REVERT: E 662 MET cc_start: 0.7856 (mtm) cc_final: 0.7116 (mpp) REVERT: E 758 MET cc_start: 0.6951 (mpt) cc_final: 0.4918 (ttm) REVERT: F 662 MET cc_start: 0.7917 (mtt) cc_final: 0.7353 (mpp) REVERT: F 663 MET cc_start: 0.7573 (mmm) cc_final: 0.7185 (mmm) REVERT: F 718 LEU cc_start: 0.8764 (mm) cc_final: 0.8381 (mm) REVERT: G 539 GLN cc_start: 0.7761 (mm110) cc_final: 0.7384 (mm110) REVERT: G 634 ASP cc_start: 0.8572 (p0) cc_final: 0.8141 (p0) REVERT: G 662 MET cc_start: 0.7747 (mtm) cc_final: 0.7104 (mpp) REVERT: G 663 MET cc_start: 0.8132 (mmm) cc_final: 0.7588 (mmm) REVERT: G 718 LEU cc_start: 0.8535 (mm) cc_final: 0.8144 (mm) REVERT: H 125 VAL cc_start: 0.8631 (t) cc_final: 0.8399 (t) REVERT: H 662 MET cc_start: 0.8092 (mtm) cc_final: 0.7352 (mpp) REVERT: H 663 MET cc_start: 0.8472 (mtp) cc_final: 0.8222 (tpp) REVERT: I 662 MET cc_start: 0.7716 (mtm) cc_final: 0.6926 (mpp) REVERT: I 663 MET cc_start: 0.8238 (mtp) cc_final: 0.7753 (mmm) REVERT: I 718 LEU cc_start: 0.8718 (mm) cc_final: 0.8331 (mm) REVERT: I 758 MET cc_start: 0.7044 (mpt) cc_final: 0.6547 (mpt) REVERT: J 655 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.8154 (p0) REVERT: J 662 MET cc_start: 0.7812 (mtm) cc_final: 0.7233 (mpp) REVERT: J 735 MET cc_start: 0.7485 (mtp) cc_final: 0.7285 (mtt) REVERT: J 758 MET cc_start: 0.7175 (mpt) cc_final: 0.6725 (mpt) REVERT: K 226 MET cc_start: 0.8011 (mtp) cc_final: 0.7269 (mtp) REVERT: K 662 MET cc_start: 0.7565 (mtt) cc_final: 0.7316 (mtt) REVERT: K 735 MET cc_start: 0.8176 (mtp) cc_final: 0.7333 (ttm) REVERT: K 758 MET cc_start: 0.7157 (mpt) cc_final: 0.6541 (mpt) REVERT: L 662 MET cc_start: 0.7939 (mtt) cc_final: 0.7563 (mpp) REVERT: L 718 LEU cc_start: 0.8659 (mm) cc_final: 0.8299 (mm) REVERT: L 758 MET cc_start: 0.7025 (mpt) cc_final: 0.6550 (mpt) outliers start: 164 outliers final: 116 residues processed: 364 average time/residue: 0.5552 time to fit residues: 376.1965 Evaluate side-chains 316 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 199 time to evaluate : 6.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 654 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 655 ASN Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 216 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 216 ASN Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 354 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 654 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 10.0000 chunk 493 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 647 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 chunk 742 optimal weight: 40.0000 chunk 601 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 444 optimal weight: 40.0000 chunk 780 optimal weight: 6.9990 chunk 219 optimal weight: 50.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 ASN B 803 ASN ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 803 ASN E 803 ASN ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 803 ASN ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 803 ASN K 469 HIS K 803 ASN ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 69840 Z= 0.395 Angle : 0.693 7.951 94584 Z= 0.372 Chirality : 0.049 0.164 10620 Planarity : 0.004 0.034 12396 Dihedral : 6.078 47.731 9518 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.54 % Favored : 80.46 % Rotamer: Outliers : 3.15 % Allowed : 11.51 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.08), residues: 8952 helix: -1.78 (0.25), residues: 384 sheet: -3.45 (0.10), residues: 1728 loop : -3.21 (0.07), residues: 6840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 577 HIS 0.004 0.001 HIS A 469 PHE 0.021 0.002 PHE H 254 TYR 0.024 0.002 TYR B 574 ARG 0.005 0.001 ARG J 133 *********************** 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 444 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 211 time to evaluate : 5.876 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: A 539 GLN cc_start: 0.8009 (mm110) cc_final: 0.7611 (mm110) REVERT: A 634 ASP cc_start: 0.8537 (p0) cc_final: 0.7967 (p0) REVERT: A 662 MET cc_start: 0.7932 (mtm) cc_final: 0.7444 (mpp) REVERT: A 663 MET cc_start: 0.8167 (mmm) cc_final: 0.7553 (mmm) REVERT: A 718 LEU cc_start: 0.8618 (mm) cc_final: 0.8253 (mm) REVERT: B 205 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8554 (pt) REVERT: B 621 MET cc_start: 0.7158 (mmp) cc_final: 0.6916 (mmm) REVERT: B 662 MET cc_start: 0.7740 (mtm) cc_final: 0.6769 (mpp) REVERT: B 663 MET cc_start: 0.8056 (tpp) cc_final: 0.7856 (mpp) REVERT: B 735 MET cc_start: 0.7582 (mtp) cc_final: 0.6351 (ptp) REVERT: C 243 ILE cc_start: 0.9381 (mt) cc_final: 0.9177 (mm) REVERT: C 621 MET cc_start: 0.7573 (mmm) cc_final: 0.6672 (mmm) REVERT: C 662 MET cc_start: 0.8007 (mtt) cc_final: 0.7299 (mpp) REVERT: C 663 MET cc_start: 0.8411 (mtp) cc_final: 0.7409 (tmm) REVERT: C 758 MET cc_start: 0.7190 (mpt) cc_final: 0.6679 (mpt) REVERT: D 621 MET cc_start: 0.7583 (mmm) cc_final: 0.6581 (mmm) REVERT: D 662 MET cc_start: 0.7884 (mtm) cc_final: 0.7347 (mpp) REVERT: D 663 MET cc_start: 0.8172 (mmm) cc_final: 0.7611 (mmm) REVERT: D 758 MET cc_start: 0.7490 (mpt) cc_final: 0.6861 (mpt) REVERT: E 125 VAL cc_start: 0.8727 (t) cc_final: 0.8518 (t) REVERT: E 205 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8532 (pt) REVERT: E 634 ASP cc_start: 0.8389 (p0) cc_final: 0.8001 (p0) REVERT: E 662 MET cc_start: 0.7809 (mtm) cc_final: 0.7162 (mpp) REVERT: E 663 MET cc_start: 0.8027 (mpp) cc_final: 0.7708 (mpp) REVERT: E 735 MET cc_start: 0.7023 (ptp) cc_final: 0.6713 (pmm) REVERT: E 758 MET cc_start: 0.7182 (mpt) cc_final: 0.5120 (ttm) REVERT: F 243 ILE cc_start: 0.9377 (mt) cc_final: 0.9171 (mm) REVERT: F 430 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7766 (pp) REVERT: F 621 MET cc_start: 0.7556 (mmm) cc_final: 0.6611 (mmm) REVERT: F 662 MET cc_start: 0.7871 (mtt) cc_final: 0.7309 (mpp) REVERT: F 663 MET cc_start: 0.7692 (mmm) cc_final: 0.7115 (mmm) REVERT: F 718 LEU cc_start: 0.8845 (mm) cc_final: 0.8465 (mm) REVERT: G 539 GLN cc_start: 0.7932 (mm110) cc_final: 0.7535 (mm110) REVERT: G 634 ASP cc_start: 0.8643 (p0) cc_final: 0.8121 (p0) REVERT: G 662 MET cc_start: 0.7971 (mtm) cc_final: 0.7330 (mpp) REVERT: G 663 MET cc_start: 0.8185 (mmm) cc_final: 0.7613 (mmm) REVERT: G 718 LEU cc_start: 0.8528 (mm) cc_final: 0.8142 (mm) REVERT: H 124 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7164 (p0) REVERT: H 125 VAL cc_start: 0.8622 (t) cc_final: 0.8415 (t) REVERT: H 226 MET cc_start: 0.8291 (mtp) cc_final: 0.7917 (mtp) REVERT: H 662 MET cc_start: 0.8105 (mtm) cc_final: 0.7630 (mpp) REVERT: H 663 MET cc_start: 0.8500 (mtp) cc_final: 0.7581 (tmm) REVERT: H 735 MET cc_start: 0.6942 (ptp) cc_final: 0.6656 (pmm) REVERT: I 124 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7357 (p0) REVERT: I 247 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8648 (mptt) REVERT: I 621 MET cc_start: 0.7814 (mmm) cc_final: 0.6900 (mmm) REVERT: I 662 MET cc_start: 0.7850 (mtm) cc_final: 0.7279 (mpp) REVERT: I 663 MET cc_start: 0.8326 (mtp) cc_final: 0.7584 (mmm) REVERT: I 758 MET cc_start: 0.7107 (mpt) cc_final: 0.6593 (mpt) REVERT: J 621 MET cc_start: 0.7980 (mmm) cc_final: 0.6484 (mmm) REVERT: J 662 MET cc_start: 0.7895 (mtm) cc_final: 0.7272 (mpp) REVERT: K 205 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8530 (pt) REVERT: K 662 MET cc_start: 0.7600 (mtt) cc_final: 0.7374 (mtt) REVERT: K 735 MET cc_start: 0.7941 (mtp) cc_final: 0.7104 (ttm) REVERT: L 124 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7283 (p0) REVERT: L 247 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8699 (mptt) REVERT: L 430 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7801 (pp) REVERT: L 621 MET cc_start: 0.7579 (mmm) cc_final: 0.6598 (mmm) REVERT: L 662 MET cc_start: 0.7988 (mtt) cc_final: 0.7361 (mpp) REVERT: L 718 LEU cc_start: 0.8802 (mm) cc_final: 0.8409 (mm) REVERT: L 758 MET cc_start: 0.7110 (mpt) cc_final: 0.6603 (mpt) outliers start: 233 outliers final: 169 residues processed: 390 average time/residue: 0.6020 time to fit residues: 438.6446 Evaluate side-chains 380 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 201 time to evaluate : 5.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 620 VAL Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain G residue 654 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 654 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 100 GLU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 216 ASN Chi-restraints excluded: chain I residue 247 LYS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 654 LEU Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 216 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 718 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 100 GLU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 216 ASN Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 247 LYS Chi-restraints excluded: chain L residue 354 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 654 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 8.9990 chunk 783 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 510 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 870 optimal weight: 5.9990 chunk 722 optimal weight: 9.9990 chunk 403 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 288 optimal weight: 40.0000 chunk 457 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 ASN C 803 ASN F 618 ASN ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 803 ASN ** H 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 803 ASN ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 618 ASN ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 618 ASN ** L 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 69840 Z= 0.149 Angle : 0.562 7.287 94584 Z= 0.295 Chirality : 0.046 0.218 10620 Planarity : 0.003 0.028 12396 Dihedral : 5.341 24.082 9516 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 2.22 % Allowed : 12.75 % Favored : 85.04 % 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: -4.19 (0.08), residues: 8952 helix: -1.81 (0.25), residues: 384 sheet: -3.14 (0.10), residues: 1680 loop : -3.00 (0.07), residues: 6888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 577 HIS 0.004 0.001 HIS K 531 PHE 0.018 0.001 PHE L 580 TYR 0.022 0.001 TYR B 574 ARG 0.002 0.000 ARG F 228 *********************** 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 398 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 234 time to evaluate : 6.137 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: A 247 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8213 (mptt) REVERT: A 539 GLN cc_start: 0.7725 (mm110) cc_final: 0.7378 (mm110) REVERT: A 634 ASP cc_start: 0.8509 (p0) cc_final: 0.7945 (p0) REVERT: A 662 MET cc_start: 0.7940 (mtm) cc_final: 0.7379 (mpp) REVERT: A 663 MET cc_start: 0.8169 (mmm) cc_final: 0.7600 (mmm) REVERT: A 718 LEU cc_start: 0.8651 (mm) cc_final: 0.8293 (mm) REVERT: A 758 MET cc_start: 0.7156 (mpt) cc_final: 0.6529 (mpt) REVERT: B 226 MET cc_start: 0.7817 (mtp) cc_final: 0.7520 (mtp) REVERT: B 662 MET cc_start: 0.7667 (mtm) cc_final: 0.6870 (mpp) REVERT: B 735 MET cc_start: 0.7644 (mtp) cc_final: 0.6360 (ptp) REVERT: B 758 MET cc_start: 0.6878 (mpt) cc_final: 0.5315 (mtp) REVERT: C 247 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8365 (mtmm) REVERT: C 621 MET cc_start: 0.7271 (mmm) cc_final: 0.6676 (mmm) REVERT: C 662 MET cc_start: 0.7872 (mtt) cc_final: 0.7088 (mpp) REVERT: C 663 MET cc_start: 0.8288 (mtp) cc_final: 0.7765 (mmm) REVERT: C 728 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9185 (tp) REVERT: C 758 MET cc_start: 0.7046 (mpt) cc_final: 0.6469 (mpt) REVERT: D 247 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8209 (mptt) REVERT: D 539 GLN cc_start: 0.7837 (mm110) cc_final: 0.7473 (mm110) REVERT: D 621 MET cc_start: 0.7448 (mmm) cc_final: 0.6078 (mmm) REVERT: D 634 ASP cc_start: 0.8661 (p0) cc_final: 0.8194 (p0) REVERT: D 655 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.8035 (p0) REVERT: D 662 MET cc_start: 0.7851 (mtm) cc_final: 0.7336 (mpp) REVERT: D 663 MET cc_start: 0.8240 (mmm) cc_final: 0.7777 (mmm) REVERT: D 758 MET cc_start: 0.7177 (mpt) cc_final: 0.6596 (mpt) REVERT: E 125 VAL cc_start: 0.8709 (t) cc_final: 0.8482 (t) REVERT: E 205 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8450 (pt) REVERT: E 226 MET cc_start: 0.7390 (mtp) cc_final: 0.7072 (mmm) REVERT: E 662 MET cc_start: 0.7768 (mtm) cc_final: 0.7097 (mpp) REVERT: E 663 MET cc_start: 0.7937 (mpp) cc_final: 0.7620 (mpp) REVERT: E 735 MET cc_start: 0.7015 (ptp) cc_final: 0.6697 (pmm) REVERT: E 758 MET cc_start: 0.7037 (mpt) cc_final: 0.5010 (ttm) REVERT: F 247 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8391 (mtmm) REVERT: F 430 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7789 (pp) REVERT: F 621 MET cc_start: 0.7256 (mmm) cc_final: 0.6632 (mmm) REVERT: F 662 MET cc_start: 0.7804 (mtt) cc_final: 0.7247 (mpp) REVERT: F 663 MET cc_start: 0.7607 (mmm) cc_final: 0.7087 (mmm) REVERT: F 718 LEU cc_start: 0.8824 (mm) cc_final: 0.8457 (mm) REVERT: F 728 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9121 (tp) REVERT: G 247 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8226 (mppt) REVERT: G 634 ASP cc_start: 0.8624 (p0) cc_final: 0.8123 (p0) REVERT: G 662 MET cc_start: 0.7920 (mtm) cc_final: 0.7321 (mpp) REVERT: G 663 MET cc_start: 0.8223 (mmm) cc_final: 0.7688 (mmm) REVERT: G 718 LEU cc_start: 0.8573 (mm) cc_final: 0.8194 (mm) REVERT: G 758 MET cc_start: 0.6877 (mpt) cc_final: 0.5178 (ttm) REVERT: H 124 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6869 (p0) REVERT: H 125 VAL cc_start: 0.8651 (t) cc_final: 0.8390 (t) REVERT: H 580 PHE cc_start: 0.8204 (t80) cc_final: 0.7943 (t80) REVERT: H 621 MET cc_start: 0.7208 (mmm) cc_final: 0.6015 (mmm) REVERT: H 662 MET cc_start: 0.8162 (mtm) cc_final: 0.7465 (mpp) REVERT: H 663 MET cc_start: 0.8487 (mtp) cc_final: 0.8230 (tpp) REVERT: H 718 LEU cc_start: 0.8935 (mm) cc_final: 0.8363 (tp) REVERT: H 735 MET cc_start: 0.6906 (ptp) cc_final: 0.6588 (pmm) REVERT: I 124 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7002 (p0) REVERT: I 621 MET cc_start: 0.7432 (mmm) cc_final: 0.6778 (mmm) REVERT: I 662 MET cc_start: 0.7835 (mtm) cc_final: 0.7156 (mpp) REVERT: I 663 MET cc_start: 0.8292 (mtp) cc_final: 0.7776 (mmm) REVERT: I 726 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7899 (tt) REVERT: I 758 MET cc_start: 0.6944 (mpt) cc_final: 0.6459 (mpt) REVERT: J 247 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8156 (mppt) REVERT: J 539 GLN cc_start: 0.7653 (mm110) cc_final: 0.7265 (mm110) REVERT: J 621 MET cc_start: 0.7768 (mmm) cc_final: 0.6247 (mmm) REVERT: J 662 MET cc_start: 0.7855 (mtm) cc_final: 0.7258 (mpp) REVERT: K 226 MET cc_start: 0.7824 (mtp) cc_final: 0.7519 (mtp) REVERT: K 634 ASP cc_start: 0.8562 (p0) cc_final: 0.8064 (p0) REVERT: K 662 MET cc_start: 0.7558 (mtt) cc_final: 0.7312 (mtt) REVERT: K 735 MET cc_start: 0.7880 (mtp) cc_final: 0.7080 (ttm) REVERT: K 758 MET cc_start: 0.6844 (mpt) cc_final: 0.5227 (ttm) REVERT: L 124 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7002 (p0) REVERT: L 430 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7721 (pp) REVERT: L 539 GLN cc_start: 0.8037 (mm110) cc_final: 0.7755 (mm110) REVERT: L 621 MET cc_start: 0.7150 (mmm) cc_final: 0.6486 (mmm) REVERT: L 662 MET cc_start: 0.7986 (mtt) cc_final: 0.7708 (mpp) REVERT: L 718 LEU cc_start: 0.8715 (mm) cc_final: 0.8333 (mm) REVERT: L 758 MET cc_start: 0.6750 (mpt) cc_final: 0.6333 (mpt) outliers start: 164 outliers final: 119 residues processed: 358 average time/residue: 0.5641 time to fit residues: 368.5724 Evaluate side-chains 333 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 198 time to evaluate : 5.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 655 ASN Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 620 VAL Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 430 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 247 LYS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain I residue 726 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 247 LYS Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 216 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 620 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 496 optimal weight: 1.9990 chunk 635 optimal weight: 0.1980 chunk 492 optimal weight: 7.9990 chunk 733 optimal weight: 20.0000 chunk 486 optimal weight: 7.9990 chunk 867 optimal weight: 7.9990 chunk 542 optimal weight: 0.0970 chunk 528 optimal weight: 8.9990 chunk 400 optimal weight: 4.9990 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 803 ASN ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 69840 Z= 0.252 Angle : 0.595 7.838 94584 Z= 0.314 Chirality : 0.047 0.188 10620 Planarity : 0.003 0.031 12396 Dihedral : 5.387 23.757 9516 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.32 % Favored : 83.68 % Rotamer: Outliers : 2.80 % Allowed : 12.71 % Favored : 84.49 % 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: -4.28 (0.08), residues: 8952 helix: -1.62 (0.25), residues: 384 sheet: -3.36 (0.10), residues: 1860 loop : -2.99 (0.07), residues: 6708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 577 HIS 0.003 0.001 HIS D 469 PHE 0.020 0.002 PHE K 594 TYR 0.017 0.001 TYR B 574 ARG 0.003 0.000 ARG D 133 *********************** 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 434 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 227 time to evaluate : 5.874 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: A 247 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8236 (mppt) REVERT: A 539 GLN cc_start: 0.7801 (mm110) cc_final: 0.7448 (mm110) REVERT: A 621 MET cc_start: 0.7245 (mmm) cc_final: 0.6292 (mmm) REVERT: A 634 ASP cc_start: 0.8553 (p0) cc_final: 0.7989 (p0) REVERT: A 662 MET cc_start: 0.7954 (mtm) cc_final: 0.7232 (mpp) REVERT: A 663 MET cc_start: 0.8184 (mmm) cc_final: 0.7737 (mpp) REVERT: A 718 LEU cc_start: 0.8632 (mm) cc_final: 0.8286 (mm) REVERT: B 205 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8468 (pt) REVERT: B 226 MET cc_start: 0.7583 (mtp) cc_final: 0.7151 (mtp) REVERT: B 609 MET cc_start: 0.8086 (mtm) cc_final: 0.7828 (mpp) REVERT: B 662 MET cc_start: 0.7577 (mtm) cc_final: 0.6665 (mpp) REVERT: B 735 MET cc_start: 0.7663 (mtp) cc_final: 0.6382 (ptp) REVERT: B 758 MET cc_start: 0.6926 (mpt) cc_final: 0.5607 (ttm) REVERT: C 621 MET cc_start: 0.7529 (mmm) cc_final: 0.6615 (mmm) REVERT: C 662 MET cc_start: 0.7929 (mtt) cc_final: 0.7118 (mpp) REVERT: C 663 MET cc_start: 0.8344 (mtp) cc_final: 0.7939 (mmm) REVERT: C 758 MET cc_start: 0.6633 (mpt) cc_final: 0.6212 (mpt) REVERT: D 247 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8221 (mppt) REVERT: D 539 GLN cc_start: 0.7885 (mm110) cc_final: 0.7513 (mm110) REVERT: D 621 MET cc_start: 0.7549 (mmm) cc_final: 0.6200 (mmm) REVERT: D 634 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8165 (p0) REVERT: D 662 MET cc_start: 0.7987 (mtm) cc_final: 0.7375 (mpp) REVERT: D 663 MET cc_start: 0.8254 (mmm) cc_final: 0.7983 (mpp) REVERT: D 758 MET cc_start: 0.7156 (mpt) cc_final: 0.6583 (mpt) REVERT: E 125 VAL cc_start: 0.8707 (t) cc_final: 0.8483 (t) REVERT: E 205 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8522 (pt) REVERT: E 621 MET cc_start: 0.6314 (mmm) cc_final: 0.5399 (mmm) REVERT: E 634 ASP cc_start: 0.8368 (p0) cc_final: 0.7951 (p0) REVERT: E 662 MET cc_start: 0.7800 (mtm) cc_final: 0.7160 (mpp) REVERT: E 663 MET cc_start: 0.7953 (mpp) cc_final: 0.7612 (mpp) REVERT: E 735 MET cc_start: 0.7072 (ptp) cc_final: 0.6704 (pmm) REVERT: E 758 MET cc_start: 0.7079 (mpt) cc_final: 0.5040 (ttm) REVERT: F 247 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8470 (mtmm) REVERT: F 430 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7721 (pp) REVERT: F 539 GLN cc_start: 0.8061 (mm110) cc_final: 0.7803 (mm110) REVERT: F 621 MET cc_start: 0.7504 (mmm) cc_final: 0.6549 (mmm) REVERT: F 662 MET cc_start: 0.7798 (mtt) cc_final: 0.7217 (mpp) REVERT: F 663 MET cc_start: 0.7648 (mmm) cc_final: 0.7146 (mmm) REVERT: F 718 LEU cc_start: 0.8785 (mm) cc_final: 0.8403 (mm) REVERT: F 728 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9109 (tp) REVERT: F 758 MET cc_start: 0.6887 (mpt) cc_final: 0.6587 (mpt) REVERT: G 226 MET cc_start: 0.8420 (mmm) cc_final: 0.8014 (mtp) REVERT: G 247 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8237 (mppt) REVERT: G 539 GLN cc_start: 0.7760 (mm110) cc_final: 0.7407 (mm110) REVERT: G 621 MET cc_start: 0.7274 (mmm) cc_final: 0.6304 (mmm) REVERT: G 634 ASP cc_start: 0.8623 (p0) cc_final: 0.8101 (p0) REVERT: G 662 MET cc_start: 0.7900 (mtm) cc_final: 0.7148 (mpp) REVERT: G 663 MET cc_start: 0.8241 (mmm) cc_final: 0.7864 (mpp) REVERT: G 718 LEU cc_start: 0.8567 (mm) cc_final: 0.8215 (mm) REVERT: G 758 MET cc_start: 0.7053 (mpt) cc_final: 0.6454 (mpt) REVERT: H 124 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7106 (p0) REVERT: H 125 VAL cc_start: 0.8626 (t) cc_final: 0.8390 (t) REVERT: H 205 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8548 (pt) REVERT: H 580 PHE cc_start: 0.8169 (t80) cc_final: 0.7910 (t80) REVERT: H 621 MET cc_start: 0.7436 (mmm) cc_final: 0.6203 (mmm) REVERT: H 662 MET cc_start: 0.8212 (mtm) cc_final: 0.7553 (mpp) REVERT: H 663 MET cc_start: 0.8490 (mtp) cc_final: 0.7614 (tmm) REVERT: H 735 MET cc_start: 0.7029 (ptp) cc_final: 0.6649 (pmm) REVERT: I 124 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7078 (p0) REVERT: I 621 MET cc_start: 0.7664 (mmm) cc_final: 0.6796 (mmm) REVERT: I 662 MET cc_start: 0.7852 (mtm) cc_final: 0.7212 (mpp) REVERT: I 663 MET cc_start: 0.8366 (mtp) cc_final: 0.7752 (mmm) REVERT: I 726 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7873 (tt) REVERT: I 758 MET cc_start: 0.6643 (mpt) cc_final: 0.6251 (mpt) REVERT: J 247 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8172 (mppt) REVERT: J 539 GLN cc_start: 0.7714 (mm110) cc_final: 0.7325 (mm110) REVERT: J 621 MET cc_start: 0.7926 (mmm) cc_final: 0.6557 (mmm) REVERT: J 662 MET cc_start: 0.7631 (mtm) cc_final: 0.7184 (mpp) REVERT: J 809 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8410 (p) REVERT: K 205 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8451 (pt) REVERT: K 226 MET cc_start: 0.7629 (mtp) cc_final: 0.7191 (mtp) REVERT: K 580 PHE cc_start: 0.8246 (t80) cc_final: 0.7953 (t80) REVERT: K 634 ASP cc_start: 0.8577 (p0) cc_final: 0.8089 (p0) REVERT: K 662 MET cc_start: 0.7618 (mtt) cc_final: 0.7183 (mtt) REVERT: K 735 MET cc_start: 0.7973 (mtp) cc_final: 0.7089 (ttm) REVERT: K 758 MET cc_start: 0.6923 (mpt) cc_final: 0.6315 (mpt) REVERT: L 124 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7093 (p0) REVERT: L 430 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7738 (pp) REVERT: L 539 GLN cc_start: 0.7994 (mm110) cc_final: 0.7714 (mm110) REVERT: L 621 MET cc_start: 0.7456 (mmm) cc_final: 0.6509 (mmm) REVERT: L 662 MET cc_start: 0.7978 (mtt) cc_final: 0.7699 (mpp) REVERT: L 718 LEU cc_start: 0.8754 (mm) cc_final: 0.8367 (mm) REVERT: L 758 MET cc_start: 0.6784 (mpt) cc_final: 0.6418 (mpt) outliers start: 207 outliers final: 161 residues processed: 395 average time/residue: 0.5550 time to fit residues: 402.5400 Evaluate side-chains 392 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 213 time to evaluate : 5.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 216 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 247 LYS Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 620 VAL Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain G residue 654 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 247 LYS Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 216 ASN Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain I residue 726 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 247 LYS Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 809 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 216 ASN Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 718 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 354 ASP Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 634 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 8.9990 chunk 346 optimal weight: 0.9990 chunk 518 optimal weight: 30.0000 chunk 261 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 551 optimal weight: 3.9990 chunk 590 optimal weight: 40.0000 chunk 428 optimal weight: 0.0470 chunk 80 optimal weight: 9.9990 chunk 681 optimal weight: 10.0000 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN ** B 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 711 ASN ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 69840 Z= 0.220 Angle : 0.581 8.090 94584 Z= 0.304 Chirality : 0.046 0.164 10620 Planarity : 0.003 0.029 12396 Dihedral : 5.276 22.848 9516 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 2.93 % Allowed : 12.64 % Favored : 84.43 % 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: -4.17 (0.08), residues: 8952 helix: -1.76 (0.25), residues: 384 sheet: -3.19 (0.10), residues: 1884 loop : -2.93 (0.07), residues: 6684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 577 HIS 0.003 0.001 HIS K 531 PHE 0.024 0.002 PHE E 594 TYR 0.020 0.001 TYR B 574 ARG 0.003 0.000 ARG K 133 *********************** 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 445 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 228 time to evaluate : 5.883 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: A 247 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8196 (mppt) REVERT: A 539 GLN cc_start: 0.7786 (mm110) cc_final: 0.7433 (mm110) REVERT: A 621 MET cc_start: 0.7086 (mmm) cc_final: 0.6388 (mmm) REVERT: A 634 ASP cc_start: 0.8533 (p0) cc_final: 0.7968 (p0) REVERT: A 662 MET cc_start: 0.7892 (mtm) cc_final: 0.7214 (mpp) REVERT: A 663 MET cc_start: 0.8237 (mmm) cc_final: 0.7858 (mpp) REVERT: A 718 LEU cc_start: 0.8655 (mm) cc_final: 0.8315 (mm) REVERT: A 758 MET cc_start: 0.7283 (mpt) cc_final: 0.6709 (mpt) REVERT: B 205 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8428 (pt) REVERT: B 226 MET cc_start: 0.7589 (mtp) cc_final: 0.7207 (mtp) REVERT: B 634 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8168 (p0) REVERT: B 662 MET cc_start: 0.7687 (mtm) cc_final: 0.7010 (mpp) REVERT: B 663 MET cc_start: 0.8021 (mpp) cc_final: 0.7714 (mpp) REVERT: B 735 MET cc_start: 0.7655 (mtp) cc_final: 0.6338 (ptp) REVERT: B 758 MET cc_start: 0.6716 (mpt) cc_final: 0.6508 (mpt) REVERT: C 621 MET cc_start: 0.7578 (mmm) cc_final: 0.6812 (mmm) REVERT: C 662 MET cc_start: 0.7818 (mtt) cc_final: 0.7135 (mpp) REVERT: C 663 MET cc_start: 0.8324 (mtp) cc_final: 0.7932 (mmm) REVERT: C 758 MET cc_start: 0.6641 (mpt) cc_final: 0.6312 (mpt) REVERT: D 247 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8153 (mppt) REVERT: D 539 GLN cc_start: 0.7860 (mm110) cc_final: 0.7492 (mm110) REVERT: D 621 MET cc_start: 0.7601 (mmm) cc_final: 0.6143 (mmm) REVERT: D 634 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8152 (p0) REVERT: D 662 MET cc_start: 0.7982 (mtm) cc_final: 0.7373 (mpp) REVERT: D 663 MET cc_start: 0.8241 (mmm) cc_final: 0.7987 (mpp) REVERT: D 758 MET cc_start: 0.7176 (mpt) cc_final: 0.6607 (mpt) REVERT: E 125 VAL cc_start: 0.8730 (t) cc_final: 0.8498 (t) REVERT: E 205 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8482 (pt) REVERT: E 621 MET cc_start: 0.6502 (mmm) cc_final: 0.5487 (mmm) REVERT: E 634 ASP cc_start: 0.8383 (p0) cc_final: 0.7968 (p0) REVERT: E 662 MET cc_start: 0.7772 (mtm) cc_final: 0.7172 (mpp) REVERT: E 663 MET cc_start: 0.7958 (mpp) cc_final: 0.7612 (mpp) REVERT: E 735 MET cc_start: 0.7042 (ptp) cc_final: 0.6670 (pmm) REVERT: F 430 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7692 (pp) REVERT: F 539 GLN cc_start: 0.8020 (mm110) cc_final: 0.7768 (mm110) REVERT: F 621 MET cc_start: 0.7589 (mmm) cc_final: 0.6771 (mmm) REVERT: F 662 MET cc_start: 0.7824 (mtt) cc_final: 0.7254 (mpp) REVERT: F 663 MET cc_start: 0.7726 (mmm) cc_final: 0.7264 (mmm) REVERT: F 718 LEU cc_start: 0.8867 (mm) cc_final: 0.8485 (mm) REVERT: F 728 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9127 (tp) REVERT: G 226 MET cc_start: 0.8449 (mmm) cc_final: 0.8069 (mtp) REVERT: G 247 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8141 (mppt) REVERT: G 539 GLN cc_start: 0.7770 (mm110) cc_final: 0.7420 (mm110) REVERT: G 621 MET cc_start: 0.7052 (mmm) cc_final: 0.6376 (mmm) REVERT: G 634 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8120 (p0) REVERT: G 662 MET cc_start: 0.7900 (mtm) cc_final: 0.7139 (mpp) REVERT: G 663 MET cc_start: 0.8263 (mmm) cc_final: 0.7875 (mpp) REVERT: G 718 LEU cc_start: 0.8587 (mm) cc_final: 0.8239 (mm) REVERT: G 758 MET cc_start: 0.7057 (mpt) cc_final: 0.6531 (mpt) REVERT: H 124 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7087 (p0) REVERT: H 125 VAL cc_start: 0.8692 (t) cc_final: 0.8448 (t) REVERT: H 205 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8485 (pt) REVERT: H 580 PHE cc_start: 0.8112 (t80) cc_final: 0.7873 (t80) REVERT: H 621 MET cc_start: 0.7681 (mmm) cc_final: 0.6340 (mmm) REVERT: H 662 MET cc_start: 0.8245 (mtm) cc_final: 0.7581 (mpp) REVERT: H 663 MET cc_start: 0.8455 (mtp) cc_final: 0.7571 (tmm) REVERT: I 124 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7031 (p0) REVERT: I 247 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8435 (mtmm) REVERT: I 621 MET cc_start: 0.7640 (mmm) cc_final: 0.6654 (mmm) REVERT: I 662 MET cc_start: 0.7951 (mtm) cc_final: 0.7330 (mpp) REVERT: I 663 MET cc_start: 0.8369 (mtp) cc_final: 0.7754 (mmm) REVERT: I 726 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7891 (tt) REVERT: I 758 MET cc_start: 0.6826 (mpt) cc_final: 0.6432 (mpt) REVERT: J 247 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8165 (mppt) REVERT: J 539 GLN cc_start: 0.7650 (mm110) cc_final: 0.7267 (mm110) REVERT: J 621 MET cc_start: 0.7930 (mmm) cc_final: 0.6607 (mmm) REVERT: J 662 MET cc_start: 0.7769 (mtm) cc_final: 0.7208 (mpp) REVERT: J 718 LEU cc_start: 0.8871 (mm) cc_final: 0.8489 (mm) REVERT: J 758 MET cc_start: 0.7176 (mpt) cc_final: 0.6759 (mpt) REVERT: K 205 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8413 (pt) REVERT: K 226 MET cc_start: 0.7640 (mtp) cc_final: 0.7249 (mtp) REVERT: K 580 PHE cc_start: 0.8256 (t80) cc_final: 0.8014 (t80) REVERT: K 634 ASP cc_start: 0.8560 (p0) cc_final: 0.8129 (p0) REVERT: K 662 MET cc_start: 0.7783 (mtt) cc_final: 0.7472 (mtt) REVERT: K 663 MET cc_start: 0.8043 (mpp) cc_final: 0.7820 (mpp) REVERT: K 735 MET cc_start: 0.7962 (mtp) cc_final: 0.7031 (ttm) REVERT: K 758 MET cc_start: 0.6900 (mpt) cc_final: 0.5445 (ttm) REVERT: L 124 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6985 (p0) REVERT: L 430 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7720 (pp) REVERT: L 539 GLN cc_start: 0.7963 (mm110) cc_final: 0.7698 (mm110) REVERT: L 662 MET cc_start: 0.7922 (mtt) cc_final: 0.7705 (mpp) REVERT: L 718 LEU cc_start: 0.8733 (mm) cc_final: 0.8348 (mm) REVERT: L 735 MET cc_start: 0.7637 (mtp) cc_final: 0.7428 (mtt) REVERT: L 758 MET cc_start: 0.6873 (mpt) cc_final: 0.6427 (mpt) outliers start: 217 outliers final: 166 residues processed: 401 average time/residue: 0.5661 time to fit residues: 416.1525 Evaluate side-chains 395 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 210 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 634 ASP Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 216 ASN Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 620 VAL Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 654 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 216 ASN Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 247 LYS Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 526 VAL Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 205 LEU Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 216 ASN Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 247 LYS Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 472 ASN Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain I residue 726 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 247 LYS Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 232 VAL Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 718 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 354 ASP Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 430 LEU Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 634 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 7.9990 chunk 831 optimal weight: 9.9990 chunk 758 optimal weight: 10.0000 chunk 808 optimal weight: 30.0000 chunk 830 optimal weight: 7.9990 chunk 486 optimal weight: 6.9990 chunk 352 optimal weight: 20.0000 chunk 634 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 730 optimal weight: 20.0000 chunk 764 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 69840 Z= 0.536 Angle : 0.794 10.006 94584 Z= 0.428 Chirality : 0.053 0.194 10620 Planarity : 0.004 0.038 12396 Dihedral : 6.339 24.555 9516 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.81 % Favored : 78.19 % Rotamer: Outliers : 3.12 % Allowed : 12.93 % Favored : 83.95 % 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: -4.60 (0.08), residues: 8952 helix: -1.69 (0.25), residues: 384 sheet: -3.67 (0.10), residues: 2076 loop : -3.15 (0.07), residues: 6492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 577 HIS 0.006 0.002 HIS D 469 PHE 0.038 0.003 PHE B 594 TYR 0.022 0.002 TYR A 574 ARG 0.005 0.001 ARG E 133 *********************** 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 438 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 207 time to evaluate : 5.948 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: A 247 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8329 (mptt) REVERT: A 539 GLN cc_start: 0.8001 (mm110) cc_final: 0.7686 (mm110) REVERT: A 621 MET cc_start: 0.7469 (mmm) cc_final: 0.6691 (mmm) REVERT: A 634 ASP cc_start: 0.8613 (p0) cc_final: 0.7972 (p0) REVERT: A 662 MET cc_start: 0.8047 (mtm) cc_final: 0.7527 (mpp) REVERT: A 663 MET cc_start: 0.8297 (mmm) cc_final: 0.7670 (mmm) REVERT: A 718 LEU cc_start: 0.8618 (mm) cc_final: 0.8254 (mm) REVERT: A 758 MET cc_start: 0.7542 (mpt) cc_final: 0.6984 (mpt) REVERT: B 103 MET cc_start: 0.7230 (mtt) cc_final: 0.7022 (mtt) REVERT: B 205 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8447 (pt) REVERT: B 226 MET cc_start: 0.8050 (mtp) cc_final: 0.7600 (mtp) REVERT: B 609 MET cc_start: 0.8133 (mpp) cc_final: 0.7818 (mpp) REVERT: B 621 MET cc_start: 0.6299 (mmm) cc_final: 0.4893 (mmm) REVERT: B 662 MET cc_start: 0.7690 (mtm) cc_final: 0.7187 (mpp) REVERT: B 663 MET cc_start: 0.7956 (mpp) cc_final: 0.7700 (mpp) REVERT: B 735 MET cc_start: 0.7799 (mtp) cc_final: 0.7562 (mtt) REVERT: B 758 MET cc_start: 0.6925 (mpt) cc_final: 0.6590 (mpt) REVERT: C 662 MET cc_start: 0.7944 (mtt) cc_final: 0.7379 (mpp) REVERT: C 663 MET cc_start: 0.8476 (mtp) cc_final: 0.7488 (tmm) REVERT: C 758 MET cc_start: 0.7061 (mpt) cc_final: 0.6515 (mpt) REVERT: C 790 TYR cc_start: 0.8121 (m-80) cc_final: 0.7835 (m-80) REVERT: D 247 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8290 (mptt) REVERT: D 621 MET cc_start: 0.7900 (mmm) cc_final: 0.6431 (mmm) REVERT: D 662 MET cc_start: 0.8052 (mtm) cc_final: 0.7487 (mpp) REVERT: D 663 MET cc_start: 0.8230 (mmm) cc_final: 0.7976 (mpp) REVERT: D 758 MET cc_start: 0.7417 (mpt) cc_final: 0.6859 (mpt) REVERT: E 125 VAL cc_start: 0.8698 (t) cc_final: 0.8460 (t) REVERT: E 247 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8401 (mptt) REVERT: E 621 MET cc_start: 0.7061 (mmm) cc_final: 0.5972 (mmm) REVERT: E 634 ASP cc_start: 0.8464 (p0) cc_final: 0.8030 (p0) REVERT: E 662 MET cc_start: 0.7763 (mtm) cc_final: 0.7219 (mpp) REVERT: E 735 MET cc_start: 0.7166 (ptp) cc_final: 0.6736 (pmm) REVERT: F 662 MET cc_start: 0.7791 (mtt) cc_final: 0.7175 (mpp) REVERT: F 663 MET cc_start: 0.7610 (mmm) cc_final: 0.7271 (mmm) REVERT: F 718 LEU cc_start: 0.8776 (mm) cc_final: 0.8383 (mm) REVERT: F 728 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9062 (tp) REVERT: G 226 MET cc_start: 0.8646 (mmm) cc_final: 0.8436 (mtp) REVERT: G 247 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8323 (mptt) REVERT: G 539 GLN cc_start: 0.7985 (mm110) cc_final: 0.7688 (mm110) REVERT: G 621 MET cc_start: 0.7429 (mmm) cc_final: 0.6626 (mmm) REVERT: G 634 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8086 (p0) REVERT: G 662 MET cc_start: 0.8010 (mtm) cc_final: 0.7475 (mpp) REVERT: G 663 MET cc_start: 0.8235 (mmm) cc_final: 0.7647 (mmm) REVERT: G 718 LEU cc_start: 0.8702 (mm) cc_final: 0.8322 (mm) REVERT: G 735 MET cc_start: 0.7244 (ptp) cc_final: 0.7023 (pmm) REVERT: G 758 MET cc_start: 0.7243 (mpt) cc_final: 0.6706 (mpt) REVERT: H 125 VAL cc_start: 0.8644 (t) cc_final: 0.8409 (t) REVERT: H 205 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8501 (pt) REVERT: H 247 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8377 (mptt) REVERT: H 621 MET cc_start: 0.7989 (mmm) cc_final: 0.6393 (mmm) REVERT: H 662 MET cc_start: 0.8314 (mtm) cc_final: 0.7773 (mpp) REVERT: H 735 MET cc_start: 0.6834 (ptp) cc_final: 0.6531 (pmm) REVERT: I 124 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7244 (p0) REVERT: I 662 MET cc_start: 0.8154 (mtm) cc_final: 0.7567 (mpp) REVERT: I 663 MET cc_start: 0.8373 (mtp) cc_final: 0.7625 (mmm) REVERT: I 758 MET cc_start: 0.6973 (mpt) cc_final: 0.6535 (mpt) REVERT: J 247 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8302 (mptt) REVERT: J 621 MET cc_start: 0.8071 (mmm) cc_final: 0.6812 (mmm) REVERT: J 662 MET cc_start: 0.7891 (mtm) cc_final: 0.7340 (mpp) REVERT: J 718 LEU cc_start: 0.8746 (mm) cc_final: 0.8348 (mm) REVERT: J 758 MET cc_start: 0.7349 (mpt) cc_final: 0.6931 (mpt) REVERT: J 809 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8439 (p) REVERT: K 103 MET cc_start: 0.7219 (mtt) cc_final: 0.7016 (mtt) REVERT: K 205 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8434 (pt) REVERT: K 226 MET cc_start: 0.8053 (mtp) cc_final: 0.7595 (mtp) REVERT: K 621 MET cc_start: 0.6154 (mmm) cc_final: 0.5658 (mmm) REVERT: K 634 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8120 (p0) REVERT: K 735 MET cc_start: 0.8018 (mtp) cc_final: 0.7089 (ttm) REVERT: K 758 MET cc_start: 0.6985 (mpt) cc_final: 0.6381 (mpt) REVERT: L 124 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7251 (p0) REVERT: L 621 MET cc_start: 0.7222 (mmm) cc_final: 0.5656 (mmm) REVERT: L 662 MET cc_start: 0.8068 (mtt) cc_final: 0.7361 (mpp) REVERT: L 758 MET cc_start: 0.7156 (mpt) cc_final: 0.6628 (mpt) outliers start: 231 outliers final: 180 residues processed: 395 average time/residue: 0.6085 time to fit residues: 445.6386 Evaluate side-chains 391 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 196 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 412 ASN Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 620 VAL Chi-restraints excluded: chain E residue 760 ASN Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 620 VAL Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 212 ASN Chi-restraints excluded: chain G residue 216 ASN Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain G residue 634 ASP Chi-restraints excluded: chain G residue 654 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 247 LYS Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 412 ASN Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 526 VAL Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain H residue 718 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 247 LYS Chi-restraints excluded: chain I residue 354 ASP Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 472 ASN Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 620 VAL Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 127 MET Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 247 LYS Chi-restraints excluded: chain J residue 354 ASP Chi-restraints excluded: chain J residue 412 ASN Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 809 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 245 THR Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 412 ASN Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 620 VAL Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain K residue 654 LEU Chi-restraints excluded: chain K residue 718 LEU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 354 ASP Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 634 ASP Chi-restraints excluded: chain L residue 654 LEU 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: 7.9990 chunk 854 optimal weight: 0.9990 chunk 521 optimal weight: 20.0000 chunk 405 optimal weight: 1.9990 chunk 594 optimal weight: 30.0000 chunk 896 optimal weight: 20.0000 chunk 825 optimal weight: 1.9990 chunk 713 optimal weight: 0.4980 chunk 74 optimal weight: 5.9990 chunk 551 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 69840 Z= 0.150 Angle : 0.588 10.391 94584 Z= 0.303 Chirality : 0.047 0.185 10620 Planarity : 0.003 0.029 12396 Dihedral : 5.250 24.055 9516 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 2.15 % Allowed : 13.72 % Favored : 84.13 % 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: -4.28 (0.08), residues: 8952 helix: -2.06 (0.24), residues: 384 sheet: -3.32 (0.10), residues: 1932 loop : -2.95 (0.07), residues: 6636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 80 HIS 0.004 0.001 HIS B 531 PHE 0.028 0.001 PHE B 594 TYR 0.018 0.001 TYR A 574 ARG 0.003 0.000 ARG D 741 ********************** 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 387 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 228 time to evaluate : 6.070 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: A 247 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8263 (mtmm) REVERT: A 539 GLN cc_start: 0.7774 (mm110) cc_final: 0.7429 (mm110) REVERT: A 621 MET cc_start: 0.7145 (mmm) cc_final: 0.6394 (mmm) REVERT: A 662 MET cc_start: 0.7964 (mtm) cc_final: 0.7290 (mpp) REVERT: A 663 MET cc_start: 0.8214 (mmm) cc_final: 0.7792 (mpp) REVERT: A 718 LEU cc_start: 0.8584 (mm) cc_final: 0.8241 (mm) REVERT: A 758 MET cc_start: 0.7320 (mpt) cc_final: 0.6747 (mpt) REVERT: B 205 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8391 (pt) REVERT: B 609 MET cc_start: 0.8124 (mpp) cc_final: 0.7823 (mpp) REVERT: B 621 MET cc_start: 0.5821 (mmm) cc_final: 0.4770 (mmm) REVERT: B 634 ASP cc_start: 0.8648 (p0) cc_final: 0.8176 (p0) REVERT: B 662 MET cc_start: 0.7731 (mtm) cc_final: 0.7088 (mpp) REVERT: B 663 MET cc_start: 0.7875 (mpp) cc_final: 0.7578 (mpp) REVERT: B 758 MET cc_start: 0.6677 (mpt) cc_final: 0.6396 (mpt) REVERT: C 621 MET cc_start: 0.7296 (mmm) cc_final: 0.6266 (mmm) REVERT: C 662 MET cc_start: 0.7941 (mtt) cc_final: 0.7407 (mpp) REVERT: C 790 TYR cc_start: 0.8192 (m-80) cc_final: 0.7960 (m-80) REVERT: D 247 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8253 (mtmm) REVERT: D 539 GLN cc_start: 0.7882 (mm110) cc_final: 0.7530 (mm110) REVERT: D 621 MET cc_start: 0.7696 (mmm) cc_final: 0.6148 (mmm) REVERT: D 634 ASP cc_start: 0.8575 (p0) cc_final: 0.8180 (p0) REVERT: D 662 MET cc_start: 0.8041 (mtm) cc_final: 0.7478 (mpp) REVERT: D 663 MET cc_start: 0.8341 (mmm) cc_final: 0.8089 (mpp) REVERT: E 125 VAL cc_start: 0.8741 (t) cc_final: 0.8508 (t) REVERT: E 205 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8510 (pt) REVERT: E 621 MET cc_start: 0.6687 (mmm) cc_final: 0.5655 (mmm) REVERT: E 662 MET cc_start: 0.7697 (mtm) cc_final: 0.7127 (mpp) REVERT: E 663 MET cc_start: 0.7953 (mpp) cc_final: 0.7636 (mpp) REVERT: E 735 MET cc_start: 0.7081 (ptp) cc_final: 0.6613 (pmm) REVERT: F 621 MET cc_start: 0.6536 (mmm) cc_final: 0.5413 (mmm) REVERT: F 662 MET cc_start: 0.7775 (mtt) cc_final: 0.7282 (mpp) REVERT: F 663 MET cc_start: 0.7733 (mmm) cc_final: 0.7258 (mmm) REVERT: F 718 LEU cc_start: 0.8743 (mm) cc_final: 0.8353 (mm) REVERT: F 728 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9164 (tp) REVERT: G 226 MET cc_start: 0.8275 (mmm) cc_final: 0.8037 (mtp) REVERT: G 247 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8265 (mtmm) REVERT: G 539 GLN cc_start: 0.7848 (mm110) cc_final: 0.7483 (mm110) REVERT: G 621 MET cc_start: 0.7125 (mmm) cc_final: 0.6355 (mmm) REVERT: G 634 ASP cc_start: 0.8635 (p0) cc_final: 0.8096 (p0) REVERT: G 662 MET cc_start: 0.8038 (mtm) cc_final: 0.7376 (mpp) REVERT: G 663 MET cc_start: 0.8149 (mmm) cc_final: 0.7775 (mpp) REVERT: G 718 LEU cc_start: 0.8536 (mm) cc_final: 0.8190 (mm) REVERT: G 758 MET cc_start: 0.7067 (mpt) cc_final: 0.6529 (mpt) REVERT: H 125 VAL cc_start: 0.8619 (t) cc_final: 0.8413 (t) REVERT: H 205 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8404 (pt) REVERT: H 247 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8261 (mtmm) REVERT: H 580 PHE cc_start: 0.8132 (t80) cc_final: 0.7882 (t80) REVERT: H 621 MET cc_start: 0.7746 (mmm) cc_final: 0.6506 (mmm) REVERT: H 662 MET cc_start: 0.8295 (mtm) cc_final: 0.7645 (mpp) REVERT: H 663 MET cc_start: 0.8468 (mtp) cc_final: 0.7569 (tmm) REVERT: H 735 MET cc_start: 0.6868 (ptp) cc_final: 0.6577 (pmm) REVERT: H 751 MET cc_start: 0.8823 (ppp) cc_final: 0.8511 (pmm) REVERT: I 124 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7289 (p0) REVERT: I 247 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8343 (mtmm) REVERT: I 621 MET cc_start: 0.7516 (mmm) cc_final: 0.6554 (mmm) REVERT: I 662 MET cc_start: 0.7884 (mtm) cc_final: 0.7309 (mpp) REVERT: I 663 MET cc_start: 0.8269 (mtp) cc_final: 0.7798 (mmm) REVERT: I 758 MET cc_start: 0.6842 (mpt) cc_final: 0.6539 (mpt) REVERT: J 243 ILE cc_start: 0.9199 (mt) cc_final: 0.8967 (mt) REVERT: J 247 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8276 (mtmm) REVERT: J 539 GLN cc_start: 0.7727 (mm110) cc_final: 0.7376 (mm110) REVERT: J 621 MET cc_start: 0.7971 (mmm) cc_final: 0.6876 (mmm) REVERT: J 662 MET cc_start: 0.7757 (mtm) cc_final: 0.7212 (mpp) REVERT: J 718 LEU cc_start: 0.8697 (mm) cc_final: 0.8295 (mm) REVERT: J 758 MET cc_start: 0.7201 (mpt) cc_final: 0.6781 (mpt) REVERT: J 809 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8363 (p) REVERT: K 205 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8380 (pt) REVERT: K 580 PHE cc_start: 0.8246 (t80) cc_final: 0.8015 (t80) REVERT: K 634 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8170 (p0) REVERT: K 735 MET cc_start: 0.7916 (mtp) cc_final: 0.6973 (ttm) REVERT: K 758 MET cc_start: 0.6709 (mpt) cc_final: 0.6131 (mpt) REVERT: L 124 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7115 (p0) REVERT: L 539 GLN cc_start: 0.7991 (mm110) cc_final: 0.7739 (mm110) REVERT: L 621 MET cc_start: 0.6690 (mmm) cc_final: 0.5332 (mmm) REVERT: L 662 MET cc_start: 0.7947 (mtt) cc_final: 0.7546 (mpp) REVERT: L 735 MET cc_start: 0.7618 (mtp) cc_final: 0.7410 (mtm) REVERT: L 758 MET cc_start: 0.6970 (mpt) cc_final: 0.6469 (mpt) outliers start: 159 outliers final: 128 residues processed: 353 average time/residue: 0.5612 time to fit residues: 362.7193 Evaluate side-chains 355 residues out of total 7404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 212 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 127 MET Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 247 LYS Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 412 ASN Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 449 THR Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 150 ASP Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 526 VAL Chi-restraints excluded: chain F residue 620 VAL Chi-restraints excluded: chain F residue 634 ASP Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain F residue 728 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 150 ASP Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 247 LYS Chi-restraints excluded: chain G residue 412 ASN Chi-restraints excluded: chain G residue 449 THR Chi-restraints excluded: chain G residue 620 VAL Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 127 MET Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 247 LYS Chi-restraints excluded: chain H residue 277 ILE Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 526 VAL Chi-restraints excluded: chain H residue 609 MET Chi-restraints excluded: chain H residue 620 VAL Chi-restraints excluded: chain H residue 634 ASP Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 127 MET Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 245 THR Chi-restraints excluded: chain I residue 247 LYS Chi-restraints excluded: chain I residue 404 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 449 THR Chi-restraints excluded: chain I residue 526 VAL Chi-restraints excluded: chain I residue 634 ASP Chi-restraints excluded: chain I residue 655 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 150 ASP Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 211 LEU Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 232 VAL Chi-restraints excluded: chain J residue 245 THR Chi-restraints excluded: chain J residue 247 LYS Chi-restraints excluded: chain J residue 449 THR Chi-restraints excluded: chain J residue 545 VAL Chi-restraints excluded: chain J residue 620 VAL Chi-restraints excluded: chain J residue 809 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 127 MET Chi-restraints excluded: chain K residue 150 ASP Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain K residue 277 ILE Chi-restraints excluded: chain K residue 421 VAL Chi-restraints excluded: chain K residue 449 THR Chi-restraints excluded: chain K residue 634 ASP Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 124 ASP Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 421 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 526 VAL Chi-restraints excluded: chain L residue 620 VAL Chi-restraints excluded: chain L residue 634 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 20.0000 chunk 567 optimal weight: 5.9990 chunk 760 optimal weight: 4.9990 chunk 218 optimal weight: 30.0000 chunk 658 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 715 optimal weight: 6.9990 chunk 299 optimal weight: 0.4980 chunk 734 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 HIS ** G 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 803 ASN L 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.144467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.083938 restraints weight = 214953.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.085586 restraints weight = 110416.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.087100 restraints weight = 78542.105| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 69840 Z= 0.334 Angle : 0.663 15.010 94584 Z= 0.348 Chirality : 0.049 0.209 10620 Planarity : 0.003 0.028 12396 Dihedral : 5.607 22.786 9516 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.32 % Favored : 81.68 % Rotamer: Outliers : 2.23 % Allowed : 13.71 % Favored : 84.06 % 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: -2.02 (0.24), residues: 384 sheet: -3.36 (0.10), residues: 1932 loop : -3.01 (0.07), residues: 6636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 577 HIS 0.003 0.001 HIS L 469 PHE 0.035 0.002 PHE B 594 TYR 0.020 0.002 TYR A 574 ARG 0.003 0.001 ARG K 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9417.27 seconds wall clock time: 172 minutes 34.18 seconds (10354.18 seconds total)